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Knowledge Base is your tool to finding answers about common questions. Browse all Knowledge Base articles below. 

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".

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.

12/04/2020    SCIEX OS | MultiQuant Software

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

Summary of potential causes of poor HPLC peak shape


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.

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.


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.

12/04/2020    MultiQuant Software

Are PPGs Used for Tuning and Calibrating the QTRAP® or TripleQuad™ LC-MS/MS 7500 Systems?

No, a new calibrant, the MS Tuning Solution, was introduced for tuning and calibrating the QTRAP® or TripleQuad™ LC-MS/MS 7500 Systems.


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.

12/02/2020    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.

12/02/2020    Clinical | Analyst Software

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.

12/02/2020    MultiQuant Software

How to Sum the Concentrations of Isomers in SCIEX OS Software

To add the concentrations of different isomers together when processing data in SCIEX OS Software, open a processing method in the Analytics mode of the software. Select the Calculated Columns tab in the processing method and then select Add Formula to create a custom calculation for adding the isomers.  

12/02/2020    SCIEX OS

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.

12/01/2020    SCIEX OS

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. 

12/01/2020    SCIEX OS | MultiQuant Software

How to Open a Reporter Query Used with SCIEX OS or MultiQuant Software Report Templates

This article discusses the three ways to open a query (a file with the extension .query), a file linked to a report template that can be used to perform more complicated calculations or sorting functions in a results table.

Where Is the License File Saved to Activate a SCIEX Library Used with SCIEX OS Software?

For libraries imported into SCIEX OS Software and used with LibraryView 1.x Software, the license file needs to be saved to the directory C:\Program Files\AB SCIEX\LibraryView\LibraryViewFramework\Server in order to unlock the library and activate it.

11/10/2020    LibraryView Software

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.

11/10/2020    Analyst Software

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.

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.

11/10/2020    Analyst Software

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.

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.


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.

11/10/2020    MasterView Software

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.

Which Glycan Notation Is Used in the BioPharmaView™ Software?

The glycan notation used in BioPharmaView™ Software is the Oxford style.

Is the Digital PicoView® Ion Source Compatible with Analyst® TF Software 1.8.x?

Both Analyst® TF Software 1.8.x and the software for the Digital PicoView® Nanospray Ion Source will work together with the Windows 10 operating system. This was tested and confirmed separately by both manufacturers, SCIEX and New Objective. 

11/08/2020    Analyst 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."

11/08/2020    Academia Omics | Pharma CRO

Electronically Resetting the X-series QTOF MS Systems (X500R and X500B)

The steps required to reset the X-series QTOF MS Systems (X500R and X500B) are described here.


What Is the Part Number for the Solvent Guides Used in the Amplifex™ Diene Reagent Kit?

This article provides the part number for the solvent guides used in the Amplifex™ Diene Reagent Kit.

11/06/2020    Amplifex Keto Reagent

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.

11/06/2020    Academia Omics

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.

11/06/2020    SCIEX OS

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.

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.

11/06/2020    Pharma CRO | Analyst Software

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.


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.

11/06/2020    SCIEX OS

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.

11/06/2020    QTRAP Systems | Triple Quad Systems

Are the Ion Sources Interchangeable Between the QTRAP® and TripleQuad™ 6500+ and 7500 Systems?

The ion sources for the SCIEX QTRAP® and TripleQuad™ 6500+ and 7500 LC-MS/MS Systems are not interchangeable. The OptiFlow® Pro Ion Source cannot be used on the QTRAP or TripleQuad 6500+ Systems. Likewise, the IonDrive™ Turbo V, Turbo V™, and OptiFlow Ion Sources cannot be used with the QTRAP and TripleQuad 7500 Systems. 

11/06/2020    QTRAP Systems | Triple Quad Systems

Creating a ProteinPilot Software Winner Proteins Results List as FASTA File

This article describes the steps for creating a FASTA file from a ProteinPilot™ software report of winner proteins.

Flags or Custom Results Are Not Showing Correctly on a SCIEX OS Software Report

A mismatch of index can occur when internal standard values from a SCIEX OS software results table are processed within a query, causing the text for the reported values to appear bolded and in red, even when there is no reason for flagging these values in the report itself. This phenomena is observed for results tables created in versions of SCIEX OS Software 1.6.1 or lower and has been fixed in versions of SCIEX OS software 1.7 or greater.

11/05/2020    SCIEX OS

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).


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.

11/05/2020    QTRAP Systems | Triple Quad Systems

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".


