Knowledge Base Article

Migrating an Analyst® Software Compound Library to Sciex OS Software

To migrate compounds in an Analyst® software library to Sciex OS software, navigate to the Library module in Sciex OS software, and select Analyst Compound Library in the import options. The imported library must be named. Instructions for naming the library are included here.

Setting the Low Limit Value in the MPX 2.0 Software for Real-Time Data-Dependent Decision (RTD3) Flagging

When setting up MPX 2.0 software's carryover detection feature in the Define limit values screen (step 3), the low limit for each component must be defined using the lower limit of quantitation (LLOQ) or from the cut-off limit determined from the standard curve.

How do I modify the parameter translation file for mass tolerance and threshold for reporting iTRAQ ratios

Mass tolerance and threshold values for reporting iTRAQ ratios can be tuned by editing a configuration file.

Protocol for Downgrading SCIEX OS 1.4 to 1.3

If downgrading from SCIEX OS 1.4 to 1.3 is required, follow the instructions below.

What Are the Standard Addition Columns in a SCIEX OS Software Results Table?

Sciex OS software allows users to process standard addition results by selecting the Standard Addition option in the Components tab of the processing method in the Analytics mode. What do the new standard addition column headers mean?

Locating the Most Recent Quantitation Method Used in MultiQuant™ Software

To locate the most recently used quantitation methods used in MultiQuant™ software, select the File menu and then select the Recent Quantitation Methods option. This menu option allows for the most recently accessed methods to be viewed.

Choosing the Peak Selection Criteria when Using SCIEX OS AutoPeak Integration Algorithm

This articles explains what type of peak selection criteria can be used with the SCIEX OS AutoPeak integration algorithm.

Applying the Saturation Correction when Working with SCIEX OS AutoPeak Integration Algorithm

Saturation correction can correct for detector saturation effects. To make these changes in SCIEX OS software when working with the autopeak integration algorithm, select the saturation correction button in the method and specify the threshold value.

Why Does My Area Ratio Show as N/A in MultiQuant™ Software?

Area ratios that give a value of N/A in MultiQuant™ software are likely due to an internal standard not being integrated or only being designated, but not assigned, to an analyte.

Analyst® Software Sub-projects Cannot Be Used with Custom Quant Table Settings

To create and apply custom results table settings in Analyst® software, sub-projects cannot be in use.

Installing ProteinPilot™ 4.5 and 5.0.x Software on the Same PC

For software users who need to view the older group files, maintaining a separate computer with ProteinPilot™ software 4.0 installed is the recommended best approach. Alternatively, both versions, 5.0.x and an older version, can be installed on the same computer, but this is an unsupported configuration.

Unable to Import Batch Files in XLSX Format in the Batch Editor in Analyst® 1.7 Software

Importing an XLSX batch file into Analyst® 1.7 software may cause an error, and the batch file import will not be successful. The XLSX format is only available if the version of Microsoft Office that is installed is a 32-bit application. Users with a 64-bit version of Office will see these batch import errors, and must install additional software components to support XLSX type spreadsheets with Analyst software.

How to delete Results Table Settings in Analyst Quantitation Mode

Where to find the 'remove' button for the results table settings

Manually Integrate script is installed but when running the script an error message appears saying that the script is not installed.

On Windows 7 I have the Manually Integrate script installed but when running the script an error message appears saying that the script is not installed.

What File Format Can Report Templates Be Created In?

Report templates—used to create reports from results tables generated in Sciex OS, MultiQuant™ and Analyst® software—must always be in the format of a Word document with a file extension .docx. However, the output report itself can be created in several formats including Word, HTML, PDF, and CSV.

Upgrading to Analyst® TF Software 1.8.1: Batch Editor No Longer Displays Autosampler ekspert nanoLC400 as an Option

After upgrading Analyst® TF software 1.8 to version 1.8.1, the Eksigent control software no longer displayed the option to chose the ekspert™ nanoLC 400 autosampler. To resolve this issue, in the Eksigent control software, the autosampler driver for the nanoLC 400 must be unregistered and then re-registered.

MultiQuant™ Software v2.0 Will Not Launch with a 2.0 License

The MultiQuant™ software 2.0 license will not launch the 2.0 version of MultiQuant software. Instead, MultiQuant software 2.0.2, 2.1 or 2.1.1 must be installed.

Direct LIMS Transfer in SCIEX OS Software Does Not Require a Template

Transferring data to a LIMS system from a results table created in SCIEX OS software does not require a template. Once the results table is saved and locked, under the Reporting menu, select Transfer results to LIMS, and two LIMS export options will appear in the LIMS transfer dialog box.

How is the GETSTAT Function Used in SCIEX OS Software?

The calculated columns for a processing method in SCIEX OS software allow users to add a formula that pulls the statistics pane calculations into the results table as a custom column. This can be done using the GETSTAT function.

How Does SCIEX OS Software Calculate the Ion Ratio for a Component?

SCIEX OS software uses the regression parameter defined for the first component in the results table to calculate the ion ratio for all of the components in the results table.

Reporting Values for Calculated Concentration that Are Not Equal to N/A from a Results Table

To filter results table data in a report based on the calculated concentration not equal to N/A, add the if statement $Calculated_Concentration<>"N/A".

What Is the Difference Between .wiff and .wiff2 Data Files?

There are two data file formats for data sets acquired using SCIEX mass spectrometers: 1) .wiff and 2) .wiff2. Instruments using Analyst® software to acquire data will write data sets in the .wiff format. Instruments acquiring data using SCIEX OS software (version 2.0 or lower) will write data sets in the .wiff2 format. The newer versions of SCIEX OS software (version 2.1 and greater) write data in both the .wiff and .wiff2 format.

Shimadzu Pumps Do Not Start when Selecting Equilibrate in Analyst® Software

Selecting Equilibrate in Analyst® software does not always turn on the Shimadzu LC pumps. To get the LC pumps to respond, users must follow a specific start up procedure and recognize when the system has gone into standby mode.

How to Setup Standard Addition in SCIEX OS Software

If the standard addition feature is enabled in SCIEX OS software, then the results table contains new columns, including Standard Addition Accuracy that compares the Standard Addition Calculated Concentration for a sample to the Standard Addition Actual Concentration. Standard addition is enabled in the quantitation method on the Integration tab under the Options menu.

Release Notes for Analyst® TF 1.7.1 Software with Components for LC Devices

Analyst® TF 1.7.1 Software with Components for LC Devices Release Notes are attached. Please consult this guide for the newly added support for the NanoCell Interface, Exion LC series of devices and the Analyst Device Driver.

Differences between iTRAQ® Reagents Application Kit - Protein (4374321) and iTRAQ® Reagent 4Plex or 8Plex Kits

This article describes the different workflows for the iTRAQ® Reagents Application Kit - Protein (4374321) and the iTRAQ Reagents - 4plex or 8plex kits.

LC Methods Not Opening in Analyst® Device Driver Software

Sometimes, the LC portion of a method in Analyst Device Driver (ADD) will not open successfully; yet the associated Analyst® software acquisition method file (.dam) is able to be opened, and the LC conditions can also still be viewed. To resolve this issue, avoid copying files between project folders or re-activate the hardware profile.

What Are the Functions Available to Each Security Configuration Role in Analyst® Software?

Individual users of Analyst® software can be assigned a particular role in Analyst software in the Security Configuration mode. The various roles are designed to limit a user's access to certain functions within the software depending on the role assigned. Below is a chart that shows how access to these functions decreases for the various default roles.

Analyst® 1.7 Software Installation Error in Windows 10

Upgrading from Analyst® 1.6.3 to Analyst 1.7 software in a Windows 10 environment will cause an installation error, and Analyst 1.7 software will not launch. Analyst 1.7 with Hotfix 1 must be installed alone, and previous versions of Analyst software cannot also be installed concurrently.

Data for Custom Calculations Show as Not Calculated on a Report

In reports created from results tables in Analyst® and MultiQuant™ software, queries are used to compute the values for custom calculations, but occasionally the data appears as "Not calculated" on the report. This issue appears when the query file linked to the report template is not saved to the same folder as the report template.

How Are the Ion Ratio Flagging Rules Set Up in SCIEX OS 1.5 Software?

To set up the ion ratio flagging rules in SCIEX OS software, select a processing method and then select edit. The rules can be changed under Flagging Rules and Ion Ratio Acceptance options under this menu.

LeadScape Software and LeadSampler (LS-1) Compatibility with Exion AD Pumps

The Exion AD pumps sold by SCIEX are compatible with Sound Analytics' LeadScape software and the LeadSampler (LS-1) autosampler.

Can I Do Any Data Processing in Keystone™ Viewer Software?

No, Keystone™ viewer software provides data viewing capabilities only.

Why Is There a .Special File Placed in the SCIEX OS Software Project Folders?

SCIEX OS software creates a special placeholder file (with a file extension of .special) and places these files in the root of every known SCIEX OS project sub-folder. SCIEX OS software uses both the project folder names and the .special files to identify its known folders, and it will not recognize the folder if the .special files are removed.

Equilibration Issue with Exion and Photo Diode Array (PDA) and Analyst® Software

When an Exion LC system with a photo diode array (PDA) detector will not communicate with the Analyst® software, reactivate the hardware profile and restart Analyst services.

How to check Operating System Locale on Windows 7

SCIEX software is (unless stated otherwise in release notes) only supported on systems with a Locale of en-US United States. The process to accurately check your system locale is described below.

How Is the New SCIEX OS Software Quantification Algorithm Better than the Original Analyst® Software Classic Algorithm?

The quantification algorithms for finding and integrating peaks in SCIEX software programs have improved significantly since the Analyst® software classic algorithm was introduced. Users of the SCIEX OS software will see two main advantages when integrating peaks with the new AutoPeak algorithm.

What File Formats Can Be Converted with the Newest Version of ProteoWizard Software?

This newest version of ProteoWizard software, version 3.0.20258-97f41f698, can now convert files to the txt format, as well as the three original file types (MGF, mzML and mzXML). For SCIEX software users, the txt file might be a useful option; however, the quality of the output file from ProteoWizard has not tested.

Can the Pressure Trace Be Monitored or Saved in SCIEX OS 1.4 Software?

Currently the pressure traces for many liquid chromatogram instruments can be monitored in real-time in the SCIEX OS software, but not be saved to a specific location.

Incorrect Argument Error when Adding Standards to a Results Table in SCIEX OS Software

When adding multiple standard samples with the same name to a results table in SCIEX OS software, an error was generated: "Incorrect Argument. An item with the same key has already been added." This article explains the workflow that generates this error and provides a workaround.

Resolving the Analyst® Software RackBuilder.exe Error Message: Failed To Open Database AutosamplerPoetDb

When running the RackBuilder.exe, an error message is received: "Failed to open database AutosamplerPoetDb". This error can be cleared by setting the Windows User Account Control (UAC) settings to level 4 (Never notify) and then rebooting the computer.

Saving Consecutive Batches for the Echo® MS System to the Same Data File Impairs Peak Splitting, Automatic Processing

For data acquired with the Echo® MS system, peak splitting is performed after acquisition is complete. If a subsequent batch is acquiring data to a file while the system is splitting peaks written to that file during the previous acquisition, then a resource conflict occurs.

How to Adjust the Ion Ratio in MultiQuant Software

Where are ion ratios modified in a MultiQuant software quantitation method (.qmethod file)?

How Do You Convert a Non-scheduled MRM Method to a Scheduled MRM Method in Analyst?

Converting a non-scheduled MRM method to a scheduled MRM method requires that the retention time of each transition is updated in the Analyst software method.

Setting Up Email Notifications and Emailed Reports in Cliquid® Software

To set up email notifications in Cliquid® software, launch the software and select the User Profile option. To start email notifications and the option to have reports emailed, the user's email address will need to be entered in the user profile.

How Very High Concentration Samples Are Handled in MPX 2.0 Software

MPX™ 2.0 software contains a feature for automated carryover monitoring, which can identify samples above a certain threshold.

How to Save Application and System Event Logs in Windows 10

The Windows event logs often contain crucial data about the performance of SCIEX software. Follow these steps in Analyst® software to save your system and application event logs so that they can be analyzed by the SCIEX support team.

Where Can I Find More Information about Software IQ/OQ Testing Plans?

More information about software validation services can be found by emailing complianceservices@sciex.com.

How do I tell if the source exhaust is blocked or flooded? What is the cause and how do I fix it?

Procedures to diagnose exhaust issues.

Can the Loops ForEachSample and ForEachVisibleSample Be Used in the Same SCIEX OS Software Report Template?

No, the loops, ForEachSample and ForEachVisibleSample, cannot be used within the same SCIEX OS software report template. Similarly, ForEachAnalyte and ForEachVisibleAnalyte cannot be used together in the same report template.

What Sample Plate Formats Are Supported on the Echo® MS System?

The Echo® MS System is only compatible with specialized, acoustically clear microplates that were specifically designed to ensure the optimal and repeatable performance of droplet ejection. These specialized plates are available in both 384- and 1536-well formats.

Missing Columns when Exporting the Protein Summary from ProteinPilot™ Software 5.0.2?

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

Analyst® Software Error: Failed to Write Method to Datafile Caused by Symantic Antivirus

Disabling the Sonar technology in the Symantic Antivirus program prevents the Analyst® software error "Failed to write method to datafile".

How to Print an Acquisition Method in Analyst® Software

To print an acquisition method in Analyst® software directly from the .wiff file, open data file under the Explore mode and then click on the i icon in the toolbar for the data file's information. Activate the file info pane by selecting it, and then go to File > Print > Pane.

What Is the Correct Format for the Client License Text for Software Using a Concurrent License?

To create and set up the license on the client PC for software using concurrent license server, the license text should be formatted as follows: SERVER [SERVERNAME.DOMAIN.COM or IP ADDRESS] ANY [PORT NUMBER] VENDOR ScxMSSW0 USE_SERVER

Recommendations for Waters Driver Packs with Different Analyst® Software Security Modes

When installing Analyst® software with the Waters' Driver Pack 4 (DP4) or the Driver Pack 4 supplemental release (DP4 SR1), consideration must be given to the Analyst security mode setting that is selected.

Why Don't I get Hits when the Precursor Mass Tolerance Is Set to 0.01 Da when Searching SCIEX Libraries?

Searches of SCIEX libraries with the precursor mass tolerance set to 0.01 Da may not yield any hits. This is due to the fact that some of SCIEX libraries contain spectra that were acquired with inaccurate precursor m/z.

Unable to Add Users to the Security Database in Analyst® Software

When Analyst® or SCIEX OS software is launched under the local admin account, an error message is received: “The current user is not added to the security database.” This error message appears because the software was originally installed under a non-admin account.

Low Virtual Memory Warning

If you receive warnings that your virtual memory is low youll need to increase the minimum size of your paging file

MultiQuant™ Software Will Not Launch after Installation

After successfully installing MultiQuant™ software and launching the software for the first time, the license activation screen does not appear and the license can not be installed.

Tips for Setting Up a Test in Watson LIMS™ Software for Use with Analyst® Software

This article summarizes some helpful hints for setting up a test in Thermo Fisher™ Watson LIMS™ software for use with Analyst® software.

Changing the Extension on the Analyst® Software Data File Acquired to a Temp Folder

If an Analyst® software data file is acquired to a temp or a cache folder, the data file may not have the .wiff or .wiff.scan file extension name. The data file extension name must be changed to .wiff or wiff.scan when the user attempts to move the files to a new location.

Where Are the Files Containing the Hardware Profiles Stored in Analyst® Software?

The hardware profiles created in Analyst® software are stored in the API Instrument project folder in the Configuration sub-directory: C:\Analyst Data\Projects\API Instrument\Configuration.

How Is the ITC Parameter Accessed in Analyst® TF Software?

Changing the ion transmission control (ITC) parameter in Analyst® TF Software helps to assess if the QJet® ion guide on a Triple TOF® system needs to be cleaned. This article explains how to access the ITC parameter within the Analyst software.

How To Create an Unsecured PDF Report in Sciex OS Software

In order to create reports in SCIEX OS software in the portable document format (PDF) that are unsecured, the PDF setting in the SCIEX OS config file will need to be updated. Please follow below instructions to edit the config file.

Where Can I Find Micro HILIC Columns to Separate Hydrophilic Peptides?

Hydrophilic interaction chromatography (HILIC) columns for separating hydrophilic peptides can be found in the SCIEX column catalog (https://sciex.com/products/hplc-products/microlc-products/micro-hplc-columns).

Primer Purity Requirements for Sequencing and Fragment Analysis Using the GenomeLab™ GeXP Genetic Analysis System

When ordering nucleic acid primers for use in either DNA sequencing or fragment analysis using the GenomeLab™ GeXP Genetic Analysis System or older CEQ genetic analyzers, be sure to select primers that--at the minimum--have been purified via solid phase extraction.

Can Biologics Explorer Software Be Installed on a PC with One Partition?

Biologics Explorer software needs to be installed on a computer with both a C: and D: drive partition; however, it is also possible to install this software on a PC with just one (C: drive) partition if a patch is also installed.

Applying Results Table Column Settings to Another Results Table in SCIEX OS Software

To apply the custom result table column settings from one Sciex OS software results table to another, open a results table in the Analytics mode. Then set the custom column order that you want to be displayed by clicking the More button, and then choose Table Display Settings.

Sciex OS Software Startup Always Defaults to License Activation Screen

Every time Sciex OS software is launched, the license activation screen continues to appear with all fields blank, even though previous launches of the software indicate that the software license was installed successfully. Reinstalling the software as an administrator using a local admin user will resolve this issue.

Preventing IP Address Conflicts with SCIEX 5500/6500+ Series MS and Waters' Acquity LC Instruments

To eliminate the possibility of any IP address conflict, the Waters IP addresses should be changed when operating with a SCIEX 5500/6500+ series instrument. To change the IP address on a Waters' LC components, use the Waters DHCP configurator located in the following folder: C:\\Program Files\Waters Instruments\Waters DHCP Server Configuration.exe.

What Fields in DiscoveryQuant™ Software Standard Template Are Default Names?

In DiscoveryQuant™ software version 3.0.2 and version 3.0.2 with HotFix 2, default names are generated for the sample, acquisition method, and data file name fields if they are not defined in the imported LIMS file.

Protocols for Protein Precipitation in Samples before Using iTRAQ® Kits

To prepare samples prior to iTRAQ® reagent labeling, use the following protocols.

Filtering Audit Trail Events Using a Set of Specified Criteria in SCIEX OS Software

The audited events in the audit trail can be filtered using a set of specified criteria in SCIEX OS Software by selecting the Filter icon in the upper task bar on the Audit Trail screen.

MultiQuant™ Software Report Error: Object Reference Not Set to an Instance of an Object

If the MultiQuant™ software error "Object reference not set to an instance of an object" appears when creating a report, then the report template was not selected in the Create Report dialog. Check the file being used in the Report template field is a true report template. If not, replace it with a correctly formatted report template.

Where Is the Data Stored from a Photo Diode Array (PDA) Interfaced wtih Analyst® Software?

When using a Waters photo diode array (PDA) with Analyst® software connected through an analog digital converter (ADC) connection, the data is stored in an Analyst data file (.wiff) and can also be viewed and processed in PeakView® software.

SQLite Exception Error in the Regulated Version of SCIEX OS Software

While setting up the regulated version of SCIEX OS software (CFR features activated), the following error message appeared when accessing the Audit Map portion of SCIEX OS software: "System.Data.SQLite.SQLiteException : unable to open database file." To resolve this issue, change the Windows permissions so that the user has full access to Audit Trail files.

How to Install Skyline Software on an Off-Line Computer

To download Skyline software on a computer that is not connected to the internet, use the Unplugged installer or the Administrator installer:

Tracking Pressure in Real-Time for an Exion LC System in Analyst® 1.7 Software

The ability to access a real-time report of pressure versus time trace is not available in the Analyst® software for the Exion LC systems. So far, this feature is only available for Agilent LC systems when using the Analyst Device Driver.

Reporter Template Suite Software: The Summary Table Always Starts on the Second Page

When a report is generated from a results table in MultiQuant™, Analyst® or SCIEX OS software, the summary table will only start appearing on the second page of the report, and the first page is left blank after the header. To resolve this issue, open the report template and select and highlight the summary table. In the Microsoft Word Layout menu, select Paragraph. De-select the option Keep with next.

What Causes BioPharmaView™ Software To Stall when Processing Data or Running Batches?

BiopharmaView™ software will stall when processing data when more than one instance of the software is open or if there are some corrupted files in the processing queue folder in the BioPharmaView program files folder.

How To Provide Selective Access to Analyst® Software Projects

To set access for select users at the project level in Analyst® software, the security configuration must be updated.

Reporter: Unable to Report Custom Columns Created in the Analyst® Software Results Table

When a user creates a custom column in an Analyst® software results table and creates a report template using a custom tag for the custom column, the data for this custom column is not output to the report. The report template will not read the custom column unless [Custom] is added to the column name in the results table

Custom Calculations and Flagging Rules for Carryover in SCIEX OS Software

This article contains instructions on how to set up a new processing method in SCIEX OS software that has the custom calculations and flagging rules for carryover.

Why Do I Receive Memory Concerns Warning when Processing Data in MultiQuant™ Software?

When processing a large data set in MultiQuant™ software 3.0.3, users may see a Memory Concerns message, "The Results Table you opened may cause out of memory computer issues. To free-up memory close other applications and any other opened results table." This message is a warning, not an error message, regarding the amount of memory required to process and display a large data set.

MultiQuant™ Software: Concentration Upper Limits Flag Incorrectly Assigned when No Peak Detected

In Multiquant™ software using a quantitation method with upper limits for concentrations set causes samples with N/A for peak area to be flagged for concentration.

Reporter 3.2: Adding Custom Columns to a Report Template

Custom columns can be added to a report template so that custom data values values can be read into a report created with Analyst® Reporter 3.2 (via Analyst software).

BioPharmaview™ Software: Simultaneous Analysis of Disulfide Bridges and Cysteine Modification Not Possible

Disulfide bond mapping in BioPharmaView™ software is described in the user guide. However, creating a disulfide bridge table in addition to analyzing cysteine modifications simultaneously is not described and cannot be done.

Is There an Equivalent to Single User Mode in SCIEX OS Software 2.0?

Single user mode is a security mode in Analyst® software that allows for any user that is logged in to a PC using any Windows account to access the software as an administrator. However, there is not currently an equivalent to single user mode in the SCIEX OS software. The security mode options in SCIEX OS software are limited to integrated mode and mixed mode.

Do you have any recommendations for the inclusionexclusion lists size for the Analyst TF 1.6 software

Do you have any recommendations for the inclusionexclusion lists size for the Analyst TF 1.6 software

How To View Metric Plots in the Analytics Mode in SCIEX OS Software

To view trends (such as internal standard peak area) over a range of samples in a results table, a metric plot can be created in the Analytics mode of SCIEX OS software by selecting the column with the values of interest and then selecting Create metric plot from the More menu.

How To Change Results Table Peak Review Settings in Analyst® Software

While reviewing a results table in the Quantitate mode of Analyst® software, the peak review settings can be changed to view more than one chromatogram and to adjust the x-axis and y-axis automatic zoom settings.

Getting Started with OneOmics™ Suite 3.4

This article describes the required registration, browser setup, software setup, and first steps for uploading data to the Data Store in the web-based and cloud-powered OneOmics™ suite.

Password Guidance for Secure Network Account or Special Acquisition Account for SCIEX OS or Analyst® Software

This article provides some guidance for using a secure network account (SNA) with SCIEX OS software or a special acquisition account (SAA) with Analyst® software.

Setting Up MRM Transitions if Q1 Mass Is Identical to that of a Second Compound

To set up a MRM transitions where the Q1 mass for one compound is identical to a second compound in Analyst® software, change the Q1 mass of the second compound by 0.1 -0.05 Da. After making this adjustment, the software will accept the duplicate mass for Q1.

Queue TIC Plot Does Not Resize Properly when the Window Size Is Adjusted in DiscoverQuant™ Software 3.0.2

The patch, DiscoveryQuant™ 3.0.2 Patch for Scrollbars and Plot Resize Issue, needs to be installed to resolve the TIC plot not resizing when using DiscoveryQuant software 3.0.2.

What Is the Exact Mass that iTRAQ® Reagents Add to Peptides?

SCIEX does supply the masses of the labels in the iTRAQ® Reagent 4plex and 8plex kits, but masses with more significant figures can be found at www.unimod.org.

What SCIEX Mass Spectrometer Data Files Work with Keystone Converter Software?

Keystone Converter Software can convert nominal mass (.wiff1) files, but it does not work with SCIEX OS software files or TripleTOF system files.

How Is the Full Screen Option Enabled in SCIEX OS Software?

Select the Full Screen Mode option to use SCIEX OS as the primary application. Users cannot close the software or access other software programs.

Can I Install SCIEX OS and Analyst® Software on the Same Computer for Data Acquisition?

Analyst® software and SCIEX OS software can be installed on the same PC, but SCIEX does not support workflows that use both the Analyst and SCIEX OS software to acquire data from the same mass spectrometer.

How Many Client Workstations with SCIEX OS Software Does the Central Administrator Console (CAC) Software Support?

The Central Admin Console (CAC) software can support 100 client workstations with the SCIEX OS software installed.

Verifying if the Data File is Acquired with Checksum On or Off in Analyst® Software

After opening a data file in Analyst® software in Explore mode, select the Verify Checksum radio button; a new window will appear to indicate whether or not the checksum feature has been turned on for the data file.

Reinstalling Analyst® Software without Uninstalling Analyst® Device Driver Will Cause Acquisition Methods To Fail

When installing the Analyst® Device Driver with Analyst® software, the order of installation of the programs is important. The Analyst software must be installed first, and then the Analyst Device Driver is installed next.

What Is the Best Way to Back Up My Library Compounds in LibraryView™ Software?

This article provides some guidance on best practices for backing up your library compounds stored in LibraryView™ software. Its recommended that a snapshot is created of the library every time the library is updated or edited.

Common Project Area Folder Write Access Error in SCIEX OS Software

When creating a new project in SCIEX OS software, the following error was received: The current user does not have write access to the requested project. This issue was resolved by copying the common-project-area folder in the SCIEX OS Data folder over from a different PC with an intact root directory.

Analyst® Software Freezes when the Hardware Profile Includes a LC System

In situations where Analyst® software will only launch acquisition methods successfully with a MS-only hardware profiles, but crashes when a Shimadzu LC autsaompler with a rack controller is added to the hardware profile, check to see if the Rack Controller is checked on the autosampler portion of the hardware profile.

Agilent Infiniti II HPLC System and SCIEX 6500+ Systems

When an Agilent Infinity II HPLC system is experiencing difficulty communicating with a SCIEX QTRAP or TripleQuad 6500+ System while running samples, this procedure must be followed for bringing the HPLC system online and building methods.

Cliquid Error Retrieving the COM class factory for component with CLSID

Cliquid will run samples successfully but will be unable to process them and will report Error Retrieving the COM class factory for component with CLSID 36977493A67011Dc8Dcc00104BC5f89A at the bottom of the window.

Recovering a Lost or Corrupted Acquisition Method in Analyst™ Software

To recover or recreate an acquisition method that was lost or corrupted in Analyst™ Software, click in the information pane of an older data file, and then right click and choose Save Acquisition Method.

How to Group Analytes in an Analyst® Software Results Table

To place multiple analytes (or multiple transitions for the same analyte) into a group within a results table in Analyst® software results table, follow the steps outlined in this article.

Waters Driver and SCIEX Software Compatiblity Guide

Please consult the attached guide, "Waters tested Sciex Configuration Guide," to determine if a Waters driver will work with a particular version of Analyst® software. Please make sure Waters UPLC firmware is compatible with the driver pack or ICS version.

Adding an Arrow in MultiQuant™ Software to Display the Expected Retention Time during Peak Review

In MultiQuant™ software, an arrow can be added to the peak review chromatogram window to represent the expected retention time. To do this, right click within the peak review pane and select Options from the list. A Peak Review Options popup window will appear. Check the option Mark Expected RT with Arrow under the Appearance tab. Then select OK. 

MultiQuant™ Software Error: "Update Column Settings Failed"

The MultiQuant™ software error "Update Column Settings Failed. Object reference not set to an instance of an object" is due to a memory leak problem, which can be quickly fixed by closing and reopening the program.

How to merge Analyst Acquisition Methods

Where to find, how to install and to use the 'Merge MRM' Script in Analyst.

What Happens During Q0 Dissociation when "Simple" or "Enhanced" Options Are Used in SCIEX OS Software?

Declustering is achieved with the SCIEX Triple Quad 7500 system using a voltage differential between the QJet® ion guide and the IQ0 lens or a voltage differential between IQ0 and Q0 (the quadrupole ion guide before Q1). This article explains how Q0 dissociation is achieved using simple or enhanced modes in the SCIEX OS software and how the D Jet™ ion guide is involved in enhanced-mode dissociation.

How Can I Tell if Zeno SWATH Pulsing Is Working Correctly on My ZenoTOF 7600 System?

To verify that Zeno SWATH pulsing is working on a ZenoTOF 7600 system, users should run a SWATH® acquisition method with and without additional Zeno pulsing using standards from the SWATH acquisition performance kit.

Creating Windows User Groups for Analyst® Software Security Configuration

Windows User Groups are established for each role established in the Analyst® software security configuration.

Multi-Page Printing Subsequent pages identical to the first.

A corruption in the local user profile can cause Analyst to print pages incorrectly with multipage documents having all pages as the first.

Can the ChemoView™ Software LIMS Template Be Edited?

Yes, the LIMS template for ChemoView™ software can be edited and customized. Once changes are saved in the report template, the report output will reflect the changes.

ProteinPilot™ Search Error: Unhandled Exception: Out Of Memory Exception

During a search with ProteinPilot™ Software 5.0, 5.0.1 and 5.0.3, the error "Unhandled Exception: Out Of Memory Exception" appears. This issue is due to the LC/MS reconstruct crashing within the ProteinPilot Software when data sets with a high MS1 scan speed are being processed.

Creating a New Report Style in Cliquid® Software

To create a new report style in Cliquid® software, go to the Administrator Tasks (Home) menu, then select Manage Report Styles and Create a Report Style.

SCIEX Software Activation with Offline Workstation

How to activate Analyst, MultiQuant or SCIEX OS software with a computer which is not connected to the internet

Converting WIFF2 Files from SCIEX OS Software to the mzML and mzXML Format

The ProteoWizard tool (http://proteowizard.sourceforge.net/downloads.shtml) for mzML and mzXML conversion has been updated to work with the WIFF2 files that are produced by SCIEX OS software.

How Are the Correct Solenoid Valves for a Shimadzu Pump Added to an Analyst Hardware Profile?

The solenoid valves for Shimadzu pumps can be set up by editing the hardware profile and changing the pump configuration.

How Is the Peptide Score Calculated in BPV Flex™ Software 2.1?

The BPV Flex™ Software 2.1 peptide score indicates the probability that the peaks in a given MS/MS spectrum will match those of the theoretical peptide fragments by random chance. Therefore, the score calculation is derived from observed MS/MS fragments and the corresponding intensities, as well as the number of theoretical MS/MS fragments.

How Can an Ion Library Group File Generated by ProteinPilot™ Software Be Uploaded to BaseSpace?

The procedure for uploading a group file generated by ProteinPilot™ software is described here. The group file is used as an ion library in BaseSpace and is uploaded using the CloudConnect MicroApp within PeakView® software.

What Is a Regular Expression?

A regular expression (regex), also called a rational expression, is a sequence of alphanumeric and/or special characters that can define a search pattern depending on their context.

Does SCIEX OS Software Have Functionality To Help My lab Achieve Compliance with Regulations?

Yes. SCIEX OS software has all the key data integrity features required to reduce your regulatory risk, including configurable security, electronic signatures, and audit trails.

Analyst® Software: How to Increase the Number of Waiting Samples in the Queue

By default the number of samples that can be submitted from the Analyst® Software queue is 100 samples. To change the number of waiting samples shown in the queue, select the Configure mode, and then navigate to the Tools menu. Select Settings and then Queue Options. Type in a desired number for Max Num Waiting Samples, and then click OK.

During PPG Tuning Some Mass-Charge Ratios Appear as NA

While tuning and calibrating the MS in Analyst® software, some masses in the calibration table are showing up as NA in the table despite clearly being present.

How to Backup or Move Masterview Libraries

How to Backup or Move Masterview Libraries

Should I Install Windows Updates on My Acquisition Computer?

Windows updates should not install automatically on your acquisition workstation, but once you receive notification that there are new updates, these can be installed when Analyst® software is not acquiring data.

Trouble Importing Sample List into Lipidomics Workflow Manager Project

In order to import a sample list successfully into Lipidomics Workflow Manager 1.0.5, the following software must be also installed: Microsoft Office 2010 and Access 2007 Runtime.

DiscoveryQuant Cannot set spectrum for experiment X

DiscoveryQuant Optimize will not complete optimization with the error message Cannot set spectrum for experiment followed by a number which can be any one of your scan functions.

How to Check if Unknown Samples Are Within Calibration Curve Range in SCIEX OS Software

To check if unknown samples are within the calibration curve range in a SCIEX OS software results table, additional calculated columns will need to be added to the results table.

Manage Mode Is Greyed Out in ChemoView 2.0.3 Software

After logging into ChemoView software, only the Process pane was accessible. The Manage pane was greyed out. This was resolved by changing all users in Analyst software to administrators in the Security Configuration mode.

Can ethanol be substituted for isopropanol when performing iTRAQ protocol for 4Plex and 8Plex

Can ethanol be substituted for isopropanol when performing iTRAQ protocol for 4Plex and 8Plex

Incorrect Argument Error when Creating MultiQuant™ Software Results Table

To resolve the Incorrect Argument error that occurs when creating a MultiQuant™ software results table, data should be transferred within the Analyst® software project folder to a new PC and not as individual .wiff and .wiff.scan files.

How Can Library Hit Results Be Filtered by Score in a SCIEX OS Software Results Table?

To filter library hit results in a SCIEX OS software by library score and to remove any results without a proper score (presenting with N/A), a custom filter can be used in the Analytics mode.

Chromatograms do not populate on printed reports linked image cannot be displayed

When generating large reports after a number of Chromatograms the box will be filled with the text linked image cannot be displayed

Is the E Lens™ Technology Used in the OptiFlow® Pro Ion Source Compatible with Atmospheric Pressure Chemical Ionization??

No, the E Lens™ Technology integrated into the SCIEX Triple Quad™ 7500 LC-MS/MS System has been designed for electrospray ionization (ESI) mode of analysis and is not compatible with atmospheric pressure chemical ionization (APCI).

Generating a Service Package in Sciex OS Software

To generate a service package in Sciex OS software that contains the event logs, select Configuration, About, and Generate a Support Package.

Resolving the PeakView™ 2.2 and MultiQuant™ 3.0.3 Software Error after Upgrading to .NET 4.7.2

After upgrading PeakView™ software to version 2.2 or MultiQuant™ software to version 3.0.3, the following error message was generated: "The procedure entry point nextafterf could not be located in the dynamic link library MSVCR120_CLR0400.dll." The workaround is to remove .NET Framework 4.7.2 and then install the .NET 4.0 software.

Will ProteinPilot™ 5.0.2 Software Function on a Windows 7 64-Bit System?

ProteinPilot™ 5.0.2 software has only been tested on Windows 10 SP1 64-bit with Microsoft Office version 2016.

What Are the Reasons for Hybrid Electrodes Probe Blockage?

Common issue reported with hybrid electrodes probes.

Top 10 des bonnes pratiques de l’utilisateur pour minimiser les contamination des systèmes LC/MS

French Translation of Knowledge Article 000017896

Scheduled MRM not supported in Multiquant you do not have the required license to open files containing scheduled MRM data

Scheduled MRM not supported in Multiquant you do not have the required license to open files containing scheduled MRM data

Removing Rows Releated to Internal Standards from a MultiQuant™ Software Table

If its not desirable to view the internal standard information in a MultiQuant™ software results table, de-select the IS button by clicking on the binoculars icon in the Components & Groups column.

How Inclusion or Exclusion Lists Are Imported into Analyst® TF Software

This article describes how a text file can be created to import an inclusion or exclusion list into Analyst® TF software when building an IDA method.

Will Keystone™ Viewer Software Open Any AnIML file, or Just ANIML files Converted by Keystone Converter Software?

Keystone™ viewer software displays an AnIML file, including those that were not created by Keystone converter software.

Reporter 3.2: Including Only the Results for the Quantifier Ion in a Report

To include only the data associated with the quantifier ion in a report, group the quantifier and qualifier ion for a particular analyte, and then use the For Each AnalyteGroup loop around the information to be reported.

Acquity AAO Service Did Not Start

Steps are provided for editing the service properties of the AAO file to resolve the error "Cannot start service from the command line or a debugger." Editing the service properties will direct the AAO file to reopen in the event that it closes.

CAD Gas Setting Displays Incorrectly in the File Information for Analyst® 1.6.x or Higher

If a data file was acquired using simplified CAD gas settings and opened in the Analyst® software without the correct hardware profile active, the CAD gas setting in the file information will be displayed incorrectly.

Data File Sample Information Is Incorrect for Data acquired with Different SCIEX OS Software Versions

If data is acquired with one version of SCIEX OS software, and then data is appended to the data file (.wiff) with another version of SCIEX OS software, then the software version recorded in the data file is incorrect. The earlier software version will be shown in the File Info section, and the newer version will not be captured in the file information.

File Locking Prevents Addition of Remaining Injections to Existing Analyst® Software Data Files

To add injections to an existing data file, ensure that the Analyst® software data file is not in use or locked by another software program.

The Peakfinding Algorithm in SimGlycan® Software Improves Search Results on SCIEX Datasets

The Peak Detection & Picking feature in SimGlycan® software versions 5.9.2 and higher offer an improved peak-picking algorithm that is faster and more efficient at handling data from SCIEX TripleTOF® LC-MS/MS System instruments.

License File Was Not Emailed when AID Key Was Entered without Dashes

When activating a software license key online (at https://licensing.sciex.com/), the license key number must be entered with dashes after every fourth character in the AID- key (e.g., AID-xxxx-xxxx-xxxx-xxxx-xxxx-xxxx-xxxx-xxxx).

Plate Template Used for Tissue Imaging on MALDI TOF/TOF Instruments?

To use the Mass Spectrometry Imaging Starter Kit design by LaserBio Labs™, your tissue needs to be mounted onto a blank LC MALDI plate. This blank MALDI plate fits a 123 mm x 81 mm plate holder. A starter template is provided here to create a customized plate for MALDI data acquisition.

Error Message for National Instruments GPIB Driver Received during Analyst® Software Installation

To resolve the error message received for the National Instruments GPIB driver during Analyst® software installation, install the driver from the GPIB folder on the Analyst software installation disk manually.

How do I debug MultiQuant Queries

Often when developing MultiQuant queries it can be useful to see the calculations which are performed during the query. By setting MultiQuant queries to debug mode you can view the files generated in excel allowing you to fix any errors in the calculations

How Many Vials of Each iTRAQ® Reagent Are in the Multiplex Kit?

Each iTRAQ reagent multiplex kit (PN 4352135) contains 5 vials of of the following iTRAQ reagent labels: 114, 115, 116, and 117.

How can I change the sample which is used in a MultiQuant quantitation method or results table as a typical sample to set expected retention time and integration parameter for each MRM transition

This article gives a guidance how to change the typical sample used in MultiQuant software

Why doesn't a TrEMBL FASTA file work for a ProteinPilot search?

This is a known issue, and the TrEMBL database is not recommended for use with ProteinPilot software. The TrEMBL database is automatically annotated and not reviewed and could contain redundancies in terms of protein sequences, protein ascension numbers, etc.

Exporting reports and data graphic from the 32Karat method

Procedure to export reports (e.g. % area report, etc.) and data graphics (electropherograms with annotations) from the method.

Injection volume must be a positive value

If the Regional Settings in an Acquisition Computer with Analyst® Software is not set to US English , this can course the Error message: "Batch not submitted-Injection volume must be a positive value" during submitting a Batch.

What Software Is Supported for Analysis of Data from the Echo® MS System?

Once data collection from a well plate has been completed on the Echo® MS System, a .csv file is created for each well, in addition to another file that contains all of the data from the well plate. The .csv files can be imported into any data visualization software for further analysis, or the .wiff2 data can also be reviewed in SCIEX OS software. The data set contains the sample name, well location, component name, peak area, peak height, and peak width.

MultiQuant™ Software Error: Currently Running in Another Windows Session

To resolve the MultiQuant™ software error "Currently running in another Windows session on this computer. Switch to the other session and close the software", shut down Analyst® and MultiQuant software and services under both accounts, and then relaunch software under one account.

How to Export Results for Specific Analytes from SCIEX OS Software

To report only the results for specific analytes from SCIEX OS Software, a results table will first need to be opened in the Analytics mode. Start by selecting one of the analytes of interest from the Components and Group Tab. If multiple analytes need to be reported, then select additional analytes by holding the Ctrl key down and selecting each additional analyte with the mouse. Then in the Reporting menu, select Export Results > Export and Save Results Table.

Using the 25 Micron ESI Electrode with the DuoSpray™ Source?

A 25 micron ESI electrode can be used with the IonDrive™ Turbo V source and the DuoSpray™ source.

How Many User Roles Are Available in ChemoView™ Software?

ChemoView™ software supports two user roles, technician and administrator. Each role allows access to different rights and functions within the software.

How to Generate MRM Ratios in Analyst Software

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

Reporter Error: Cannot Retrieve Analyte: the Specific Index ("-1") Is Out of Range

If the following error is received when creating a report for a results table in MultiQuant™ or SCIEX OS software "Cannot retrieve analyte: the specific index ("-1") is out of range", ensure that the individual tags within the loop are for the same sample type (e.g., use internal standard tags if For Each Internal Standard is used for the loop).

Calculating the Theoretical Average Mass for an Intact Protein in BioPharmaView™ Software

BioPharmaView™ software uses the isotopic masses published by NIST online at: https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl. Please note that the results generated will be the same throughout all SCIEX software (e.g., PeakView™ and ProteinPilot™ software).

Where Are the Report Templates for BioPharmaView™ Software Stored?

The file folder locations of the report templates for BioPharmaView™ software are listed in this article.

How do I store iTRAQ® labeled peptides?

Store iTRAQ® reagent labeled peptides at -20 or -80 degrees Celsius. Avoid having the peptides undergo multiple freeze/thaw cycles. iTRAQ-labeled peptides can degrade over time.

Can a Method Built in MPX™ Software Be Converted to a Method Used with SCIEX OS Software?

No, methods built in MPX™ software cannot be converted for use in SCIEX OS software. Files built in MPX software are not supported in SCIEX OS software.

Altering Parameters in PPG Tuning Methods Causes Mass Shift and Resolution Issues

Changing any of the source or compound parameters in a PPG tuning method (such as Q1PosPPG.dam located in the API Instrument project folder in the Analyst Data folder) causes mass shift and resolution issues in the resulting data file.

How to Generate a Service Package in Analyst® Software

Generating a service package allows the technical support team to pinpoint and resolve software issues more quickly. To diagnose an issue with Analyst® software, download and install the Analyst Diagnostics Tool (ADT).

Finding the Archived Results in Chemoview™ Software

All result reports are archived in Chemoview™ software in the Results Archive tab. Users can browse the report by job date, or search job by date, .wiff file name and sample name.

Can You Print a Quantitation Method in MultiQuant™ Software?

MultiQuant™ software does not have an option to print the quantiation method. However, the quantitation method can be copied or exported as text file into Excel and printed.

What Are the Peptide Sequences in the Six-Peptide Mixture (PN 4465940)?

The six-peptide mixture (part number 4465940) is used for the calibration of mass spectrometers. The kit contains the following six peptides and their mono-isotopic masses: bradykinin (2-9 clip) (904.4681), angiotensin I (1296.6853), glu1-fibrinopeptide (1570.6774), ACTH (1-17 clip) (2093.0867), ACTH (18-39 clip) (2465.1989), and ACTH (7-38 clip) (3657.9294).

Installing SciexOS 1.4 on a PC where Other SCIEX Software Was Previously Installed

SciexOS 1.4 uses the LibraryView™ Framework in the background to manage libraries and library searching. Older versions of the framework may be on the PC that can interfere with the installation of 1.4. Also, older version of Microsoft SQL server and .NET Framework can cause the installation process to fail. This article contains information on steps to take to remove older versions of the aforementioned tools.

Why it is not recommended to open Audit Trail Archives with Newer Versions of Software

Opening/reading Audit Trail files should only be performed with the same version of Analyst software as they were acquired.

What Integration Algorithms Are Used by SCIEX OS Software?

The SCIEX OS software has three integration algorithms that can be used to integrate peaks, and these options are listed in the Project Default Settings in the Analytics module: MQ4, AutoPeak and Summation.

Common Issues when Using 32 Karat Software for Peak Integration

Peak integration with the 32 Karat software can be improved using the suggestions found here.

How Does the Quadrupole Transmission Function in the TripleTOF® Systems Work?

For TOFMS, all ions pass through Q1 in RF mode. In general, Q1 and Q2 perform "hops" over the mass range, ensuring an appropriate envelope of masses is passed into the TOF analyzer. The general explanation found here for the QSTAR® systems can also be used to explain TripleTOF® systems as well.

Can Analyst® and SCIEX OS Software be Installed on Separate Computers and then Used Alternately for Acquisition?

Switching between Analyst® and SCIEX OS software for acquisition, either on the same or different computers, is not a supported workflow.

Can the SCIEX OS Software Central Administrator Console (CAC) Run on a Citrix Server?

The SCIEX OS Software Central Administrator Console (CAC) should run on a Citrix Server, but this configuration has not been tested and is not officially supported.

How Does the Score in the Peptide Sequencing Section of BioPharmaView™ Software 2.1 Work?

Each peptide is displayed in a table after processing the peptide digest in BioPharmaView™ software. A score is given to each peptide after it is compared to the theoretical proteolytic digest.

Application Event Log Error - Analyst Event ID - 2 - Category FMAN [CompDocDrvDLL][Error][File: CreateOpenCompDoc.cpp][Line 569]

This article describes the cause of this Event which can effect network acquisition

Re-installing a MPX License by Dropping the License Directly into the Program Files

If MPX driver software does not accept a license saved on the desktop during the license installation process, drop the license into the MPX bin folder in the program files.

How to Access the SCIEX OS Software Help Menu

To access the SCIEX OS software help menu, click on the question mark in the upper, right-hand corner.

How To Enable the New Intact Protein Quant Feature in SCIEX OS 1.7 Software

The Intact Quant feature in Sciex OS 1.7 software platform enables the quantitative processing of intact proteins without sample prep and allows for the complete and compliant intact reconstruction of protein data sets. To activate this feature, an additional, add-on software license, SCIEX OS IntactQuant 1.7 (part number 5078597), must be installed in the C:\ Program Files\SCIEX\SCIEX OS folder.

Where Can I Download SCIEX Software?

Full versions of many our software programs can be downloaded from the SCIEX website at https://sciex.com/software-support/software-downloads.

How To Reset a QTOF System Mass Spectrometer

Power cycling a QTOF mass spectrometer can help resolve communication issues. The The TripleTOF® system, the X500 QTOF system, and the ZenoTOF system instruments (X500-, 5600-, 6600- and 7600-series instruments) are all reset in the same way. This article describes the reset procedure for these instruments.

How Do You Obtain a Token for ChemSpider Software?

The Formula Finder Settings panel in Sciex OS software requests a ChemSpider security token after selecting the ChemSpider Service. To obtain a token, users will have to register on the ChemSpider website.

MarkerView 1.2.1 error Could not get method information for A1_MS_1.t2d when trying to download data

MarkerView 1.2.1 error Could not get method information for A1_MS_1.t2d when trying to download data

How Do I Activate My SCIEX License Key?

To activate a SCIEX license key, log into www.sciex.com with your username and password. Navigate to https://sciex.com/support/activate-software and complete the required fields.

Reporter Templates Cannot Be Edited Due to Missing XML Tags

When opening a template, an error was received from the Template Content Control Manager, "Error: Specified argument was out of range of valid values." To resolve this error, the Template Content Control Manager needs to be reinstalled.

Adding Negative Ion Mode Experiment Information to Analyst® Software Quant Methods

Adding a negative ion mode experiment to an Analyst® software quantitation methods can be done by opening an older quantitation method in Analyst and then using Save As to save a copy of the older method. The negative ion mode information can be added by toggling the Data Source options in that drop down menu.

Differences between “Find Any” and “Find” in FormulaFinder in SCIEX OS Software

In SCIEX OS software, the “Find Any” function in Formula Finder considers just the monoisotopic peak to be within the m/z tolerance. Both odd (in italics) and even electron elemental compositions are provided. When using “Find Any” element ranges “From” and “To” are considered. The “Find” function in Formula Finder uses all constraints, including the mass tolerance for all selected peaks in the isotope pattern and the settings from the Options dialog.

How Do You Set Up for Manual Tuning Using Tee Infusion?

Before setting up your manual tuning method for source/gas optimization, your MS instrument must be set up for continuous infusion with high LC flow.

How Does the Size of a Converted AnIML File Compare to the Original Wiff File Size?

The converted AnIML file created using the Keystone™ converter software is 1.6 to 1.8 times bigger for data sets with multiple reaction monitoring (MRM) data. This is because the original .wiff.scan file is compressed, but then it is uncompressed as part of the conversion and storage process when creating the AnIML file.

Is It Possible To Convert an Acquisition Method Built in Analyst® Software to a MS Method for SCIEX OS Software?

A MS acquisition method built in Analyst® software cannot be opened directly in SCIEX OS software 2.2, but it can be converted to a usable MS method in SCIEX OS software using the Convert file feature in the MS Method workspace.

Can the Eksigent Nano III ion source fittings withstand the back pressure when using a UPLC

Can the Eksigent Nano III ion source fittings withstand the back pressure when using a UPLC

The ExionLC 2.0 System Status Icon in the Analyst®Software Is Red But Shows as Ready

Sometimes when an error occurs on the ExionLC 2.0 system, the LC status icon in the Analyst® software turns red — but the LC status may be listed as Ready. To reset the LC system, deactivate the hardware profile and then activate it again.

Differences in Date-Time Stamp for a Results Table Audit Map in Analyst® Software

In the Audit Trail Manager in Analyst® software, the audit map associated with a Results Table (accessed under the Results Tables node) might have a modified date-time that is different than the modified date-time shown with the project node (accessed under the Projects node) or in a Windows folder.

What is the Maximum Sampling Speed of the Echo® MS System?

There are two modes for the Echo® MS system, normal and fast. The normal mode maximum sampling speed is 1 sample/s. In fast mode, the maximum sampling speed is 3 samples/s.

How Can I Set the Integration Algorithm in the SCIEX OS Software?

To set the integration algorithm prior to processing quantitation data, select the Project Default Settings option in the Projects menu in the SCIEX OS software under the Analytics tile.

Adjusting Settings on a New Installation of DiscoveryQuant Software to Trigger a Run

A new installation of DiscoveryQuant (DQ) software was not triggering injections with an Acquity UPLC. Adjustments to the settings in DiscoveryQuant included changing the autosampler type, building a new hardware profile, re-establishing communications between the LC and MS, specifying a plate location, and disabling the Look Ahead injection type.

PA800 How To - Installing the LIF Aperture and Probe Stabilizer

Installing the LIF Aperture and Probe Stabilizer

How To Generate a List of All Installed Programs and Windows Updates

To generate a list of all programs installed on a PC and a list of Windows updates, select the Programs and Features icon in the control panel. A list of all installed Windows updates can be created from the View Installed Updates screen.

Checking for Administrator Rights on a Windows 10 PC before Installing Analyst®/SCIEX OS software

There are three simple steps to determine which Windows users are listed as administrators before installing SCIEX software.

Is Watson LIMS Software 7.6.1 SP1 Compatible with Analyst® Software 1.7.2 on Windows 10?

Yes, Watson LIMS software 7.6.1 SP1 is compatible with Analyst® software 1.7.2 on Windows 10. Please run as administer when installing both the Watson and the Analyst software to ensure LIMS integration between the two.

Can Report Templates from Analyst® or MultiQuant™ Software Be Used with SCIEX OS?

Report templates used previously with Analyst® or MultiQuant™ software should work with SCIEX OS, with the exception of MultiQuant templates that include a table query.

Starting an Analyst Software Data File (.wiff) with a Space

Can an Analyst® software data file name start with a space? The answer is yes. It is not a good practice to start the file name (.wiff) with a space, but Analyst software does allow the user to do that by using the format of "Subfolder name\ Datafile name" in the data column of the batch.

Optimal CE Voltages for Peptide Analysis on TripleTOF® Systems

The collision energy (CE) and the collision energy spread (CES) values needed for peptide analysis (during protein IDA identification and SWATH® acquisition) can be optimized using Information in the rolling CE setting embedded in the Analyst® TF software.

What Is the Latest Nano Acquity Driver that Is Supported by Windows 7 OS (32 and 64 bit)?

The latest Nano Acquity driver that supports the Windows 7 operating system (both 32- and 64-bit) is the ACQUITY UPLC M-Class Driver Pack version 1.55.

Custom Calculations or Flagging Rules Not Working after SCIEX OS Software Upgrade or Reinstall

After a reinstall or upgrade of SCIEX OS software, the custom calculations and flagging rules of a processing method may not work properly. A config file for the software will need to be edited to restore functionality.

How Do I Create a Dump File?

A SCIEX technical support agent may ask you to create and send a dump file to provide a snapshot of a SCIEX software application's processes, loaded modules and memory at a certain time point. This article explains how a dump file is created.

Adding Users to the SCIEX OS Software Security Database

To add users to SCIEX OS software Security Database, the user who installed the software needs to navigate to the User Management section in the Configuration mode and select the plus sign next to the User name or group drop-down menu.

Compatibility of ProteinPilot Software 4.5 Beta with Microsoft Office 2016

ProteinPilot software 4.5 beta is not compatible with Microsoft Office 2016.

Why Use the Enterprise Edition of SimGlycan® Software?

SimGlycan Software (a product of PREMIER Biosoft) predicts glycan and glycopeptide structures from SCIEX mass spectrometer-acquired MS/MS data. Some of the advantages of using the enterprise edition of SimGlycan software include being able to create glycan templates so that novel glycan structures can be added to the database.

Enabling and Disabling the Data File Checksum Feature in SCIEX OS Software

To enable or disable the data file checksum feature in SCIEX OS software, navigate to the Configuration workspace in SCIEX OS software. Under the Projects tab under Data File Security, select the checkbox for Enable checksum writing for wiff data creation.

Increasing the Maximum Injection Volume for an MPX™ Software System

To change the default injection volume in MPX™ 1.2.1 software, the MaxInjectVolume line in the MPX configuration file (Multiplex.INI) can be edited. Additionally, the value added to the injection volume field in the Analyst software batch editor (on the Sample tab) will override the configured MPX injection value during an acquisition run.

How Is CEQ/GeXP Data Exported in the ABI Format?

This document explains how to export data files acquired with the CEQ/GeXP software into an ABI format for data reprocessing purposes.

What is the Source of the Atomic Weight Information in BPV Flex Software?

BPV Flex software uses the same source of atomic weight information as BioPharmaView™ software. The theoretical value required for the intact workflow uses the average molecular weight; the peptide workflow uses the monoisotopic weight.

Unknown Retention Time Values for Analytes in IDA Method Inclusion or Exclusion Lists in SCIEX OS Software

When setting up an information dependent acquisition (IDA) method, there is an option for including the retention time (RT) for analytes in an inclusion or exclusion list. In the inclusion/exclusion table, users can limit the masses in the list to a certain retention time with a specific width. However, sometimes the retention time is unknown, and its not clear what value to add for RT column.

Can the Probes and Electrodes for the OptiFlow® Ion Source Be Used with the OptiFlow Pro Ion Source?

The probes and electrodes for the OptiFlow® Ion Source can be used with the OptiFlow Pro Ion Source.

Where Is Guided Optimization Found in the SCIEX OS Software?

The SCIEX OS software offers various guided optimization methods in the MS Method mode.

Chromatograms Are Not Appearing in Reports Created with Reporter Template Suite

When using MultiQuant™ or SCIEX OS software to create a report with Reporter Template Suite software, chromatograms are not appearing in the report. Instead, the report shows the text "This image is not available" where the image should appear. If the tag, Picture: Peak Review, is used, then the Label field must contain a value that matches the name of a column in the results table or it must be blank.

Creating Reports where Internal Standard Peaks Appear Normalized to the Analyte Peak in Chromatograms

When viewing an analyte's chromatogram in a report, the internal standard peak that is overlaid with the analyte's is not normalized in the report's chromatogram and part of the peak appears out-of-bounds in the peak review image. If you see an internal standard peak in the peak review pane of MultiQuant™ Software or SCIEX OS Software that is not normalized to the analyte's peak size, double click on the x-axis of that particular chromatogram.

How to Save Application and System event logs in Windows 7

The Windows event logs often contain crucial data about the performance of SCIEX software. Follow these steps to save your system and Application event logs so that they can be analysed by the SCIEX support team.

Troubleshooting Amplifier Reset

An Amplifier Reset alert simply means that the pump has emptied and refilled. As the pump has a finite volume then this refilling is expected if running for a long time or at a high flow rate. Note that an Amplifier Reset is an Alert not an Error. If an Amplifier Reset occurs the pump will refill and continue to pump at the programmed rate. An Amplifier Reset will not cause the sample batch or queue to stop. If an Alert message appears indicating that an Amplifier Reset has occurred the first step is to determine if this is a natural reset or not. In the following section are steps described how to determine the cause of an amplifier reset.

Does ProteinPilot™ Software 5.0.2 Support MALDI TOF/TOF™ Systems?

Description of which ProteinPilot™ software versions still support 4800 and 5800 MALDI TOF/TOF™ systems.

What is my Source Exhaust and how does it work?

Description of the Source Exhaust components and common requirements to maintain optimal performance

What is SimGlycan Software?

SimGlycan® software is a comprehensive glycan and glycopeptide drawing and structure analysis software.

PA800 How To - Cartridge Removal

Video demonstration of Cartridge Removal on the PA800 system

Changing Parameter Settings Options in Analyst® Software

Changing the options available for individual parameter settings in Analyst® software can be done by selecting Configure or Tune mode and then going to Tools > Settings > Parameter Settings.

Where Can LIF Emission and UV Bandpass Filters Be Ordered?

UV bandpass filters used with the fixed wavelength UV detectors or emission filters for the laser induced fluorescence (LIF) detector can be ordered from common optics companies such as Andover Optics or Newport Optics.

When Should I Use Retrieve Configuration in Analyst® Device Driver Configure Mode?

In Analyst® Device Driver, when adding or changing a CTC PAL3 autosampler configuration, the Retrieve Configuration command must be performed in the Configure mode in the CTC PAL3 LC sampler dialog.

Can the Installation Repair Tool in SCIEX OS Software Be Used for a Central Administrator Console (CAC) Software Install?

No, the Installation Repair Tool in SCIEX OS software can not be used to assess the installation of the Central Administrator Console (CAC) software.

Tuning 4500,5500 and 6500 using Instrument Optimization

Walk through of instrument optimization

Can a LIMS System Be Connected Directly to SCIEX OS Software?

Yes, SCIEX OS software supports the ability to send results directly to Watson LIMS. Other LIMS connections are possible through a third-party provider, Data Innovations.

Where Is the Download for the SCIEX All-In-One 2.0 with NIST 2017 Library?

To download the SCIEX All-in-One HR-MS/MS library 2.0 and NIST 2017 MS/MS library (PN 5061635), go to the downloads page on the SCIEX website, and select the All-in-One library and the NIST library and download them both. Activate and install the licenses for each library.

How To Create a Metric Plot in Analyst® Software

In Analyst® software, there are multiple ways to view a metric plot in order to see trends quickly after generating a results table.

Can Both Analyst® Software and SCIEX OS Software be Used for Acquisition on the Same PC?

No, Analyst® and SCIEX OS software cannot be used for acquisition on the same computer. Analyst software will be removed from an acquisition PC if it is upgraded to use SCIEX OS software for acquiring data.

Exporting Libraries from MasterView™ Software to a New Computer

To use the set of libraries imported into MasterView™ software on another PC – or to switch between two sets of libraries – consider using the command line tools to export the library snapshot.

Changing the Comparison Sample Assignment in Analytics in SCIEX OS Software

When reviewing a results table in the Analytics workspace of SCIEX OS software, users can change the comparison sample assignment from the one that was originally included in the processing method by selecting the option, Use the selected sample as the comparison sample.

How Do I Open a Port in Windows Firewall for the Central Administrator Console (CAC) Software?

This article describes how to open the port for the Central Administrator Console (CAC) server when Windows Defender is used as the Windows firewall software.

Adding a New Fragmentation Rule for EAD Data from a ZenoTOF 7600 System to the Mascot Server

The steps for adding Mascot server fragmentation rules for an electron activated dissociation (EAD) cell on a ZenoTOF 7600 system are discussed in this article, as well as how to set up these rules in the Mascot Daemon client software version 2.6 or 2.8.

Overlaying Two or More Extracted Ion Chromatograms (XICs) in Analyst® Software Explore Mode

To overlay extracted ion chromatograms (XICs) in Analyst® software Explore mode, click on the first XIC, then select Overlay in the Explore menu, and then select the second XIC. The second XIC will now appear in the same screen as the first XIC.

MultiQuant™ Software's sMRM Feature May Require an Extension License

If an installation of MultiQuant™ software will not process sMRM data, an extension license may be need to be installed.

MPX Softare Error: MPX Driver Is Not in the Active Analyst® Hardware Profile

To resolve the MPX software error "MPX driver is not in the active Analyst® hardware profile", remake the Analyst software hardware profile from scratch.

System Error Causing SCIEX OS Software Acquisition Stoppage Resolved by Clearing Data Folder

Sample acquisition using Sciex OS 1.5 software was stopped, resulting in a system error. The drive where the SCIEX OS Data folder was stored was full, so backing up and clearing out older data allowed for data acquisition to proceed.

Creating a Hardware Profile in Simulation Mode in SCIEX OS Software

To create a hardware profile in simulation mode in SCIEX OS software, select Simulate Device under the Settings tab when adding instruments to a hardware profile in the Configuration mode.

Two Methods for Finding the Number of Points Collected across a Peak in Analyst® Software

Determining the number of points across a peak in Analyst software can be done two ways: 1) View - Graph Information, and 2) Tools - Settings - Appearance Options - Other Graph Option - Yes (with scan number ) under Chromatogram.

Integrated Syringe Error Message Recieved while Using Manual Tune Mode in Analyst® Software

While running Analyst® software in Manual Tune mode during compound optimization, an error message is received: "The current sample cannot be run because the syringe pump has stalled. The syringe plunger may be stalled in the syringe barrel." To resolve this issue, move the syringe holder back and clear error. If this doesn't work, replace the syringe, or if still needed, reset the MS.

Purpose of the Gel and Water Rinses in the SCIEX Capillary IsoElectric Focusing Shutdown Method

The purpose of the gel rinse followed by the water rinse in the SCIEX capillary isoelectric focusing (cIEF) shutdown method is to keep the capillary conditioned for use the next day.

Adding a Custom Column to a Results Table in SCIEX OS Software

To add a custom column to a results table in SCIEX OS Software, select Add custom column from the More menu. Provide a name for the custom column and then select OK.

Why Does Activating the Hardware Profile in Analyst® Software Change the Date of the Instrument Data File?

For SCIEX Triple Quad™ and QTRAP® Systems, the Analyst® software creates backup instrument data parameter setting files when deactivating a hardware profile. Each time the hardware profile is activated, it loads the correct backup file according to the mode of the default instrument data and parameter setting files; because the file is changed, the date on the instrument data file also changes.

How do I measure Peak Signal to Noise in Analyst Software

This article describes how to measure signal to noise using Explore or Quantitate mode with Analyst Software.

MultiQuant™ Software Feature Unavailable Error Message

When installing a MultiQuant™ 2.0 software license, a MultiQuant Feature Unavailable error message is received. Installing the correct version of MultiQuant will resolve this issue.

Can the Lipidyzer™ Platform Be Upgraded to a Windows 10 Compatible Version?

Lipidyzer™ platform 1.0.5 is only Windows 7 compatible, and there are no upgrades available that allow the software to be used on a Windows 10 system.

Directly Transferring Data from MultiQuant Software to a LIMS System

Data Innovation is a third party company that can set up a direct connection from MultiQuant to a LIMS system. http://www.datainnovations.com/support/driver-downloads

Locating the Computer ID(s) on a PC with a Windows Operating System

The computer ID, also known as the physical or MAC address, is a number used when activating a software license on Sciex.com and contains a series of 12 characters followed by a space and then another 12 characters. This article explains a few different ways to generate the computer ID on a Windows 10 system. (These same steps apply to a Windows 7 system as well.)

Where Are Acquisition Method Files (Both LC and MS) Saved for SCIEX OS Software Projects?

Each SCIEX OS software project has its own, separate MS and LC acquisition method files. This article describes where the method files are typically stored.

How to Export UV Data into a Text File in SCIEX OS Software

Open a data file that also contains UV data in SCIEX OS software in the Explorer module. Locate the Show menu and select UV/DAD/ADC Channel. Once UV trace is displayed, click Data and Peaks Table under the Show menu to display the table. Export the data by right clicking on the table and selecting Export Data as Text from the menu.

What Are the New Visualization Features in the OneOmics Suite for DIA-NN Software Output Files?

The DIA Results app, a new software feature in the cloud-based OneOmics suite for processing DIA-NN software output (TSV file), helps visualize proteomics data so that protein quantification results can be interpreted in the Analytics and Browser sections.

I am seeing inconsistent HPLC Peak shape. What may be the cause of this?

Summary of potential causes of poor HPLC peak shape

Renaming Analyst® Software Data Files

Renaming an Analyst® software data file (.wiff and .wiff.scan) after forgetting to do so in the batch may prevent the data file from being reopened later.

Is Cliquid® 3.4 Software Compatible with MPX™ 2.0 Software?

MPX™ Software is compatible with Cliquid® software and can be operated through the Cliquid software console; however, the Cliquid software Walk-up mode is not available.

Does SCIEX OS 1.4 Support Queries?

SCIEX OS 1.4 does not support table queries in the Analytics component of the software.

Creating an Ion Library for DIA-NN Software Using the Ion Library Generator in OneOmics™ Suite 3.3

This article describes how to create an ion library for DIA-NN in the OneOmics™ suite 3.3 using the Ion Library Generator.

Replacing the Sciex OS 1.0 License with a Sciex 1.2

Sciex OS 1.0 users must upgrade to Sciex OS 1.2. New license keys for Sciex OS 1.2 were distributed to Sciex 1.0 users. After removing the Sciex OS 1.0 license from C:/program files/Sciex/Sciex OS, the Sciex OS 1.2 license file should be installed from the desktop using the license activation screen in the Sciex OS 1.2 software.

Transferring the Custom Column Settings from One MultiQuant™ Software Results Table to Another

To transfer the custom column settings from one MultiQuant™ software results table to another, select Column Settings and then export the .cset file. Open the new results table and then import the .cset file.

Data Files Should Be Copied at the Project Folder Level in Analyst® Software

The best way to copy Analyst® software data and method files is to copy and paste at the project level.

Saving Custom Columns As Default Columns in MultiQuant™ Software

To routinely add the same custom columns to each newly generated MultiQuant results table, custom columns can be added to the table in the Batch Editor in Analyst® software that is created before acquiring a data set.

How to Restore the Batch Rack Code in Analyst® Software when Using CTC Autosampler

While creating a batch in Analyst® software with a CTC autosampler in the hardware profile, the drop-down menus appear blank for rack position, plate position, and plate code and do not contain the usual text selections. Reselecting the rack code value of 1 will restore the drop-down menu text.

How To Organize Data Using Sub-Folders in Analyst® Software

When setting up a batch in Analyst® software, a sub-folder can be created in the project's data folder to organize data by date or acquisition time. To create the sub-folder, type a backslash next to the data file name in the Data File column.

Will Software Validation Ensure that Our Lab Is 21CFRpart11 Compliant?

The SCIEX software validation service ensures that Analyst® software is configured correctly, that the necessary procedures are documented, and that objective evidence of these activities is provided to ensure 21CFRpart11 compliance.

How Can I Adjust the Dynamic CE Table in SCIEX OS Software?

Sometimes the dynamic collision energy (CE) for peptides needs to be adjusted to get better fragmentation of the precursor ion. This article describes how to adjust the dynamic CE table.

Chromatograms Are Randomly Missing from the Report after Upgrading Microsoft Office

When a report is created using Sciex OS, MultiQuant™, or Analyst® software, one of the chromatograms is randomly missing. This issue is due to Microsoft Office 365 Apps for Enterprise or Business being installed, and this version of Office is not currently compatible with the current versions of SCIEX software.

How to find Computer ID for Windows XP

Description of how to use the Command Prompt of Windows XP to find the Computer ID used when licensing Sciex software.

Issue with Ion Ratio Calculations in MultiQuant™ Software 3.0.3 Resolved with HotFix 2

When removing a standard from the calibration curve of an analyte in MultiQuant™ Software 3.0.3, an error occurs where the ion ratio for analytes farther down the list gets improperly calculated and changed. This issue is resolved by installing HotFix 2.

Removing Server Path Names in the MultiQuant™ Software LIMS Transfer Dialog

In order to enter the correct server address to enable LIMS transfers in MultiQuant™ software, delete the FilesFolderOptions.xml file in the folder C:\Users\User.Name\AppData\Roaming\AB SCIEX\MultiQuant3 and then restart the software.

Multiple Period Experiments Cannot Be Processed in BioPharmaView™ Software 2.x and 3.x

Data processing for intact proteins and peptide mapping in BioPharmaView™ software versions higher than 2.x do not allow for multiple period experiments.

How Are Peptides Named in BPV Flex Software after in Silico Digestion?

The general rule for naming peptides in BPV Flex software is: the first peptide resulting from a proteolytic cleavage is named T1 for sequences displayed from the N-terminus to the C-terminus; moving toward the C-terminus, the second proteolytic cleaved peptide is named T2, and so forth.

What is the Analyst® Diagnostic Tool and How Can It Help Me?

Analyst® Diagnostic Tool is an information-gathering program that is designed to provide insight on performance issues with Analyst software and the computer's operating system.

Power Down and Power Up the TripleTOF® System

How to power down and up the TripleTOF systems

Can I Use My Own Calibrant Solution to Tune the QTRAP® or TripleQuad™ LC-MS/MS 7500 System?

To tune and calibrate a SCIEX QTRAP® or TripleQuad™  LC-MS/MS 7500 system, a new calibrant, called the MS Tuning Solution, was recently introduced and must be used to tune the new instrument.

Is SCIEX OS Software Compatible with Cliquid® Software?

No, SCIEX OS software cannot coexist with the Cliquid® software on the same PC.

Installing Analyst® 1.7 Software on a Processing PC with Win 10

Described below are two procedures for installing Analyst® 1.7 software on Windows 10: 1) for a PC with a SCIEX-issued version of Windows 10 and 2) for a PC not purchased from SCIEX.

Why is my Graph Selection Window in SCIEX OS transparent?

Why is my Graph Selection Window in SCIEX OS transparent?

How can I convert .wiff to NetCDF format

Explanation of how to convert .wiff files to NetCDF using the Translat.exe program which is included with Analyst software

Can Multiple Users Log In to Windows while Analyst® MD Software Is Acquiring Data?

If a user starts a batch using Analyst® MD Software and then signs out of their Windows account while Analyst Software is acquiring data, the software will close and suspend the run. It is not recommended to sign out of a user's Windows account if Analyst MD Software is acquiring data.

Displaying Analytes Horizontally and Samples Vertically on a Report

To create a report where the analytes appear horizontally (as column headers) and sample names appear vertically (at the start of a row) in a report, the For Each Analyte tag will need to be nested within the For Each Sample tag.

What Are the New Features in the ProteinPilot™ Software Found in the OneOmics™ Suite 3.3?

This article describes the new software features recently implemented in ProteinPilot™ software 5.0.3 in the OneOmics™ suite version 3.3. The version of ProteinPilot software found in the OneOmics suite has nearly the same features as the desktop version of ProteinPilot software.

General Guidance for Antivirus and Backup Software Used on Acquisition PCs

The antivirus or backup software on Analyst® software acquisition workstations should be configured in a manner that will disable real-time scanning and archiving of files in the Analyst Data folder.

Can Xcalibur Software 3.x and Eksigent Software 4.3 Operate on Windows 10?

SCIEX's Eksigent software and Thermo Scientific's Xcalibur software have not officially been tested together on a Windows 10 operating system. The Eksignet software can be installed on a Windows 10 PC, but then it cannot be configured with any Xcalibur software versions. However, both software types can be configured together on a system running Windows 7, 64-bit.

Location of the Analyst® Software Configuration Files

The configuration files contain the processing parameters for library searching in Analyst® software. These parameters can be changed under the ConfirmationLibrarySearch.config or MultipleCandidateLibrarySearch.config files, and these files are typically saved under C:\Program Files (x86)\AB SCIEX\AnalystReporter\Resources\AlgorithmConfigFiles.

Resolving Hexadecimal Errors when Creating Reports in MultiQuant™ Software

If the error "Incorrect Argument. Hexidecimal value 0x1F is an invalid character" is received when creating reports with MultiQuant™ software, trailing spaces from the sample name need to be removed.

What is the Supported Control Software for the Echo® MS System?

The Echo® MS System is controlled by SCIEX OS software, version 1.6.10. This is the only supported software for direct control of this instrumentation. SCIEX OS software supports an open application programming interface (API) for the creation of integrated control through third-party automation software packages.

Analyst® Device Driver 1.3 Tutorial

The Analyst® Device Driver 1.3 Tutorial is a guide for the device driver usage and contains troubleshooting tips.

Where Are Report Templates Located for MasterView™ Software?

Report templates for MasterView™ software are located under the following root directory: C:\Users\Public\Documents\AB SCIEX\MasterView\Templates

ProteinPilot Software Datafile Cannot be Searched because two files are acquired under same file name

Searching for ProteinPilot software files using Windows Explorer cannot be done because there are two files acquired under the same file name. This is a long known issue for all ProteinPilot versions that only one file per file name can be searched using ProteinPilot software.

MultiQuant™ Software Installation Error Due to Some Prerequisite Components Needing Reinstallation

A successful MultiQuant™ software installation requires that the SCIEX Reporter software and a .pdf reader program, PDF Factory, be installed prior to the installation of MultiQuant.

What Sample Matrices Are Supported on the Echo® MS System?

The sample matrices that can be supported on the Echo® MS system must correspond to one of the supported liquid classes, either AQ or SP.

Unable To Change Sample Loop Volume With Analyst® Hardware Configuration For ExionLC™ AD System

After replacing the sample loop for a different volume on an ExionLC™ AD system, the volume of the loop can be changed on the LC controller panel but not within Analyst® software hardware configuration.

What is the Limit of the Path Length for the SCIEX OS Software Installer to Ensure a Successful Install?

The SCIEX OS software installation folder path is limited to 118 characters or less.

Can a WIFF or WIFF2 File from SCIEX OS Software Be Split into Subset Data Files?

There is currently no script or software that allows for splitting a multi-sample data file from SCIEX OS software (i.e., .wiff or .wiff2) into individual subset files.

What Is the Maximum Length of Characters for the Path to the Installation Folder for SCIEX OS Software?

Please ensure that the path to the installation folder for SCIEX OS software is 118 characters or less. If it is longer, the installation of SCIEX OS software will not proceed.

SCIEX Registered Software Webpage Lists All Recently Activated Licenses

The SCIEX Registered Software webpage (https://sciex.com/support/registered-software) lists all recently activated licenses.

Locating 66-Vial Plates in the Analyst® Software Plate Code Selection

Analyst® Device Driver supports 66-vial plates, but they are not initially found in the plate code selection of the Analyst software batch editor. To view this plate option, the rack code needs to be changed to 2 Drawer Plates and then the user can find both of the 66-well plate code options: 66VialGen PlateR and 66VialGenPlateC.

Multiwash Section in Analyst® Device Driver 1.3 Software Is Grayed Out when Configured with Agilent 1290 MultiSampler

The Analyst® Device Driver 1.3 software includes a Multi-wash section on the Multisampler tab when the LC portion of an Analyst software method is open, but it is grayed out. If the multi-wash hardware accessory is not installed on the autosampler, the Multi-wash screen will not be available for editing.

Where Is the License for a LibraryView™ Software Library Installed?

If the LibraryView™ software library cannot be viewed through the software after installing it, the location of the library license needs to be checked. It should be installed to C:\Program Files\AB SCIEX\LibraryView\bin.

Maximum Setting for Collision Energy (CE) during Compound Optimization

The maximum value that can be used for collision energy (CE) during compound optimization in Analyst® software is 130, even though the CE value can be set to 180 in the parameter settings.

PA800 How To - Capillary Removal

Capillary Removal

Unable to Configure a Shimadzu LC System after Upgrading to Analyst® 1.7 Software

A Shimadzu LC system may not be recognized and may not be able to be configured after an upgrade to Analyst® 1.7 software if a computer image on the PC was not sourced from SCIEX.

Can I Use the TOMKit Library with SCIEX OS and/or LibraryView™ Software?

The TOMKit Libraries are newer library entities, and they are not compatible with SCIEX OS or LibraryView™ software. The TOMKit libraries are for use with Agilent instruments only currently.

Building a Quant Method in SCIEX OS Software for DAD Data

Peaks from DAD or UV chromatograms that were acquired during an LC/MS experiment can be quantified in SCIEX OS software. Open a new quantitation method in SCIEX OS software, and then select the representative sample. On the Components tab, select the drop down menu in the Experiment Index column. Select the DAD experiment for each transition and add the desired wavelength to quantitate in the Start - Stop (Wavelength) column.

Which Version of Watson LIMS Is Compatible with SCIEX OS Software 1.7?

SCIEX OS software 1.7 has been tested with Watson LIMS server/client version 7.6, Oracle server/client 12.2.0.1.0 SE (64-bit) and 12.2.0.1.0 (32-bit).

How Do I Import and Export ChemoView Settings

ChemoView settings can be Exported so that they can be backed up or transferred between instruments or computers using the Import function.

Reporter Error: Template Not in Your Trusted Location

If a reporter error shows that the template is not in the trusted location when trying to save or move a report template, then the Trusted Locations list in Word must be updated to include locations where SCIEX reports and templates are edited.

What Default URL Is Used for Configuring the Mascot Server with ProteinPilot™ Software?

Configuring the Mascot server from the ProteinPilot™ software requires the default URL to be used.

Where Are the SCIEX OS Software Project Audit Trail Archives Stored?

The audit trail records for a SCIEX OS software project are stored in the Audit Data sub-folder for the project. The audit trail file name is ProjectAuditEvents.atds.

What Curtain Gas Setting Should Be Used on the QTRAP® 6500 System?

The QTRAP® 6500 system has a limit of 50 psi for the curtain gas. Curtain gas settings should not be higher than 40-45 psi.

Is It Possible To Monitor More MRMs Per Well than Specified for the Echo MS System?

Yes. The specified four MRMs per well is based on the peak width from a single droplet ejection.

License Error when Launching LipidView™ 1.2 Software on Windows 10

When launching LipidView™ 1.2 software on Windows 10, a license error appears indicating that the license has expired, even when a permanent license has been installed. To resolve this issue, right click on the LipidView software icon and select Run as Administrator to launch the software.

Setting Up Manual Integration (Percentage Rule) in SCIEX OS Software

To set up the parameter Manual Integration (Percentage Rule) in SCIEX OS software, a results table and peak review will need to be open in Analytics mode. In the peak review pane, select the Peak review display settings button under the Options menu. Then select the Appearance tab. The manual integration percent rule can be set by clicking the drop down arrow as shown below.

Analyst® Software Error: Please Enter Positive Numeric Value Only

While attempting to select manual tune mode, users of Analyst® software may see the error message "Please enter positive numeric value only." This error results from commas instead of periods being used as decimal points in non-English based operating systems.

To Install MultiQuant™ Software, Log into Windows as an Administrator

When installing a MultiQuant™ software license, an error message appears that says "The feature you are trying to access is unavailable. Cannot find license file/License File cannot be opened." To override this error, the software and license need to be installed while logged into Windows as an administrator.

Can a Precursor-ion IDA Experiment Be Performed on a SCIEX TripleTOF System?

None of the SCIEX TOF instruments, 5600, 5600+, 6600, X500R, or X500B, can do a precursor ion IDA experiment.

General SQL Installation Errors for SCIEX OS and LibraryView™ Software

Installing any program with SQL-based software components (e.g., SCIEX OS and LibraryView™ software) requires that a certain rules are observed. These rules are set by Microsoft, and are not covered in the release notes for the SCIEX software installation that includes the additional of SQL components.

My Annual SCIEX License Suddenly Stopped Working Before It Expired, Why?

A new annual SCIEX subscription license stopped working suddenly despite having many months of use remaining.

Using 32 Karat Software with a Corporate Network or Domain

32 Karat software can be used with a company network 1) to control user logins and permissions via a Windows operating system (OS) network domain controller and 2) to allow access to network printers and hard drives.

MultiQuant™ Software's Audit Trail and Security Feature Requires a Base and an Extension License

When installing MultiQuant™ software with the audit trail and security extension license, the license installs successfully, but MultiQuant software does not launch. Instead, a -5 error code appears and the error message displayed reads, "This feature is not licensed. It cannot be used." MultiQuant requires a base license to be installed alongside its audit trail and security extension license.

Users Are Unable to Save or Submit Batches with Long File Paths in Analyst® Software 1.7.2

In Analyst® software 1.7.2, users cannot save or submit an acquisition batch if the project path is longer than 126 characters.

What Are the Advantages of the .wiff2 Data File Format?

The .wiff2 meta data file generated by SCIEX OS software is designed to offer users improved security for their data. One of the primary advantages is the .wiff2 meta data file is encrypted, which prevents software users from tampering with results.

The Report Option Is Missing from the MultiQuant™ Software File Menu

When the Report option is missing entirely from the MultiQuant™ software File menu, check that the version of Microsoft Office installed is correct.

Explanation of 32 Karat License Key Program and User License Types

32 Karat software requires a hardware license key to launch, and on older versions, a similar software license key is installed from a floppy disk.

Setup Cannot Continue Error when Installing MultiQuant™ Software

The MutliQuant™ software installation error "Setup cannot continue until all system components have been successfully installed" indicates that a Windows 10 operating system is present and the software must be reinstalled on a Windows 7 system.

Creating a Processing Method in ChemoView™ Software

To create a new processing method in ChemoView™ software, select the Add New Processing Method button.

DiscoveryQuant Quicktune DP 0 DP Scan Problem

Using DiscoveryQuant 2.1.3 Quick Tune will set the DP value to 0 and then Fine Tune will fail as it has an invalid DP value. The temporary Q3 MI scan method for the quicktune will show the MH ion with 2 DP scans both at 200v though this voltage may vary.

Is the Shimadzu LC-40 Fluorescence Detector RF-20AXS Supported in Analyst® Software?

Yes, Analyst® software 1.7.2 can directly control the Shimadzu Nexera LC-40 fluorescence detector RF-20AXS.

Can I display the pressure trace of a chromatogram when I use an Agilent LC system with Analyst

Description how to activate the pressure trace in the hardware profile

How Do I Select a Library and Perform a Library Search in SCIEX OS Software?

To select a library to use with a targeted or non-targeted screening method in SCIEX OS software, open an existing processing method or edit an embedded method from a results table. Ensure that the checkbox for Quantitation and targeted identification or for Non-targeted screening is selected. Then navigate to the Library Search option to set the library search parameters.

Are Validation Services Available To Install and Test the SCIEX OS Software in My Lab?

Yes, the SCIEX validation services team has helpful and cost-effective services for SCIEX OS software validation.

What Are the Specifications for Installing SCIEX OS Software 2.2 on an Acquisition PC?

To install SCIEX OS software version 2.2 on an acquisition workstation, the PC needs to meet specific requirements. The following PCs are supported: 1) SCIEX workstation or workstation+ and 2) SCIEX Alpha workstation 2020.

How Is a Formula Column Added to a Result Table in Analyst® Software?

To add a formula column to a results table in Analyst® software, right click on the results table and select Add Formula Column.

Which Version of DiscoveryQuant™ Software Supports the Acquity LC on Windows 10?

The Windows 10 compatible version of DiscoveryQuant™ software that supports Acquity LC is version 3.0.1 Hotfix 2.

Can SCIEX OS Software Be Installed on a PC with Windows 10 Hotfix2?

No, SCIEX OS software cannot be installed on a PC with Windows 10 hotfix2.

How Are Retention Times Updated in MultiQuant™ Software Processing Methods?

There are two ways to update retention times (RTs) in MultiQuant™ software quantitation methods. One way is temporary and the other way is permanent.

Are CloudConnect and SWATH® MicroApps within PeakView® Software Windows 10 Compatible?

The software package, PeakView® 2.2, CloudConnect 1.2 beta and SWATH® 2.0.1 software. is needed to perform the OneOmics workflow and/or SWATH protein data processing and is Windows 7 and Windows 10, 64-bit compatible.

How to Add Select Samples to a Report Created in SCIEX OS Software

To add only selected samples from a results table created in SCIEX OS software in a report, uncheck the Reportable column for the sample you do not want to report. Then edit your report template to include an If statement within a ForEachSample loop to include $Reportable="TRUE".

Valve Model Will Not Stop Equilibrating In SCIEX OS Software 2.1

When equilibrating any MS method on a SCIEX 7500 system, the "Valve Model" will never finish equilibrating even after the specified time when using SCIEX OS software 2.1.

MultiQuant™ or SCIEX OS Software: The Ion Ratios on the Report and Results Table Do Not Match

When a query file is used to calculate the ion ratio calculations in a MultiQuant™ or SCIEX OS software report, the values for the internal standards ion ratios in the report output will not match those in the results table. This issue is observed when the internal standards are not assigned to the analytes in the order in which they are listed on the quantitation/processing method.

How Many Modified Amino Acids and Modifications Can Be Added in PeakView® Software?

In general, the number of modified amino acids and modifications that can be added is unlimited in the PeakView® software.

Is It Possible to View Extracted Ions in Separate Panes in SCIEX OS Software?

To show extracted ions in SCIEX OS software, the data file must be opened in the Explore module and then Ctrl+E is used to extract the ions of interest. The Split Traces into Separate Panes option in the Graph menu allows for the extracted ions to be displayed in separate panes.

Should I Revalidate My Software?

Periodic reviews of validated systems must be performed to ensure that no changes have been made that affect the validated state of the system. If there is a change, then the software needs to be revalidated.

Integrating Peaks from a DAD or UV Chromatogram in Analyst® Software

Analyst® software Quantitate mode can be used to integrate peaks from DAD or UV chromatograms that were acquired during an LC/MS experiment.

How Can I Get a Biologics Explorer Trial License?

To obtain a Biologics Explorer (BE) 1.x trial license, send an email to biologics.explorer.orders@sciex.com with a request for a 30-day trial.

Modifying a Report Template to Report Select Sample Types Using IF Statements

An IF statement can be added to limit the sample types that need to be output to a report from a results table created in Analyst® software, MultiQuant™ software or SCIEX OS software. Below are few examples of how to write an IF statement within the loops ForEachSample or ForEachAnalyte.

Venting and Pumping Down the 5500 Series Mass Spectrometer

How to remove the vacuum and pump the machine back down afterwards

Mapped Network Drive Issue when Using SCIEX OS Software Version 2.1.6

Many customers reported issues when using a mapped network drive to store for data for SCIEX OS software version 2.1.6; however, if the data was download to a local drive, no errors were received.

Uninstalling and Reinstalling SCIEX OS 1.x Software

This article describes how to uninstall SCIEX OS software and manually remove certain files in order to completely remove the software.

Communication Issues when Switching Between ExionLC and Eksigent Hardware Profiles in Analyst® Software

Switching from a hardware profile that contains an ExionLC (or Shimadzu LC) system to a hardware profile with an Eksigent LC when both LCs are connected to the PC can cause Analyst® 1.6.3 software to crash, resulting in communications issues.

PA800 How To - Capillary Storage

Capillary Storage Details for PA800 System

Intact protein script for TripleTOF™ instruments

This knowledge article summarizes when to use the intact protein script in

Shimadzu Autosampler Rack Must Be Seated Correctly for Analyst® Software to Acquire Samples

Acquisition and equilibration errors in Analyst® software signalling a Shimadzu LC controller error may be the result of the autosampler rack not seated correctly in the autosampler housing.

MultiQuant™ MD 3.0.2 Software Will Not Open and No Error Message Appears

If MultiQuant™ MD 3.0.2 software will not open when the desktop icon is selected and there is no error message appearing, this usually indicates that the software was installed on a non-compatible operating system. MultiQuant MD 3.0.2 software must be installed on Window 7, and it will not launch in a Windows 10 enviroment.

Is the Database for DiscoveryQuant™ Software Limited to 1 GB?

Yes, the size of the Microsoft Access database file is limited to 2 GB. However, the reliability of the database degrades before reaching the 2 GB limit, so it is suggested that DiscoveryQuant™ software users create a new database before the database exceeds 1 GB.

What Is Skyline Software and What Data Types Does It Work With?

This article includes a general description of the features of Skyline software and the possible data formats from SCIEX instruments that work with Skyline.

PPG Reference Peak List Table Is Missing when Tuning and Cannot Be Opened

To view the mass calibration peak lists in Analyst® software while using the manual tuning mode, go to the Tools menu and select Settings-Appearance options-Miscellaneous-Show Mass calibration peak list.

Removing Analytes from a MultiQuant Software Method (.qmethod)

To remove an unneeded analyte's MRM transitions from a MultiQuant software method, the quantitation method must be opened and the Delete Selected Rows function must be used.

Analyst Projects dropdown is not in alphanumeric order

Analyst Projects drop down provides project list in what appears to be an unordered list

How to Electronically Reset a SCIEX 7500 System

This article describes the steps for resetting the SCIEX 7500 series instruments.

Ekspert 400 AS3 Error Message Pump volume is not sufficient to run LC method without a restroke.

Ekspert 400 AS3 Error Message Pump volume is not sufficient to run LC method without a restroke

Exporting a Centroid Spectrum from SCIEX OS Software

To export a centroid spectrum from SCIEX OS software, load a data file and open a spectrum in explore mode; click Centroid Spectrum from Process drop-down list, and then select Export from the File drop-down list.

Ekspert™ 400 LC system – Change the mobile phase

How to change mobile phase on Ekspert™ 400 LC system

CDS Autocalibration without a HPLC System in the Analyst® Hardware Profile

Analyst® software will acquire data even if the CDS autocalibration system is activated without a HPLC system in the hardware profile.

How Can Audit Trail Records Be Viewed from SCIEX OS Software?

To view audit trail records in Sciex OS Software, open the Audit Trail workspace. The Audit Trial screen will appear. Select Workstation in the left pane to view the audit trail for the workstation. Select Project in the left pane to view the audit trail for the project of interest.

Late elution of peaks on Eksigent nano Tempo Classic

Late elution of peaks on Eksigent nano Tempo Classic

Computer error: Raid status was degraded

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

How to remove unused template definitions from DiscoveryQuant 2.1.x

This document explains how to remove unused template definitions from the DiscoveryQuant Analyze setup window

Why is the Option to Sum Multiple Ions Grayed Out in SCIEX OS Software?

In order to use the Sum Multiple Ions option in the SCIEX OS software, the group name for each compound needs to be entered into the Group column.

Access to Path Is Denied Error when Installing License

When installing a Sciex software license, an error message appears that says the license was not sucessfully installed and the access to the path C:\Program Files\AB Sciex\.... is denied. This error message indicates that 1) the user doesn't have sufficient privileges to access the Program Files, or 2) the license file needs to be placed in correct location in the Program FIles manually.

Improving Peak Resolution when Using Capillary Electrophoresis

Basic tips are presented here for improving the overall resolution of capillary electrophoresis (CE) separations.

Why Do the Calculated Concentration Values Show as Degenerate in SCIEX OS Software?

In SCIEX OS software, if a value in the Calculated Concentration column displays as degenerate, this is because the values for Actual Concentration for standard samples have not been added to the results table.

Is Digital PicoView® Source Windows 10 compatible?

Digital PicoView® Source is a nano ion source from New Objectives that is Windows 10 compatible and can be used with many SCIEX mass spectrometers.

Can the Default Location of MultiQuant™ Software Queries Be Changed?

It is not possible to change the default location of MultiQuant™ software queries.

Where Are the Queries Used with MultiQuant™ Software Stored?

MultiQuant™ software queries are saved in the following folder: C:\ProgramData\AB SCIEX\MultiQuant\Queries.

Data Not Visible for New Results Table Processing in SCIEX OS Software

To create a new results table in SCIEX OS software, users must browse to data sets (.wiff files) from the Analytics mode through the Results menu. When New and then Browse are selected to start a new results table, no data set is seen when the data folder is selected in the Select Folder menu. It appears as if the raw .wiff files are missing.

What Are the Most Common Installation Issues for SCIEX OS Software 1.7?

Some of the most commonly observed installation issues with SCIEX OS software 1.7 are summarized here. Instructions on how to uninstall previous versions of SCIEX OS software are also included.

Importing a Library Package into LibraryView™ Software 1.3

To install a newly downloaded library package (.lpb file), select the import button in LibraryView™ software and then the correct file type.

What Happens to the SCIEX OS Software when the License for the Central Administrator Console (CAC) Software Expires?

If the license expires for the Central Administrator Console (CAC) software, the server data is maintained in the CAC database, but users won’t be able to launch the CAC application. The SCIEX OS software installed on the client workstations will continue to launch and work with last retrieved data while the CAC server is not reachable.

How to Remove "No Data" from Report Output Generated from SCIEX OS Software

An IF/ELSE statement can be created to filter out the “No data” response in a report in SCIEX OS software.

Detuning an Acquisition Method in Analyst® Software

If the signal seems to be saturating during acquisition on a Triple Quad™ 5500 system using Analyst® software, one option is to detune the acquisition method by using non-optimized collision energy values for the MRM transitions.

User Role Not Assigned Correctly in SCIEX OS Software

To resolve the error "You do not have the correct SCIEX OS role permissions to access this product" in SCIEX OS software, the software needs to be opened under the Windows user login that the software was installed under.

How Do I Generate a Report with Only the Quantifiers in SCIEX OS Software?

Open the Analytics workspace in SCIEX OS software and open a results table. In the More menu, click Table Display Settings. A list of column names will appear. Select Reportable to make this option visible. Selecting the Reportable column shows whether or not the result is included in reports, exports, and LIMS transfers. Under Reportable column, select Quantifiers for the component.

What Files Must Be Backed Up before an Analyst Software Reinstall?

Back up the API Instrument project folder in the Analyst Data folder prior to any reinstall or upgrade of the Analyst software. To upgrade an older version of Analyst, remove and back up the Analyst Data folder and any remaining short cuts on your workstation. Reboot the PC and install the new version of the software.

How Is a Hardware Profile Created in Simulation Mode with an Eksigent 4.x and Analyst TF Software?

Description of the steps to place the Eksigent software in the AAO system of the Analyst® software and how to run it in simulation mode.

SCIEX OS 1.5 Software Launch Errors Overcome by Starting Clearcore2 Services

The Clearcore2 Service runs in the background for SCIEX OS 1.5 software. The service will need to be started manually in the Services section of the Control Panel if SCIEX OS will not launch.

Setting the High Limit Value in the MPX 2.0 Software for Real Time Data-Dependent Decision (RTD3)

In the MPX software 2.0, the carryover detection feature requires that the values for the high or region height columns need to be defined for each component. These values are used to set the flag for the above upper concentration limit.

Can Standard Concentration Values Be Stored in a MultiQuant™ Software Quantitation Method?

No, the concentration values for a standard or quality control samples cannot be stored in or saved to the MultiQuant™ software quantitation method.

IF Statement Syntax for Calculated Columns in SCIEX OS Software 2.1.6

Reports created with SCIEX OS software use templates with embedded tags. One of the commonly used tags is the IF statement, and the basic syntax for this tag is as follows: if(<condition>;<value if true>;<value if false>)

MarkerView Microsoft Office 2013 This method or property is not available because this command is not available for reading.

When Markerview 1.2.1 is used in conjunction with Microsoft Office 2013 report generation fails with the message This method or property is not available because this command is not available for reading.

Viewing Real-Time PDA or UV-Vis Data in Analyst® Software when Employing a Shimadzu AAO

Viewing real-time photo-diode array (PDA) or UV-vis data is not possible in Analyst® software when employing a Shimadzu diode array or UV-vis detector.

Defining Analyte and Analyte Type in ChemoView™ Software

To define a new analyte in ChemoView™ software, navigate to the Manage/Analyte module, and select the Add New Analyte button.To define analyte type, select the Setup menu and chose the Analyte Types option.

Can I Install the Central Administrator Console (CAC) Software on a Server Also Running a FlexNet Licensing Server?

Yes, the SCIEX OS software Central Administrator Console (CAC) software can reside on the same server as the FlexNet Licensing Server.

SCIEX Website Login Requires that Your Email Address Is Verified

After creating your login for the SCIEX website, you will be asked to verify your email. Click on the link in the webpage that appears after your account is created or in the email sent to you by SciexNOW to activate your online account with SCIEX.

Can Analyst® Software Directly Control the Shimadzu SPD-M40 Detector?

Analyst® software 1.7.2 can directly control the Shimadzu SPD-M40 detector through the Shimadzu MIMIC 2 driver that has been incorporated into Analyst software.

Submitting and Starting Sample Batch in Analyst® Software

How to start acquiring data using Analyst software

Does My Acquisition PC Have a Bad Ethernet Card?

This article summarizes some issues that might contribute to a bad network card.

Centering a Peak in a SCIEX OS Software Peak Review Pane

To adjust the location of the peak in the window and to center it, select the peak review icon in the results table, click Options and then Peak review display settings. In the Zooming tab, select the Zoom time axis to view peak check box and add the desired retention time.

How Are SWATH™ Acquisition Files Recalibrated?

The procedure for recalibrating a SWATH™ acquisition file is outlined here.

Does a POET Error Reflect a Possible Network Connectivity Error or an Unsupported Network Drive Type?

This article describes what to do to identify this POET error in more detail. A POET error can arise when saving a results table in Analyst® software, with the error typically arising when saving the results table file to a network drive.

Considerations for Bin Sizes when Creating a TOF Acquisition Method in Analyst® TF Software

What does "bin size" mean and what is the rule of thumb for setting bin sizes when setting up acquisition methods for a TOF MS system in Analyst® TF software.

Fatal Error in MultiQuant™ Software: The File or Directory Is Corrupted and Unreadable

While opening a file or creating a results table in MultiQuant™ software, users may receive the error message "The file directory is corrupted and unreadable." Running the Windows file explorer drive check can resolve this issue.

How Can I Find the Computer ID on a Win 7 Operating System?

To locate the computer IDs (MAC or physical addresses) on a computer with a Windows 7 operating system, run the DOS command ipconfig/all, and a list of physical addresses be provided.

How Do I Obtain a Trial License for SCIEX Software?

To download and obtain a licensed trial for a SCIEX companion software, navigate to https://sciex.com/products/software#tryfree and select the software that you would like to try.

How can I create a record of the security settings from Analyst Software

Explains how to record your security settings from an Analyst workstation in either printed format or PDF file using a PDF printer.

How Is Peak Asymmetry Caluclated in Analyst® Software Quantitate Mode?

Peak asymmetry is calculated in Analyst® software Quantitate mode using the formula ((Peak end time) - (Retention Time)) / ((Retention Time - (Peak start time)).

Resolving the Report Error in SCIEX OS Software: "Error during Report generation"

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

Changing the Integration Algorithm in SCIEX OS 1.6.1 Software

To change the integration parameter used in a quantitative processing method in the Analytics module of SCIEX OS Software, select the Projects menu, and under the Projects default settings, select Quantitative Processing > Integration Defaults > Integration Algorithm.

PA800 How To - Installing the Cartridge Aperture

Procedure for Installing the Cartridge Aperture on the PA800 system

How to Improve SCIEX OS Software Performance during Data Analysis

SCIEX OS software may perform slowly during data analysis due to the location of the data files being processed. Relocating data files from a temporary location (such as the Windows desktop) to a SCIEX OS or Analyst software project folder that is located in the root directory mapped in the Configuration module of SCIEX OS software may improve the software performance. 

SCIEX OS 1-5 Software

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

How to Create an Ion Ratio Flag in a Report Template

To flag an ion ratio as pass or fail in a report, an If/Else statement needs to be added using the MQ_Ion_Ratio tag.

How to Change the Font in a Report Template?

Use these instructions to change the font of the text appearing in a report.

LightSight® Software Acquisition Mode Is Not Supported on a SCIEX 6500+ LC-MS/MS System

LightSight® software version 2.3.x acquisition mode is not supported on a SCIEX QTRAP® or Triple Quad™ 6500+ LC-MS/MS System.

Specifications for the SCIEX Pre-Assembled Capillary Cartridge for CE-SDS Applications

Specifications for the SCIEX pre-assembled capillary cartridge (part number A55625) are provided here.

Can I Use the SWATH® Variable Window Calculator 1.2 with All SCIEX QTOF Systems?

The SWATH® Variable Window Calculator 1.2 is a new updated calculator that supports all SCIEX QTOF instruments with Analyst® TF and SCIEX OS software versions.

Upgrading MultiQuant™ Software from version 3.0.1 to 3.0.x

To upgrade to MultiQuant™ software from version 3.0 to version 3.0.1, 3.0.2 or 3.0.3, the following instructions should be followed.

Setting the Security Configuration to Single User Mode in Analyst® Software

To set the security configuration to single-user mode in Analyst® software, navigate to the Configure mode, and then select the Security Configuration option. Select More from the bottom left side of the splash screen, and then select the Security tab at the top of the screen. Under the Security Mode tab, choose the Single User Mode option. Click Apply and OK.

Analyst Regression Equations

This document summarises the equations used by Analyst to calculate the regression curves used for Quantitation.

Selecting a New Tab in the Waters Method Editor Resolves LC Method Creation Error in Analyst® Software

An error results when selecting the ACQ-BSM tab when creating an LC method using the Acquity Method Editor accessed through Analyst® software. It can be resolved by selecting any other tab in the method editor screen.

Licensing Information for the SWATH Acquisition™ MicroApp in PeakView® Software

When viewing license information in the PeakView® software Help menu, the SWATH™ acquisition microapp licensing info shows in the plug-ins list, but not in the PeakView License Report screen.

How Are the Method Parameters Chosen for Autocalibration Samples in the X500 Series?

Method parameters for autocalibrations submitted in SCIEX OS batches are automatically chosen from the sample after the autocalibration.

The Analyst application cannot be started because the current user is not in the security database.

When Analyst is started the message The Analyst application cannot be started because the current user is not in the security database or has not been assigned a user type. You may also get this message if the network is not available. Please contact your administrator.

How Do I Migrate Data from a DiscoveryQuant™ 2.1 SQL Server to a DiscoveryQuant™ 3.0 SQL Server

This article describes how to migrate DiscoveryQuant 2.1.x SQL Server Data to a DiscoveryQuant 3.0 SQL Server Installation

Using the Purity Score To Assess a Match to My Library Search Results in SCIEX OS Software

All peaks from both the unknown and library spectra are used to calculate the Purity Score, which is used to assess how well a compound matches an existing library compound. A high value indicates a high probability that the unknown spectrum has been correctly identified; a low value indicates the match is less certain.

Locating the Name of a Server or PC Using the Command Prompt Window

This article describes the DOS commands used to access the name of the server or PC.

How Is a ChemSpider Software License Activated within PeakView® Software?

The software activation procedure is described step-by-step for ChemSpider, which needs to be activated within PeakView® software's FormularFinder feature.

Nomencature Used by BiopharmaView™ Software for N-Gylcan Names

BioPharmaView™ software uses predefined N-glycan structures (following the Ludger product names), or software users have the option to build their own custom modifications.

Can I Use a Regular Expression (Regex) to Filter Data in SCIEX OS Software?

A regular expression (regex) can be used to filter data in a results tables and in reports created with SCIEX OS software.

Enabling Hidden Folders in Windows 10 to Install an Analyst® Software License

Many users find that they cannot activate their Analyst® 1.7 software license file on a Windows 10 operating system because the folder where the license file is installed does not show.

How Is the Software Protection Service in Windows 7 Disabled?

The steps for disabling the Software Protection service in Windows 7 are provided here.

License Not Supported Error Appears after Installing MultiQuant™ Software

After a new MultiQuant™ software installation, the error message, "License not supported" is displayed.

Internal Standard Recovery Calculations in MultiQuant™ and SCIEX OS Software

SCIEX OS and MultiQuant™ software both calculate internal standard (IS) recovery but use different approaches. SCIEX OS software uses a built-in functionality for creating custom formulas to calculate IS recovery. MultiQuant™ software requires a query to be applied to the results table to perform the IS recovery calculation and to add a custom IS recovery column to the results table.

MPX™ Software Batch Stoppage due to Daylight Savings Time Shift

If the computer clock updates for daylight savings time while MPX™ software is submitting a batch, data corruption and batch stoppage can occur. The clock must be set up so that automatic updates to the time do not occur.

Does SCIEX OS Software Offer Tools To Assist with Achieving 21 CFR Part 11 Compliance?

The features within SCIEX OS software that help users achieve 21 CFR Part 11 compliance are explored in the article, "SCIEX OS LC/MS Software and 21 CFR Part 11 Regulations".

Can a Processing Method Built in ChemoView™ Software Be Converted for Use in SCIEX OS Software?

No, a processing method built in ChemoView™ software cannot be converted for use in SCIEX OS software. Files built in ChemoView software are not supported in SCIEX OS software.

Does SimGlycan® Software Use .wiff2 File Formats from X500 Series Instruments?

This article describes the possible file input formats for SimGlycan® software.

Converting .Xml Templates to .Docx Reporter Templates for Analyst® 1.5 to 1.6 Software

To convert the .xml files to .docx reporter templates for Analyst® software, the templates must first be updated to .docx. This is done by using the AB SCIEX Reporter Template Converter located in the following directory: C:\Program Files\ABSCIEX\Reporter Template Converter\Template Converter.

Acetic Acid Is Needed To Prepare the PepCalMix Peptides in the SWATH® Acquisition Performance Kit

This article describes the experimental issues when formic acid is used to prepare the PepCalMix for the SWATH® Acquisition Performance Kit instead of 5% acetic acid.

Obtaining a Smaller Volume Divert Valve for a 4500, 5500 and 6500 LCMS Systems

To obtain a smaller volume divert valve for a 4500, 5500 or 6500 LCMS system, a new part must be ordered from Valco, part number of C52-2006I.

Is There a "Batch-Convert" Function Available in Keystone™ Converter Software?

Yes, Keystone™ converter software offers a command line option to allow for the creation of automated processes for converting large pools of legacy data.

What Are the Options in Data Explorer Software To Improve Spectral Quality?

This document lists a couple of options on how to improve spectral quality using Data Explorer software 4.11

Activating a SCIEX Software Trial on Workstations that do not have Internet Connection

Activating SCIEX software on a computer without internet access can be made simpler by following these steps

Replacing the Logo Shown in My Report in SCIEX OS Software

To replace the logo shown in a report in SCIEX OS software after the results table is reviewed, click Reporting, then Create Report, and then save the Results Table. Click Replace Logo.

I am having trouble reaching temperature in the ALS Thermostat. What is the effective range of the ACMP Peltier?

The ACMP Peltier effectivity is based on the ambient temperature of the instrument. The operational range of the ACMP is between 4-40C.

Recommended NIST Library Processing Method Settings

The recommended library search settings when using the NIST library with MasterView™ or SCIEX OS software are listed here and include deactivating collision energy filtering.

Can an Analyst® Software Results Table Be Opened in SCIEX OS Software?

No, an Analyst® software results table cannot be opened in SCIEX OS software. The user will have to recreate the Analyst results table in SCIEX OS software.

Explore Mode - Extract Ions - Overlay Multiple Panes Automatically

Where to find the settings for automatically overlay panes when extracting multiple Ions.

Watson LIMS Needs To Be in Compatibility Mode for Use with SCIEX OS Software

When transferring data from SCIEX OS software to Watson LIMS, the Watson software did not appear to be importing the data.

What Value Should Be Used for the XIC Width in My SWATH® Acquisition MicroApp Processing Settings?

One common error when using the SWATH® Acquisition MicroApp 2.0.1 for processing SWATH data is to relate the XIC width setting in the processing software with the mass accuracy of the instrument, and set the XIC width to a value that is too low. XIC extraction widths should be set to 50 to 75 ppm, regardless of the mass accuracy of the acquired data.

How Do I Install the Intact Protein Script on the TripleTOF® 5600 and 6600 Systems?

The Intact Protein script can be installed from the Analyst® TF software directory located at: C:\Program Files (x86)\Analyst\Scripts. The ShowInTuneLayout script must be installed and enabled in order to acquire intact proteins.

Why are the peaks centroided in ProteinPilot Group files

Why are the peaks centroided in ProteinPilot Group files

How to modify the Project Results Table Settings in Analyst

All available project results table settings can be accessed and modified via Tools.

PeakView® Software 1.2 License Code Replacement

PeakView® software 1.2 displays an error message indicating that the license is about to expire. The software needs to be reinstalled, and new license code obtained.

Finding the Pulser Frequency in an Acquisition Method Built in Analyst® TF Software

In general, the pulser frequency is automatically calculated for a given mass range in the method editor using the Analyst® TF software. To see the pulser frequency value, follow the directions below.

Can a Method Built in Cliquid® Software Be Converted to a Method for SCIEX OS Software?

No, methods built in Cliquid® software cannot be converted for use in SCIEX OS software. Cliquid software method files are not supported in SCIEX OS software.

Where Can I Find Out If My Software Upgrade Is Free or a Paid Upgrade?

To determine if your software upgrade is complimentary, check the SCIEX webpage, Software Product Lifecycle at https://sciex.com/software-support/software-support-policy.

Resetting an Agilent Infinity II LC System after Receiving an ADD Error

This article explains how to reset an Agilent Infinity II LC system after receiving an ADD error by clearing the configuration.

Dionex: Is the DCMS Link 2.10 and 2.12 Compatible with Win7 32- and 64-bit?

The DCMSLink is not validated to work with a Win 7 operating system (OS) as stated in the Dionex release notes.

What Library Database File Types Can Be Imported into LibraryView™ Software 1.4?

Many different types of compound and library databases can be imported into LibraryView™ software version 1.4. The following options for source files are acceptable for importing library compounds into LibraryView software: LibraryView Package (*.lbp), DiscoveryQuant™ Compound Database (*.mdb), Analyst® Compound Database (*.mdb), Cliquid® Package (.clq), Excel file (*.xls), Overwrite Database with LibraryView Snapshot (*.lbp), and Third Party Library Package (*.tplp)

What Are the Current Limitations of the SWATH® Variable Window Calculator Tool?

The SWATH® Variable Window Calculator tool can be used with Analyst® TF 1.7 software and SCIEX OS 1.7 software and higher for many QTOF instruments. This article lists the maximum target number of Q1 windows and the maximum upper m/z limit for each QTOF instrument.

What Are the Considerations for Using Ion Pairing Reagents in My Mobile Phases?

Ion pairing reagents can greatly help with problematic chromatography, but any added ion pairing reagents also tend to stick to LC components and the column, as well as to the MS source, leading to signal suppression and diminished column performance. This article includes suggestions for a more successful experience when using ion pairing reagents and mass spectrometry.

ProteinPilot error fraglet.exe CHEMICAL EXCEPTION

ProteinPilot error fraglet.exe CHEMICAL EXCEPTION

Connecting to a New Compound Database Library in Analyst® Software

The steps needed to connect to a new compound database library in Analyst® Software are detailed in this article.

Migrating the SQL Server from DiscoveryQuant™ 2.1 Software to Version 3.0.x

Instructions are provided here for migrating the SQL server for DiscoveryQuant™ 2.1 to an installation of DiscoveryQuant 3.0.x software.

Shimadzu 30AC Autosampler External Rinse Method Definitions in Analyst® Software

On the Shimadzu 30AC autosampler, the external rinse function flushes the needle's exterior using a solution that is pushed to the rinse port by the rinse pump. When building an LCMS acquisition method in Analyst® software, the rinse method definitions can be accessed through the Flow Channel Reference radio button under the Autosampler tab.

When Does SCIEX OS Sofware Start Archiving Audit Trail Records?

In SCIEX OS software, the audit trail will be archived when it reaches 20,000 records.

Cliquid® Software Does Not Show Quantitation Values for Qualitative Transitions in the Sample List

When Cliquid® software is used to submit samples, the sample list shows only the group name instead of each individual transition (e.g., only Testosterone is shown, instead of Testosterone 1 and Testosterone 2) so only one concentration from one transition can be added. To ensure that Cliquid software reads the full transition name, an underscore in between the name and number must be added (e.g., Testosterone_1 and Testosterone_2).

Crashing on Windows 7 when in ExploreQuantitate Mode AB Sciex Analyst has stopped working

When using Analyst versions 1.6.x with Windows 7 Operating System Analyst will stop with the message AB Sciex Analyst has stopped working. This will usually happen when the mouse cursor is moved across the chromatogram pane.

Creating a Peptide Library in Skyline with a ProteinPilot™ 5.0 Software .Group File

If a user installs ProteinPilot™ 5.0 software with Skyline, old and new group files will not be able to be opened because the converter has changed. An error message will be displayed when building peptide libraries while importing a ProteinPilot group file.

How Is Quantitation Information Imported into an Analyst® Software Batch?

To import updated quantitation information into the batch, export the batch file as a text file from Analyst® software and edit the information in Excel.

How many processing cores will my ProteinPilot Software use?

The number of processing cores used by ProteinPilot Software is defined by the license file and the physical capabilities of the instrument.

How Do You Select Root Directory for a Workgroup in Analyst® Software 1.6.3?

To select a root directory for a workgroup in Analyst® software 1.6.3, the workstations should be removed from the workgroup and then re-added.

Is ProteinPilot™ Software 5.0.1 Compatible with Windows 10?

Is ProteinPilot™ Software 5.0.1 compatible with Windows10? No, it works only with Windows 7, Service Pack 1, 64-bit.

What Normalization Can I Use in MarkerView™ Software 1.3.1 when Processing My Peptide Data?

MarkerView™ software 1.3.1 software has a new Most Likely Ratio (MLR) normalization algorithm incorporated info this newest version of the software.

How Do I Configure Analyst® Software for Network Acquisition

Network data acquisition can be very useful for data integrity backup security and access purposes. This walkthrough explains how to configure Network Acquisition using Analyst Software.

Installing the SCIEX OS Software CFR License

Save the CFR license file to the C:\ Program Files\Sciex\Sciex OS folder where the SCIEX OS license is located.

What is the Maximum Length of the Project Path in Analyst® Software to Submit a Batch Successfully?

In Analyst® software 1.7.2, users cannot save or submit an acquisition batch if the name of the project path is longer than 126 characters.

Resolving SCIEX OS Software Error: Cannot Open LibraryViewServiceHost Service on Computer

When trying to access the Analytics mode in SCIEX OS software when logged into Windows as a user without administrative privileges, an error is received: "Error has occurred: Cannot open LibraryViewServiceHost service on computer '.'. LibraryView service must be running." The LibraryViewServiceHost was not started when the Analytics mode was opened, and a workaround needs to be used to launch it.

How do I reset values or changes made in the ParameterTranslation file or ProteinPilotDataDictionary file in ProteinPilot

It may be required to reset the values within these files if they have been manually adjusted incorrectly.

How to Report Regression Parameters in a Results Table Created in SCIEX OS Software

Regression parameters values (e.g., r squared, slope, linear coefficient) can now be added to a results table created in SCIEX OS software from the calculated columns that are saved under the processing method.

What Are the Specifications of the Six-Protein Mixture Supplied with the iTRAQ® Kit?

Specifications of the six-protein mixture (PN 4348363) supplied with the iTRAQ® kit include the accession numbers of the proteins and their mass per tube (in µg and nmol).

Returning the Status Column to the Analyst® Software Queue Manager

To bring back the status column to the Analyst® software Queue Manager, right click in any column of the Queue Manager and select Column Settings.

Changing the Leak Sensor Detection Detector Threshold for a Shimadzu LC System

When a leak error is observed for a Shimadzu LC system but the channel is dry, it may be that the threshold for detecting a leak is set too low.

Reporter 3.0.1 Templates The file contains custom XML elements which are no longer supported by Word.

When opening a reporter 3.0.1 XML Template in Microsoft Word 2007 SP1 then the error message The file contains custom XML elements which are no longer supported by Word. If you save this file these custom XML elements will be removed permanently

Overview of the 32 Karat Software User Privileges

An overview is provided of each user privilege in the 32 Karat software that can be assigned or removed from the user.

How Do I Prevent a Windows 10 Upgrade on my SCIEX Windows 7 Desktop

Microsoft has started to strongly encourage users to upgrade from the Windows 7 operating system to the Windows 10 operating system. This action might result in an unwanted or accidental upgrade. As of July 2016 none of the SCIEX software products have been fully tested on the Windows 10 platform. We cannot confirm therefore that the SCIEX software will perform as expected on the Windows 10 operating system.

Can Google Drive Be Used for Transferring or Storing Data Generated by SCIEX Software?

The use of Google Drive for data storage has not been tested with data sets generated on SCIEX software. Transferring and storing data using Google Drive has led to issues with data sets for some end-users because of a potential embedded encryption process in Google Drive.

Analyst® 1.7 Software License Error: Cannot Find License File

After activating the Analyst® 1.7 software license and saving it to C:/ProgramData/AB SCIEX/Analyst/License, the software would still not activate and error message -1,359 was received. Retyping the license file name to "Analyst1.7.lic" resolved the issue.

AB SCIEX Data Explorer® Software Issue: Periodic Table and Other Software Features Are Grayed Out

The AB SCIEX Data Explorer® software is an embedded software for data processing on the 4800 MALDI TOF/TOF™ and the TOF/TOF™ 5800 Systems and was recently rebranded; however, the rebranding process caused certain applications menu items to become grayed out (periodic table, isotope calculator, and elemental composition). To resolve this issue, install the patch provided in the link in this article.

Where is the method found that is created during automatic compound optimization?

When several compounds are optimized in Analyst 1.6.3, one method is created with all the MRM transitions included. The final MRM method created contains all compounds and is present at the bottom of the compound optimization report.

Upgrading Analyst® Software Requires that Cliquid® Software be Uninstalled

Upgrading Analyst® software on workstations where Cliquid® software is also installed requires that Analyst be uninstalled as well as Cliquid software. After reinstalling Analyst software, then Cliquid can be reinstalled.

Adjusting Integration Parameters to Exclude Peak Tailing Area in Analyst

Some analytes may display an undesirable amount of peak tailing, some of which may need to be excluded from the total integrated peak area. Adjusting the percent noise parameter in the IntelliQuan dialog may help to decrease the area of the peak included for integration.

How to Simulate a Hardware Profile with a Mass Spectrometer and Shimadzu LC in Analyst® Software

In Analyst® software, creating a simulated hardware profile allows a user to create acquisition methods and batches when using the software on a processing PC that is not connected to an instrument. To create a simulated hardware profile, open the Hardware Configuration Editor and select a hardware profile that you would like to simulate. Then select Edit Profile.

PA800 How To - Replacing the Ejector and Electrode

Replacing the Ejector and Electrode

How Are Analytes Deleted from a Processing Method in Sciex OS Software?

To delete unwanted analytes from a processing method in Sciex OS software, highlight the rows, right click and select Delete Rows.

Coolant leak troubleshooting tips

The document provides troubleshooting steps for coolant leak issues (to determine where the leak is coming from).

Why Is There No MRMHR Scan Type when Using the Method Wizard for a TripleTOF® LC-MS/MS System?

This article describes the MRMHR workflow for a TripleTOF® LC-MS/MS System using the Method Wizard in Analyst® TF or SCIEX OS Software. MRMHR is not a scan type. It is a description for a set of looped experiments, which can be used for a targeted approach. The looped experiments include a TOF-MS experiment followed by dedicated product ion experiments either in high-resolution or high-sensitivity mode.

Unable to Open SCIEX Cloud ProteinPilot™ Software Searches with the Desktop Version 5.0.2

The version of ProteinPilot™ Software in the SCIEX Cloud is version 5.0.3; therefore, group files created in the SCIEX Cloud cannot be downloaded to a desktop and opened in ProteinPilot Software 5.0.2. To download and read a group file on a desktop installation of ProteinPilot Software, the desktop version must be upgraded to version 5.0.3.

How to create a new Wellplate in SCIEX OS for Agilent Autosampler

Will explain how to use an existing wellplate to modify accordingly to be able to use a new customized wellplate for Agilent Infinity II Multisampler. Same procedure will also works for other Agilent Autosampler, but have some slightly different names for some of the steps.

Is It Possible To Set the Y-Axis to a Fixed Value in Analyst™ Software?

When reviewing data in the Analyst™ software Explore mode, the y-axis for the signal intensity cannot be set to a fixed value to compare results from one run to another. But this can be done in Quantitate mode while reviewing peaks in a results table by selecting Tools -> Settings -> Peak Review Settings and typing in the Intensity under Automatic Zooming -> Y axis units.

DiscoveryQuant™ Software Will Not Launch Without Analyst® Software Installed

If DiscoveryQuant™ software fails to launch, even after the software is uninstalled and reinstalled, check to see if Analyst® software is also installed. An installed version of Analyst software is a prerequisite to installing DiscoveryQuant software; DiscoveryQuant software will not launch without Analyst software.

Why Won't LipidView™ Software Load My Analyst® Software (.wiff) Data Files?

In order to load Analyst® software data files (.wiff files) into LipidView™ software, either Analyst or Analyst TF software must be installed alongside LipidView.

Can Audit Maps Be Easily Transferred from Analyst® Software to SCIEX OS Software?

No, audit maps cannot be directly transferred from Analyst® to SCIEX OS software.

Can the SWATH™ Acquisition Variable Window Calculator v 1.0 Be Used with All TripleTOF® Systems?

SWATH™ acquisition software and the variable window methods will work on the TripleTOF® 4600, 5600 and 6600 systems, but Analyst® TF 1.7 software must be installed.

How Can Concentrations above the ULOQ be Flagged in MultiQuant™ Software?

Concentrations above the ULOQ can be flagged in your MultiQuant™ software results table by setting up the Upper Limit of Calculated Concentration in the Quant method.

Analyst: How is the limit on the number of samples in the queue increased?

The limit on the number of samples added to the queue for a run can be adjusted using the Max. Num. Waiting Samples setting in the Queue Options menu.

Exporting .T2D Files in Batch Mode from the Raw Data Spotset

To export .T2D files in batch mode from the raw data spot set on a MALDI plate, locate the Remote Data Access software in the program files and install the T2DExporter.

Adding User Groups to the Analyst® Software Secruity Configuration

The steps below describe how to add user groups into the Analyst® software security configuration.

Does the Echo MS System Support All QTRAP® 6500+ System Functionality?

The Echo® MS System cannot be supported by the QTRAP® 6500+ System; instead, Echo MS is paired with the TripleQuad 6500+ System for data acquisition.

Adjusting the Dilution Factor Corrects Calculated Concentrations in Analyst® Software for Known Samples

If the dilution factor is not set correctly in an Analyst® software results table, the calculated concentration values for samples of known concentration will be incorrect.

Firewalls Can Cause CloudConnect Connection Issues

The CloudConnect service is installed and runs in the SYSTEM security context, as opposed to PeakView which runs in user context. Some IT organizations block port 443SSL for SYSTEM level programs as a security measure.

SCIEX OS Software: How to Choose the Format for a Numerical Field in a Report

By default, the format for a numerical field in a report is taken from the results table itself if the format is not set in the report template tag. If a specific numerical format is desired for a particular field in a report, certain default formats (such as the number of decimals desired or scientific notation) can be chosen in the Format field in the tag for that value. Otherwise, In the SCIEX OS software results table itself, the number format can be set for individual columns by editing the Number Format in the Results Table Display Settings options.

Is it possible to export the correlation coefficient r from a MultiQuant results table

This article gives a guidance how to export the correlation coefficient r from a MultiQuant results table. Only Available in MultiQuant Version 3.0.1.

How to Print an XPS Report after Running MS Tune in SCIEX OS Software

To print the XPS report from the most recent or a prior tuning in SCIEX OS software, navigate to this location: D:\SCIEX OS Data\Optimization and then print the file report.xps.

Aliquots of Bulk iTRAQ® Reagent Require Cold Storage Under Inert Gas

When aliquoting bulk iTRAQ® reagent, vials must be stored at -20 °C under inert gas.

How to Adjust Failed Ion Ratios in MultiQuant® Software

If the ion ratios are flagged in the MultiQuant® software results table, it usually indicates that there is some discrepancy in the integration of the peaks corresponding to the transitions used for that analyte group.

I am running Analyst 1.5.1 with or without June 2010 hotfixes and I am having failed acquisitions with my batches I generate using a HPLC utilising an AAO Analyst Access Objects driver.

Details of the requirements to run AAO HPLC Device with Analyst 1.5.1 and 150 Transitions.

How Are Calibration and Integration Parameters Defined in MultiQuant™ Software?

The default integration parameters are defined in the User Integration Defaults or User Units & Calibration Defaults under the Edit menu in MultiQuant™ software. These settings should be established before creating a quantitation method.

What Version of LibraryView™ Software Is Needed for a Win 7 64-bit System?

Install LibraryView™ software version 1.0.2 for use with Windows 7, 64-bit systems.

What Is the Settling Time in an Analyst® Software Acquisition Method?

In Analyst® software, the settling time is defined as the time that a mass spectrometer pauses after finishing a cycle until it begins the next cycle. The instrument electronics require a settling time in order to function successfully.

How to install ProteinPilot 4.5b and upgrade from ProteinPilot 4.0 to ProteinPilot 4.5b

This procedure describes the removal and install of ProteinPilotTM software 4.5b in great detail.

Eliminating air bubbles in CEQ/GeXP gel cartridges

Centrifuge protocol to help get rid of air bubbles in gel cartridges that might get into the gel lines

Will the SCIEX OS Software Central Administrator Console (CAC) Run on Windows Server 2019 in a Virtual Environment?

Yes, the SCIEX OS Software Central Administrator Console (CAC) software installed on a Windows Server 2019 will run in a virtual environment and is officially supported.

Difference between Rapid and Thorough Searches in ProteinPilot™ Software

The rapid search and a thorough search settings in ProteinPilot™ software determine which parts of the search algorithm will be invoked and effectively how deep the sample will be searched to find the right answers.

When I change integration in an Analyst® result table manually or automatically I always have to click apply and accept. Is there a possibility to make this process easier

The Audit Trail settings in Analyst software enforce that all manual integrations have to be Accepted. If you do not require the Audit Trail you can turn off this requirement by setting the audit map to No Audit Trail.

How Are Simple Queries Created in MultiQuant™ Software?

Simple queries can be created in MultiQuant™ software by selecting the Create Simple Query option in the Process menu. The formula can then be entered into the Create Query File screen.

Analyst® 1.7 Software Installation Guide

The Analyst® 1.7 Software Installation Guide is attached. Please consult this guide before installing this version of Analyst software on your PC.

Permanent License Gives an Error Message of Expired for DiscoveryQuant™ Software

After launching DiscoveryQuant™ software, an error message is received indicating the software has expired even though a permanent license is installed.

How Is an Ion Library Created in Analyst® Software?

To create an ion library in Analyst® software, each MS or MS/MS spectrum needs to be opened and then added to a small existing database.

Where Are the Event Logs for SCIEX OS Software Archived?

When event logs in SCIEX OS software become too large, the software will create an archive event log file. This file is located in the directory C:\ProgramData\SCIEX\Clearcore2.Acquisition.

Where Are the MPX™ Driver Software Event Logs Located?

To locate the MPX™ Driver software event logs, navigate to the MPX Driver folder in Program Data and locate the Log folder.

What is the IP Address Used by the Uniprot Server to Submit a ProteinPilot™ Software 5.x Search?

This article describes the website links that are being used to submit a ProteinPilot™ software (v 5.x) search.

DiscoveryQuant™ Software Produces SQL Error during Migration from Windows 7 to Windows 10

To resolve an error that prevents the SQL database from connecting with DiscoveryQuant™ software 3.0.2 in Windows 10, SQL user accounts with the password enabled must be used.

Recommended N-Glycan MALDI Sample Preparation Matrices for TOF/TOF Instruments

Depending on what type of N-glycan moiety that is being analyzed on a TOF/TOF system, refer to the table provided for recommended MALDI sample preparation techniques, matrices and acquisition methods.

Can the SCIEX QTRAP® or TripleQuad™ 7500 LC-MS/MS System Operate without E Lens™ Technology Active?

Yes, the SCIEX QTRAP® or TripleQuad™ 7500 LC-MS/MS Systems can operate without the E Lens™ Technology active. Each QTRAP and TripleQuad 7500 System comes with a blanking plug that can be inserted should there be a need to operate without the E Lens Technology.

Adding or Removing Samples from the SCIEX OS Software Results Table

Open a results table in the Analytics workspace in SCIEX OS Software. Select the More menu > Add samples. In the Select Samples dialog, select the required samples.

Analyst® Software Error Message: Failed To Set Sample Data

If the error message "Failed to set sample data" appears when using Analyst® software, the issue may be resolved by reducing the number of racks in the batch to only those that were actually used for samples.

Diverter Valve Would Not Work While Using Delay Time in Analyst® Software

The diverter valve will not work properly when using Delay Time in the acquisition method of Analyst® Software due to a mismatch between diverter valve timing and MS acquisition timing. This results in the diverter valve timing not aligning with the MS acquisition time.

Lost sensitivity on your Triple Quad or QTRAP You may need to optimize your CEM detector parameter.

This article explains how to resolve the issue of low sensitivity on a Triple Quadrupole or QTRAP instrument due to an incorrect CEM value by manually optimizing the CEM detector parameter in the Analyst software

Installing MultiQuant® Software Generates a .NET Framemwork Error

When installing MultiQuant® 3.0.2 software on Windows XP, an error message was received: "An error occurred while installing system components for MultiQuant. Setup cannot continue until all system components have been successfully installed."

How Are Submitted Batches Rearranged in the Analyst Queue?

Batches can be rearranged in the Analyst software queue using the Move Batch option. In the Move Batch window, drag the batch to be moved to the desired location to rearrange.

Can the Existing Ion Source on the X500R QTOF System Be Converted to APCI?

The source on the X500R QTOF System can be used in atmospheric-pressure chemical ionization (APCI) mode, but a different probe with a twin electrode must be installed. In addition, a different APCI tuning solution must be used and is available for purchase from SCIEX.

PA800 How To - Uninstalling the LIF Detector

Uninstalling the LIF Detector

Formatting Analyte Names in an Analyst® Software Quantitation Method

When formatting analyte names in an Analyst® software quantitation method, they should not contain any dashes. A space should be used to separate analyte names and numbers in the quantitation method to correctly group analytes.

Calibration Correction Factor (CCF) for Laser-Induced Fluorescence (LIF) Calibration

The Calibration Correction Factor (CCF) for laser-induced fluorescence (LIF) calibration is the mathematical relationship between the fluorescence from a known concentration of the analyte and the associated signal detected by the instrument. An explanation of how it is calculated is provided in this article.

PA800 How To - Removing the Ejector and Electrode

Removing the Ejector and Electrode

Convertingt MS data from .Wiff Format to a .Mgf File

To use different search engines/software, .wiff data must be converted to different format such as .mgf file before being able to submit the data for a search.

Patch for the Analyst® TF Software 1.7.1 Noise Sync Signal Issue

This patch addresses a defect in Analyst® TF software 1.7.1 that causes occasional acquisition failures resulting in the warning “Noise failing sync signal ignored" being reported in the application log file (ATF-665, -TDC error).

MultiQuant™ MD Software Will Not Launch from Desktop

MultiQuant™ MD software will not launch if the Analyst® software security setting is set to Integrated or Mixed mode. To keep these security settings, launch MultiQuant from the Companion Software mode in the left-side vertical menu in Analyst. Otherwise, change the security settings to single-user mode to open MultiQuant MD from the desktop.

Can ProteinPilot™ Software Version 5.0.2 Be Installed on a 2019 Server?

Yes, ProteinPilot™ software 5.0.2 can be run on a Windows 2019 Server. This was not officially tested or mentioned in the release notes, but many users have installed the Windows 10-compatible ProteinPilot software 5.0.2 on the Windows Server 2019 operating system and have run the software successfully in this environment.

Calculating Molecular Mass for Compounds with Isotopes in SCIEX OS

To calculate the molecular mass of compounds containing isotopes in SCIEX OS, select the Mass Calculators in the Explorer mode and then specify the chemical formula for the Mass Property tab. For isotopes, precede the chemical symbol with the weight of the isotope.

Setting up a Rack Changer in Sciex OS Simulation Mode

To set up the RackChanger in Sciex OS in simulation mode, go to Devices under Configuration mode. Select Add and choose Integrated System and follow the directions below.

How to get the error log from inside a Shimadzu CBM for a VIERROR

Description of how to access the Shimadzu Web server which can help to diagnose errors

How to deal with the Analyst User Registration Pop-Up-Window

When freshly installed and not yet registered Analyst asks in a pop-up-window for a Registration Key. Here is shown where to get it.

Which Software License Is Used for LibraryView™ 1.2 Software Installed with SCIEX OS 1.3?

When installing LibraryView™ 1.2 software alongside SCIEX OS 1.3, use a LibraryView 1.0 license, PN 5022277.

Error In MultiQuant™ Software When Generating a CSV Report

The error "Cannot save report with graphical or table elements as a text/csv file" appears when attempting to generate a report as a CSV file in MultiQuant™ software using a report template that has figures, pictures, or tables. This is due to CSV reports not being able to display figures or tables.

DiscoveryQuant™ 3.0.1 Software HotFix 2 Gives Not Registered Error

Despite being properly registered, DiscoveryQuant™ 3.0.1 software with hotfix 2 gives the error message that it is not registered and must quit. The root cause of this error is the presence of multiple instances of DiscoveryQuant software installed on the same PC.

How to Activate the Molecule Profiler Software Module in SCIEX OS Software

The Molecule Profiler software is a processing-only software module within the SCIEX OS software suite that can identify and characterize parent molecules and their metabolites. Activating the Molecule Profiler software version 1.1 simply requires the installation of an additional license; however, activation of version 1.0.1 requires an additional software download as well as license installation.

Installing the Accurate Mass Metabolite Spectral Library 1.0

Installation of the Accurate Mass Metabolite Spectral Library 1.0 requires a valid license file in order to install the compound database. The library installer creates a folder for the Accurate Mass Metabolite Spectral Library in the Start > All Programs > AB SCIEX > Accurate Mass Metabolite Spectral Library folder. The library and user documentation are copied into this location.

Ion Ratios Are Not Calculated as Expected in MultiQuant™ Software

The ion ratio value was not showing correctly due to a blank sample being included as one of the calibrators in MultiQuant™ software.

Why is Scheduled Ionization in Analyst® TF Software 1.8 Not Working with the OptiFlow® Turbo V Ion Source for Nano Flow?

Scheduled ionization in Analyst® TF software 1.8 is not configured to work optimally with the OptiFlow® Turbo V ion source ion source for nano flow. When using the OptiFlow® Turbo V ion source, scheduled ionization is always on, except when the start time in Analyst software is set to zero during pre- and post-run times. This is an issue for the nano spray users, because they will be unable to have the voltage stay on between runs for perpetual spray.

Can I Use Windows Experience Enhancers on My SCIEX Acquisition and Processing PCs?

Some PC users prefer different views and/or functionalities in the new Windows 10 interface. There are freeware/shareware programs available that allow for the customization of Windows features (such as emulation of Windows Classic settings). However, these types of Windows accessory programs have not been tested with SCIEX software; their use is not supported.

Why Does the Checksum Invalid Error Appear when Processing Data in MultiQuant™ MD Software?

If the checksum invalid error appears while trying to process data with MultiQuant™ MD software, this indicates that the data was not previously acquired with checksum feature turned on in Analyst® MD software.

After Activating My Software License Key, the License File Was Not Emailed to Me

After the software license key was activated online at the SCIEX website, the license file was not emailed to the registered email address. This occurs when the email address is not entered correctly.

Changing the Orienatation of Peak Review Chromatograms in a Reporter Template

If the peak review chromatograms are showing in the wrong orientation on an Analyst® or MultiQuant™software report, the page orientation for the actual Word document template may be set to portrait rather than landscape.

Setting Up Email Notifications for Reports in Cliquid® Software

To allow the system to deliver email notifications of reports generated in Cliquid® software, select Run Samples. In the menu option Set report options, users can choose to set up the email notifications for completed reports or indicate their preference to have a pdf version of the report emailed to them directly.

Replacing a Trial License with a Permanent License

When opening a program, an error message may appear that indicates that the license has expired, even when a permanent license is thought to be installed. For these cases, the trial license may still be installed in program files and will need to be removed and replaced with the permanent license.

Searching an EST or Other Nucleotide Databases in ProteinPilot™ Software

Searching an EST or other types of nucleotide databases in ProteinPilot™ software requires that the database be translated first.

How Do You Setup a Solenoid or Solvent Selection Valve on a Shimadzu LC?

This article describes how to setup a FCV-11 AL valve for a Shimadzu LC system.

Setting Up a New Project in Analyst® Software

To set up a new project in Analyst® software, navigate to the Tools menu and select Project.

Where Do I Put Query Files Used with Reporter Templates for MultiQuant™ or SCIEX OS Software?

Queries are used by report templates to process specific data from results tables in either MultiQuant™ or SCIEX OS Software. For a report template to utilize a query, the query file must be placed in the same directory as the report template.

Can the Existing Ion Source on the X500R QTOF System Be Converted to APCI?

The source on the X500R QTOF System can be used in atmospheric-pressure chemical ionization (APCI) mode, but a different probe with a twin electrode must be installed. In addition, a different APCI tuning solution must be used and is available for purchase from SCIEX.

Decreasing Run Time when Using the LCMS Reconstruct Algorithm in ProteinPilot™ Software

This article describes how to modify the configuration file for ProteinPilot™ software to decrease the time needed when using the LSMS Reconstruct algorithm, especially when performing large protein ID searches on data sets from a TripleTOF® 6600 LC-MS/MS System.

What is the Signal-to-Noise(S/N) Integration Threshold in SCIEX OS Software?

A signal-to-noise (S/N) integration threshold was introduced in SCIEX OS software version 2.1.6, which allows users to select peaks for integratin based on the S/N ratio.

Using an Older Version to Open a Processing Method Created in a Newer Version of SCIEX OS Software

The files created in SCIEX OS Software are not backwards compatible with other versions of the software. An error will appear when a processing method created with a higher version of SCIEX OS Software (e.g., 2.0) is opened with a previous version of SCIEX OS Software (e.g., 1.7). To open a processing method created in the latest version of SCIEX OS Software with the older version, export the processing method as a text file.

Resolving the Analyst® Software 1.7 Error: Feature Has Expired

The licensing error, Feature has expired, appears when Analyst® software 1.7 is launched. This article explains how to replace the license file to resolve the error.

How To Change Chromatography Peak Shading In MultiQuant™ Software

To change how peaks are shaded in MultiQuant™ software in the Peak Review section, right click on the chromatogram and click on Options. Under the Appearance tab, there will be a drop-down section for Fill Peaks.

Extra Backslashes Added when Using Network Location for Root Directory in Analyst® Software

If extra backslashes are added to a network location for a root directory for Analyst® software, a registry edit will be needed to prevent this issue from continuing to occur. The extra backslashes in the data file name can cause errors when trying to create a new project or save files (including results tables).

Analyst® Software Scheduled MRM Acquisition Failure Due To Unprogrammed Diverter Valve

Scheduled MRM acquisition methods created in Analyst® software may fail to start if there is a diverter valve in the hardware profile. Ensure that that valve has a time table program or that it is removed from the method's hardware profile.

Maintaining LCMS Systems under Specified (Standby) Conditions Post-Acquisition in Analyst® Software

You can choose what happens to your system after the last sample in your queue has been acquired in Analyst® software.

Analyst® 1.7 Software License Error: No Such Feature Exists. Feature: Analyst.acquisition

To resolve the Analyst® 1.7 license error "No such feature exists. Feature: Analyst.acquisition", the license key made need to be replaced. This error occurs when a processing license is installed on an acquisition workstation.

Error in SWATH MicroApps: Window Widths below 4 Da Are Not Supported

This error will appear if the SWATH configuration file is not edited to allow for window widths below 4 Da.

How to adjust, save and export the table settings in an Analyst Quantitation Table

Instructions how to modify (choose and adjust the visible columns, change the significant figures and notation), save and export an Analyst Quantitation Table.

Issue when Exporting and Importing Text Files into MultiQuant or SCIEX OS Software

Excel can insert extra characters in exported forms of the MultiQuant™ or SCIEX OS software data and corrupts this data; the resolution here is to edit the exported file and use another editor, other than Excel, that does not insert extra characters into text.

How Is Relative Retention Time Calculated?

For analytes using an internal standard, the actual retention time (RT) of the internal standard peak (for the corresponding sample) is first determined. The expected RT for the analyte is determined by multiplying the specified expected RT by the ratio of the actual to the expected RT for the internal standard.

To Prevent Contamination, Use Formic Acid Ampules

To prevent your samples from becoming contaminated, use formic acid from small volume ampules rather from a large bottle. Impurities can accrue when taking aliquots of formic acid multiple times from the same bottle, and these impurities can impact positive ion analysis especially.

Location of the Audit Trail Archives in Analyst® Software

When the Instrument Audit Trail or a Project Audit Trail in Analyst® software reaches 1000 records, a final record stating that the file has been archived is added. The audit trail is automatically saved in the Project Information folder with a name indicating the type of audit trail and the date and time.

Troubleshooting the ZenoTOF 7600 System: Tuning and Calibration

Before using the ZenoTOF 7600 system, users should run a system check to verify their instrument's performance. In the event that the MS Quick Status check fails, a link to a troubleshooting guide is included in this article.

How to Add Compound Information to LibraryView™ Software 1.1

To add information about a compound to LibraryView™ software 1.1, expand the Compounds list in the Manage pane to begin adding the compound name, and then follow the directions provided.

How Do I Change the Significant Figures of Regression Equation in Analyst

Description of how to change the display of the regression equation in Analyst

Location of the Queue Option Tab in Analyst® 1.6 Software

To find the queue option tab in Analyst® 1.6.x software, click on configure mode and then click on the Tools menu, then select Settings and then click on Queue Options.

MasterView™ Software Report Error: Object Reference Not Set to an Instance of an Object

When creating are report in the PeakView®/MasterView™ Software suite, the following error appears: "Object reference not set to an instance of an object." This error occurred because a file other than a report template was selected during the create report process.

Tips and Tricks for Cation-Exchange Chromatography for the iTRAQ® Protocol

The manual injection procedure for the iTRAQ® protocol requires a 22-gauge syringe with a 2-inch needle (purchased separately). This article lists some tips and tricks on how to set up the syringe when using cation-exchange columns for samples treated with the iTRAQ reagent.

ChemoView™ Software Error after Data Processing: Programmatic Access To Visual Basic Project Is Not Trusted

Chemoview™ software error after data processing "Programmatic access to Visual Basic project is not trusted" can be resolved by turning on the access to the VBA object model from any automation client.

C Drive Free Space Requirements when Using SCIEX OS Software

SCIEX OS software performs best when 20 GB of free space is available on the C drive (C:). Furthermore, SCIEX OS software creates log files in order to monitor both instrument (on an acquisition PC) and software (on both acquisition and processing PC's) performance. These log files incremently increase and can accumulate to a total size of 35 GB. This sets a limit of 55 GB of space needed on the C drive to use SCIEX OS software optimally.

Can I convert t2d files to mzxml file using 4700 data

Can I convert t2d files to mzxml file using 4700 data

What Type of Analyst® Software Data Is Used with Keystone™ Converter Software?

Keystone™ converter software will convert nominal mass .wiff1 files from Analyst® software 1.4.1 and later versions.

Activating Markerview 1.2.1.1 Software Requires an Activation Key Code, Not a License File

Installing Markerview 1.2.1.1. requires an activation key code, not a license file. Software activation key codes can be obtained by emailing metabolomics@sciex.com.

How to Import LibraryView Snapshot File

If reinstalling software or moving to different hardware it may be required to import a snapshot file.

Antivirus Software Symantec v12.x Interferes with Data Acquisition with Analyst® Software

Antivirus software can disrupt data acquisition with Analyst® software, Analyst TF and related SCIEX software programs such as DiscoveryQuant™, Cliquid®, LightSight®, Reporter, and MultiQuant™ software. This article provides guidance on how to configure the antivirus software to avoid conflicts with Analyst® software that could cause data acquisition issues.

Sciex OS 1.3 Error "Services Cannot Launch" Due to Windows 10 Incompatibility

An error message is received when trying to launch SCIEX OS 1.3 that indicates that services cannot start. Ensure that the software is installed on a Windows 7, not Windows 10, operating system (OS). Only SCIEX OS version 1.4 and greater are compatible with Windows 10 OS.

How to Update Retention Times in Sciex OS

To update the retention time (RT) of an analyte in Sciex OS, open a results table consisting of grouped components with different RTs, and then follow the instructions provided below.

Does the Mascot.dll script work with Analyst 1.6 on a win 7 PC

Defines the issues and workarounds required to use the script.

Multiquant 3.0.x Installation Fails. No .NET Framework 3.5 SP1 on Windows 7

Multiquant 3.0.x installation is not able to proceed on Windows 7 Operating system because the installation of .NET framework is not completed despite the inclusion of this framework within the Windows 7 Operating System.

Magnifying Chromatogram Peaks Displayed in a SCIEX OS or MultiQuant™ Software Report

The chromatograms of peaks that are displayed in a report generated in SCIEX OS or MultiQuant™ software will retain the format of the original peaks displayed in the peak review pane. To magnify the peaks displayed in a report, the zoom settings will need to be changed in the peak review settings for MultiQuant or SCIEX OS software.

What Is the Peak Split Algorithm when Using a Marker Peak with the Echo® MS System?

The marker well in the Echo® MS System is defined by the user in the acquisition batch to generate a special barcode pattern at the beginning and end of the plate run. The barcode is a pattern composed of a narrow peak, then a pause, a wide peak, then a pause, followed by a narrow peak.

Troubleshooting retention time shifts and variable pump pressure

Instructions for performing flow tests on Shimadzu Nexera and EXION AD HPLC pumps and troubleshooting common causes of inadequate pump flow.

Delete Rights Are Not Needed to Save or Overwrite a PDF Report in Analyst® Software 1.7.2

In Analyst® software 1.7.2, delete rights are not needed to save or overwrite a PDF file to the folder where the original PDF report is saved.

Library Hits Are Missing from the Library Search Reports in Analyst® Software

When using the library search report templates in Analyst® software, the library hits or the name of the compounds that has a library match does not show up in the report. This is due to an IF statement present in the pre-installed, standard, library-search templates that checks if the library hit is greater than zero ($Libs_Max_Hit_Count>0).

Separating Two Experiments Acquired within One Period in Analyst® Software

Data from two or more experiments acquired within one period in Analyst® software can be separated by opening a data file in Explore mode and double clicking the green arrow.

Installing a License for BioTool Kit in PeakView® Software 2.2

BioTool Kit software is a software module within PeakView® 2.2 software that needs to be activated by a separate license. To install a BioTool Kit license, open PeakView 2.2, navigate to the Help menu, and select BioTool Kit Activation.

Analyst.exe Unable To Locate Component pt95FKn71.dll

When Launching Analyst or Activating a Hardware Profile you receive the message Analyst.exe Unable To Locate Component with message body This application has failed to start because pt95Fkn71.dll was not found. Reinstalling the application may fix this problem.

Initiate Transfer to Watson LIMS in SCIEX OS Software Prevents Analyst® Software from Launching

When the feature Initiate Transfer to Watson LIMS is selected in SCIEX OS software, software users find that the Analyst® software installed on the same workstation will no longer launch. This is the expected behavior for Analyst software and depends on the configuration and the installation order of other SCIEX software that were installed on the same PC. 

Adding a Syringe Pump To a Hardware Profile in Analyst® Software

Adding a syringe pump to a hardware profile in Analyst® software is necessary if the user needs to use the syringe pump to infuse sample during manual tuning. This article provides instructions on how to update a hardware profile to include a syringe pump.

BioPharmaView™ Software 2.x/3.0.x Cannot Open the Data for Subsequent Samples if the Data for the First Sample Is Corrupted

BioPharmaView™ software 2.x/3.0.x cannot open the data for subsequent samples if the data for the first sample is corrupted.

What Parameters in ProteoWizard Are Needed when Converting .wiff2 Files to mzXML Files?

The parameter settings, including the PeakPicking value, that are used for converting .wiff2 files to mzXML or mzML files in ProteoWizard, are explained in more detail here.

Incorrect Peak Area Sum when Using Sum Multiple Ions Feature in MultiQuant Software 3.0.1

The Sum Multiple Ion feature in MultiQuant™ 3.0.1 software can be used to sum the fragment ions of a precursor ion. Using this feature does not create a resulting sum that matches the result when Excel is used to calculate the sum of the XIC peak areas for the same fragment ions. The reasons are explained here.

Where Can I Find Instructions for the Protein Preparation Kit?

Protein preparation instructions can be found on the SCIEX website at https://sciex.com/Documents/tech%20notes/Protein-Preparation-Kit-Protocol.pdf or https://sciex.com/products/standards-and-reagents/automated-protein-digestion-solution.

How to Set the Parameter Settings in Analyst® Software Back to Original Factory Settings

The parameters settings in Analyst® software can be set back to the original, default factory settings by selecting the Parameter Settings option from the Tools menu and then using the Factory Settings button to reset the parameters of the selected scan type.

Where Is the Executable File for Excel Saved on My Computer?

The executable file for Excel – Excel.exe – is located in the installation directory for the 64-bit version of Microsoft Office 365 at C:\Program Files\Microsoft Office\root\Office16. 

Data File not in Expected Location in Analyst® Software Project Folder

Ensure that the correct project folder is selected in Analyst® software prior to data acquisition. Data will be acquired to whichever folder is showing in the horizontal menu bar.

What are the Library Search Algorithms in SCIEX OS Software?

When setting up a new processing method in SCIEX OS software's Analytics mode, there are three different library search algorithms that the user can select under the library search parameters dialogue: candidate, confirmation and smart confirmation search.

How To Install Templates in Biologics Explorer Software

This article describes how to install the template packages in Biologics Explorer software.

Configuring a SCIEX X500 QTOF System after Downgrading SCIEX OS Software 2.0 to 1.7

After re-installing SCIEX OS software 1.7, stop the ClearCore2 service and then install the Microsoft C++ Redistributable package (vc_redis*.exe) from the install folder in the SCIEX OS 2.0 installation package. This will enable user to configure an SCIEX X500 QTOF System in the Devices workspace.

Problem Uninstalling SCIEX OS Software Stems from Hidden SQL Driver

While removing the SQL 2008 R2 Setup program during a SCIEX OS software de-installation, an error was received—indicating that the issue was due to the 2008 R2 RsFx driver, a "hidden" program that needs to be manually uninstalled using either the command prompt or regedit Windows functionalities.

Resolving a Shimadzu LC Fatal Error: Could Not Activate Profile in Analyst® Software

The LC/MS hardware profile containing a Shimadzu LC could not be activated in Analyst® software. Under the Configuration tab for the Shimadzu system controller (CBM), the serial port filed was selected and changed to TCP/IP. The IP address 192.168.200.99 was added.

What Is the Full Amino Acid Sequence of BETA-GALACTOSIDASE in the LC/MS Peptide Calibration Kit?

The full amino acid sequence for beta-galactosidase is provided in the FASTA file format. The kit (part number 4465938) contains one vial of beta galactosidase digest (625 pmol/vial).

Report Template Editing Blocked after Upgrading SCIEX OS 1.6.1 Software from a Previous Version

After updating SCIEX OS software from version 1.5 to 1.6.1, report template may be unable to be edited if Analyst® software is installed on the same PC. An error message appears in the Microsoft Word report template document: "Reporter Office addin. The provider with the name Quantitation already added to content control addin.Multiple custom type XML files found for the same provider." This article explains how to resolve this issue.

Analyst® Report Template for LIS: Why Won't the LIS System Read Past the First Line of Data?

If a CSV output file generated using the Analyst® software report template for LIS systems contains any cells with no data values, then the LIS system may not read past the empty cell. To ensure that the LIS reads the whole output file, each cell in the CSV file must contain a value of some kind.

Which License Supports LibraryView™ 1.3 Software Installed with SCIEX OS 1.4?

LibraryView™ 1.3 software installed with SCIEX OS 1.4 requires a LibraryView 1.2 license.

Sciex OS 1.5 Software Error: Processing Method Contains No Components or Is Incompatible

When opening a processing method in Sciex OS 1.5 software, an error was received, indicating that the method contained no components or was incompatible. Removing the sub-folder (C:\SCIEX OS Data\<PROJECT NAME>\Quantitation Methods\<Sub-Folder>) resulted in normal software operation.

Troubleshooting Peak Shape after Column Replacement

After replacing the analytical column, the analyte's peak shape changed, leading to ion ratio failures. Replacing the guard column resolved the peak shape issues.

Analyst® TF Software Error: Instrument Optimization Parameters Are Not Available

If the error message "Instrument optimization parameters are not available" appears when running Analyst® TF software, check the region and language settings and ensure that English (United States) is set as the default language in the Windows operating system settings.

What Fittings Are Needed To Add a Waters M-Class LC to My ZenoTOF 7600 System?

This article explains which fittings are needed to add a Waters M-Class LC to a ZenoTOF 7600 system and includes part numbers and pictures of tubing and trap loop connections.

Implementing Zeno SWATH Functionality on the ZenoTOF 7600 System

To enable the Zeno SWATH pulsing function in the SCIEX OS software for the ZenoTOF 7600 system, upgrade the software to version 3.0 and then add the Zeno SWATH extension license for SCIEX OS software.

How Does the Formula Finder Algorithm Work in Sciex OS Software?

The Formula Finder algorithm in SCIEX OS software tries to predict the possible chemical formula based on the MS and MS/MS spectrum using the precursor ion's mass accuracy, isotopic pattern and MS/MS fragmentation pattern.

Are There Differences in LIMS Column Headers between Analyst® and SCIEX OS Software?

As users switch from Analyst® to SCIEX OS software, there may be concerns about column header or formatting differences between the two software versions when importing or exporting information using a LIMS. Although similar, there are format and column differences between the SCIEX OS and Analyst software systems, and SCIEX can provide examples for both formats.

How Do You Export a Library in LibraryView™ 1.0.1 Software?

The export of a library from LibraryView™ 1.0.1 software is described here.

Sample VB Code for Hours of Instrument Usage Information from Analyst® Software Audit Trail

Information about the hours of instrument usage can be obtained from the Analyst® software Audit Trail. Audit Trail data can be retrieved using IQuantAuditTrail interface methods NumEntries & GetEntry

Updating Quantitation Method Files in Analyst® and Multiquant™ Software with a New Analyte

This article describes which method files need to be updated in Analyst® and MultiQuant™ software when new compounds are added to the method.

Can BioPharmaView™ and BPV Flex Software Coexist on the Same Computer?

BioPharmaView™ Software 3.x and BioPharmaView (BPV) Flex Software 2.x are compatible and can be installed on the same computer.

Error Code 50 Appears when Creating Reports in MultiQuant™ Software

When creating reports in MultiQuant™ Software, an error appears, "Error code 50." This error is due to a corrupt file in the project folder, and a new project will need to be created.

ConfigUpdater.exe will not update instrument firmware.

Issues with Windows Firewall preventing ConfigUpdater from updating instrument firmware via Ethernet connection.

What Information Is in the AnIML File Created by the Keystone™ Converter Software?

AnIML, an open standard XML data format for storage and sharing of experimental data, is the file format that is created when a data file is converted by the Keystone™ converter software. This article details the information that is included in the converted AnIML file.

How to Create Custom Sample Trays for a CTC Autosampler

How to configure a CTC autosampler to use custom dimensions for use with alternative plates or vial racks.

Analyst Software Batch Editor Could not open the batch data DAB Sever Error

When importing a Analyst batch from a file the import fails and the Error Could not open the batch data DAB Sever Error is displayed

Using the Same Peak Model for All Components in a Group with SCIEX OS AutoPeak Integration Algorithm

In order to use the same peak model for all components in a group in SCIEX OS software, the user must enable the Peak Selection by Group and Process by Group settings in the Project Default Settings before creating the processing method.

SCIEX OS 1.5 Installations on Windows 7 Require a TDC4 Driver Update

SCIEX OS 1.5 installations on Windows 7 require a TDC4 driver update. Please navigate to the installation folder for Sciex OS and select the Drivers folder. Inside should be a program xTDC4_driver_v1.1.0.exe which will remove version 1.0.3 and install 1.1.0.

How to Use the MAM Script in BioPharmaView™ Software 3.0.2 to Transfer Peptide Information to SCIEX OS Software

BioPharmaView™ software 3.0.2 has improved its multiple attributes monitoring (MAM) workflow, and the software now includes a script, MAM-BPV to Analytics Converter, used to create a quantitative processing method for the Analytics mode of SCIEX OS software.

Generation of a New Root Directory for SCIEX OS Software Called C:\ClearCore Data

Some users have reported the appearance of a new root directory created by SCIEX OS software that is not on the D: partition where the root directory (D:\SCIEX OS DATA) is typically located, but rather on the C: drive. This C: drive root directory has a different name (C: \Clearcore Data) and does not match the root directory that appears in the Configuration mode of SCIEX OS software in the Projects menu.

Charge Heterogeneity Buffer Vial Plate Map for Tech Bulletin IB-17031A

The plate map used in the SCIEX charge heterogeneity capillary zonal electrophoresis (CZE) assay will help guide users in setting up the method in the tech bulletin "Analysis of Monoclonal Antibody Charge Variants by Capillary Zone Electrophoresis" (Beckman Coulter IB-17031A).

Clearing an Integrated Syringe Pump Error in Analyst® Software

Different approaches are provided here to resolve an error message that appears in Analyst® software while using the integrated syringe in manual tune mode: "The current sample cannot be run because the syringe pump has reached the end of its travel. To solve this problem please refill the syringe, press "Clear Error" and resubmit the sample".

Plotting 32Karat Software Data Files that Have Been Exported as ASCII Files into Excel

To plot 32Karat software data into a graph/electropherogram format, open the ASCII file in Excel and then format the data as described.

What Is a Fraglet.exe Error when Running ProteinPilot™ Software 5.0?

A "Fraglet-exe-Error" can have many causes within the ProteinPilot™ software. In some cases, this error is caused when installing ProteinPilot on an incompatible operating system.

SCIEX OS Software: Internal Standard Data in Report Does Not Match the Results Table

If a report generated from SCIEX OS software using a template and a query contains information about internal standard samples, the internal standard information showing in the results table does not appear correctly in the report. To resolve this issue, all internal standard samples must be listed at the bottom of the SCIEX OS software processing method in the components section.

What Do SCIEX Validation Services Include?

SCIEX qualification services include testing and documentation that demonstrates that the instrument is operating correctly and includes objective evidence showing what was tested, the specification for each test, and the results.

Turning the Checksum Option On or Off in Analyst® Software

In order to turn the checksum option on in Analyst® software, select the View menu and then choose Audit Trail Manager.

How to Remove the Extra Characters from an Analyte Name in a Report

To report the analyte name in a report without additional characters showing after the name, use the TRIM and LEN functions in the expression written in the Math Field Type tag in the report template.

Adding Custom Columns to a SCIEX OS Software Report Template

In SCIEX OS software, a custom column added to a results table can be included in a report template with a custom tag.

Why Do the Results for Some Analytes Shift to a New Column in a CSV Report?

When reporting results table values to a comma-separated values (CSV) report, for some analytes, the reported information is shifted from the correct column to one column over to the left. This column-shifting issue is observed when an analyte name contains a comma.

SCIEX Trial License Key Not Received

The email address associated with your Sciex login must be verified when you request a trial license, otherwise you will not receive your trial license key by email.

Printing an Unsecured Report as a PDF with MultQuant™ or SCIEX OS Software

Reports printed as PDF files from either SCIEX OS or MultiQuant™ software are always secure because they are printed using pdfFactory. A workaround must be used to print unsecured PDF reports.

Create Acquisition Method with Agilent HPLC in Analyst® Software

Walk Through of Analyst acquisition method (.dam) creation when a Agilent HPLC is employed.

What Is the Format of a LIMS Template?

A LIMS template is used to transfer data from a MultiQuant™ software results table to a LIMS system. The LIMS template is a comma delimited file with the fields to be output listed across the top of the report. Each field in the template should be separated by a comma.

Archiving and Purging MALDI TOF/TOF™ Data and Creating Database Backups

Described herein is a general procedure on how to archive/purge data from a MALDI TOF/TOF™ system, as well as how to back up data.

No Help Topics Appear in the SCIEX OS Software Help System

Selecting the question mark in the upper right hand corner of SCIEX OS software launches the SCIEX OS Help System screen. If no information appears for a selected topic, the SCIEX OS Help.chm file located in the C:\Program Files\SCIEX\SCIEX OS\Documentation folder needs to be unblocked.

Where Can the Software for StatusScope® Remote Monitoring Service Be Accessed?

To obtain access to the software download for StatusScope® Remote Monitoring service, users who are under warranty or who have purchased the service can navigate to statusscope.absciex.com and select the link to the software download.

Is the SelexION® Device Compatible for Acquisition with SCIEX OS Software?

No, the SelexION® device is not yet supported in SCIEX OS software.

What is the Difference Between an EMC and an EMS Scan on a QTRAP® System?

The EMS and EMC scans are two different scan types that can be run on a QTRAP® system, making use of the linear ion trap (LIT) functionality. The EMS or enhanced mass scan is a full mass range MS scan in the LIT. The EMC or enhanced multiple charge scan is carried out in the LIT, where high charge state ions are selectively trapped and scanned.

Where Can I Download Skyline Software ?

This article includes the link to a free download of Skyline software.

Remote Data Access Software Error on MALDI TOF/TOF™ instruments

When setting up ProteinPilot™ Software or the imaging acquisition software for the MALDI TOF/TOF™ Systems, a RDA (Remote Data Access) software error message is received: "TOF/TOF Imaging Acquisition Software. The client components used to communicate with the instrument are newer than those found on the instrument. Please update the Remote Data Access service on the instrument."

Unable to See Chromatograms when a MultiQuant™ Software Report is Printed

If the Peak Fill option is set to "Do Not Fill Peaks" in MultiQuant software, chromatograms will be faded out when output to a report and sometimes appear as not legible.

Updating the Sample Information Column in MultiQuant™ Software Results Table

Updating the sample name column in MultiQuant™ software will fail and result in an error message if invalid characters are used in the added text. The Sample Name and Sample ID columns cannot contain the following characters: \ / : * ? " < > | = or . .

Turbo V™ Ion Source Heater Replacement

How to replace the ion source heaters in the Turbo V Ion Source

TripleTOF® System Vacuum Interface Routine Cleaning

How to clean the vacuum interface of the TripleTOF instruments

Setting Up a New Project in SCIEX OS Software

Projects can be created in the Status panel by selecting the white plus sign in a circle icon next to the projects drop down menu. Selecting the button will bring up the New Project screen where the name of the New Project will be entered. Projects can also be created in the Configuration module by selecting the Projects tab.

Can Data Files Be Renamed after Acquisition Is Complete?

It's possible to change the name of a raw data file after it has been acquired in Analyst® or SCIEX OS software. Both the .wiff and .wiff.scan files would have to be named in the exact same manner or they may become corrupted.

Importing *.xlsx Files to Build Batches in Analyst® Software

Importing *.xlsx files to build batches in Analyst® software requires Microsoft Office 32-bit to be installed, although its not recommended to use the 32-bit version of Office on a 64-bit Win 7 operating system. SCIEX recommends that the following file formats be used instead: .xls, .csv and .txt.

Can I use the Proteinpilot SW with 4700 data

Can I use the Proteinpilot SW with 4700 data

Activating Analyst TF 1.7.1 Hardware Profile in Sim Mode

When running Analyst TF 1.7.1 in sim mode on a processing workstation, an additional driver, the Chronologic driver, must be downloaded and installed.

Where are the Cliquid Software Report Templates Located?

The Cliquid® software report templates are saved in the folder D:\Analyst Data\Projects\Cliquid\Templates\ReportTemplates.

Troubleshooting the ZenoTOF 7600 System: In-Run Calibration Failures

If a calibration failure occurs while acquiring data on the ZenoTOF 7600 system, then certain measures can be followed to mitigate this issue. The troubleshooting guide provided in this article is a step-by-step path for resolving any problems with in-run calibrations. To begin troubleshooting in-run calibration failures, users should open the calibration report in the Analytics workspace of SCIEX OS software to identify the reasons behind the failure.

Bio Tool Kit Software License iNeeded for SCIEX OS 1.x and PeakView Software.

The Bio Tool Kit software can be activated within PeakView 2.x and SCIEX OS 1.x software but a separate software license is needed.

Sciex OS Software Report Error: An Item with the Same Key Has Already Been Added

An error was received while using Sciex OS software to generate a report: "Error during Report generation. An item with the same key has already been added." No report was generated. To resolve this issue, open the report template and see if a query file is linked through the Meta Field tag. If a query is linked, open the query and evaluate it for any duplicate column names. Delete any duplicate columns from the input sheet.

Unhandled exception has occurred Waters Acquity Method Editor v1.4 & 1.5

When saving or opening a method with the Waters Acquity Method Editor an unhandled exception occurs System.NullReferenceException Object reference not set to an instance of an object

SCIEX OS Software: Unable to Upload Exported Text File to Watson LIMS

In SCIEX OS software 2.1.6, if the internal standards appear in any location in the results table, instead of being grouped together at the bottom of the analyte list, and are distributed throughout the processing method, then the exported results text file cannot be uploaded to Watson LIMS.

Peak Labels from Analyst® Report Are Missing in MultiQuant™ Software Report

To add in the labels to reports generated in MultiQuant™ software, the tag for Peak Review has to be edited to show the Analyte_Peak_Name in the Label field.

PA800 How To - Installing the LIF Detector

Installing the LIF Detector

Polarity Switching Is Not Supported in Analyst® Software Versions below 1.6

To run sMRM methods with polarity switching, Analyst® software 1.6 or greater must be used.

Reasons for Data File Processing Failure with the Data Converter Version 1.3 Beta

What are the potential issues listed which can cause the SCIEX MS data converter version 1.3 beta to not work correctly?

How To Create Sub-project Folders in SCIEX OS Software

Within projects, data can be further organized in sub-folders in SCIEX OS software. This article explains how to create a sub-project using the Add Data Sub-Folders dialog in the Configuration workspace.

Where are the SCIEX OS Software Report Templates Located on My PC?

If a report template needs to be opened for editing or if a new custom template needs to be added to the template list in SCIEX OS software, then navigate to C:\ProgramData\SCIEX\Analytics\Reporter to locate or add a template.

Compound Parameters Not Loading in Analyze Mode in DiscoveryQuant™ 3.0.1 Software

Compound parameters could not be uploaded in Analyze mode in DiscoveryQuant™ 3.0.1 software after switching from a local database to SQL database due to issues with the database selected as the review database.

PA800 How To - Cartridge Removal Rebuild Reinstallation

Procedure for Cartridge Removal Rebuild Reinstallation on PA800 System

Where Can I Find My Hardware Profile in SCIEX OS Software?

The hardware profiles for instruments supported by SCIEX OS software are stored in a file called HardwareProfile.hwp that is located in the following directory: C:\ProgramData\SCIEX\Clearcore2.Acquisition.

Windows 7 and 10 Operating Systems Are Compatible with Analyst® Administrator Console 3.0

Windows 7 and 10 operating systems are compatible with Analyst® Administrator Console 3.0 software.

Adding Custom Columns to a Results Table in Analyst™ Software

To add custom columns to a results table in Analyst™ software, right click within an open results table and select the option Add Custom Column.

How Can I Sum Vitamin D2 and D3 in SCIEX OS Software?

To add the calculated concentrations for vitamin D2 and D3 together and calculate the total vitamin D, a custom calculation in SCIEX OS software will need to be created in the processing method in the Analytics mode. The calculation will add custom column named Total VitD to the results table and provide a sum of the values for the calculated concentrations for vitamin D2 and D3.

How to wire SCIEX AUXIO cable for use with a Waters Acquity HPLC System

Diagram of how to wire AUXIO connections for the Acquity HPLC including the Stop Flow on instrument error

Network Acquisition and Processing of Analyst® Software Data Files and Time Stamps

When data files acquired with Analyst® software are saved to a network server, does the time stamp on the data come from the local machine or the network server? After processing data in the Analyst project folder residing on the network server, the results files were also saved on the network server. Does the data time stamp come from the local machine or the network server?

Can I add a Compound to My Library with MasterView™ instead of LibraryView™ Software?

LibraryView™ software, but not MasterView™ software, must be used to add a compound to an existing library. You can use MasterView software to import other libraries or a new library, but not a new compound from a newly acquired MS/MS spectrum.