How to Apply an External Calibration Curve to a Results Table in MultiQuant™ Software

In MultiQuant™ software, a previously-created calibration curve can be imported into a results table and applied to the existing unknown samples. In the old results table with the calibration curve that you would like to export, ensure the standard samples are present and select the Process menu. Then select Export Calibration, name the calibration curve data, and click Save.

11/04/2020    MultiQuant Software

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.

11/04/2020    Analyst Software

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.

11/04/2020    SCIEX OS | Analyst Software

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.

11/04/2020    Analyst Software

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.

11/04/2020    SCIEX OS | MultiQuant Software

Controlled Ways to Output Data from SCIEX OS Software

The controlled ways to output data from the SCIEX OS software Analytics workspace include 1) exporting a results table; 2) Transferring  the results table data to a LIMS; and 3) Creating a report though the Reporting tab option Create Report and Save Results Table.

11/04/2020    SCIEX OS

Adding a Flag or a Custom Flag Created in SCIEX OS Software to a Report

After creating a new results table in SCIEX OS software, add the Outlier Reasons column in the quantitation method to the Input tab of a query. Then, in the AnalystCalculations tab of the query, use the search function to find the flag of interest. Have the Outlier Reasons column added to the query's Output tab, and then link the Outlier Reasons column to the report template using a custom tag.

11/04/2020    SCIEX OS

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.

10/30/2020    Analyst Software

Premium Access

To configure Data Innovations' instrument manager system with the SCIEX LIMS transfer license, SCIEX software users must contact Data Innovations, not SCIEX, for assistance with the data transfer setup. Users who purchased the LIMS license for SCIEX OS or MultiQuant™ software will need to reach out to Data Innovations directly by emailing your region’s specific sales group. This will allow Data Innovations to track your request and provide a response within 48 hr.


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 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.


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. 

10/30/2020    SCIEX OS | Analyst Software

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.

10/30/2020    SCIEX OS

Can I Change the Sorting Order for Project Folders in Analyst® Software?

Analyst® software does not have not have internal sorting logic, so to sort projects, the API functions, FindFirstFile and FindNextFile, are used to retrieve the files from the directory. The order in which the file names are returned is dependent on file system type (NTFS, CDFS or FAT).

10/29/2020    Analyst Software

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.

10/29/2020    Analyst Software

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. 

10/29/2020    Software

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.

10/29/2020    SCIEX OS

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.

10/29/2020    SCIEX OS

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.

10/29/2020    SCIEX OS

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.

10/29/2020    Analyst Software

Is There a Password Character Limit for Accessing Analyst® Software in Mixed Mode?

Passwords used to access Analyst® software in mixed mode are capped at 13 characters. If your internal IT policy for the Windows password specifies more characters, this longer password requirement may lock the user out of Analyst software in mixed mode.

10/29/2020    Analyst Software

Where is the SCIEX OS Software Security Database Found?

The SCIEX OS software security database files are located at C:\ProgramData\SCIEX\Clearcore2.Acquisition, and the file is called

10/29/2020    SCIEX OS

Reporter: Why Did the Outlier Reasons Column Change Color after Running a MultiQuant™ Software Query?

The text in the outlier reasons column will change from black to pink if the column value exceeds the cutoff value in  MultiQuant™ software. If a query is run after creating the MultiQuant software results table, the flagging color of the query overrides the flagging color of the outlier reasons column in the results table.

10/28/2020    MultiQuant Software

How to Export a Statistics Table From SCIEX OS Software to Excel

The statistics pane can be accessed from the Views menu in the Analytics module of SCIEX OS software. After opening the results table, select Statistics pane from the Views menu and a new table appears below the results table. To export the contents of the statistics table from SCIEX OS, the table can be copied to Excel by highlighting all rows, and then selecting Ctrl+C. In an open Excel spreadsheet, the selected columns and rows can be pasted using Ctrl+V.

10/28/2020    SCIEX OS

Restoring Icons to the Analyst® Software Toolbar

To restore missing toolbars in Analyst® software, select the Tools menu, and then select the Restore Default Toolbars option. This should restore the icons that were not showing previously. 

10/28/2020    Analyst Software

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. 

10/28/2020    MultiQuant Software

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.


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.

10/28/2020    Analyst Software

What Is the SCIEX OS Software Equivalent to the Area Threshold Feature in Analyst® Software?

SCIEX OS software does not have a field for the Area Threshold as found in the Analyst® software quantitation method wizard that allows users to set the criteria for peaks to appear as "not found" in a results table. Instead, a custom flagging rule must be created in SCIEX OS software to enable this type of filtering for peak area.

10/22/2020    SCIEX OS

What Cable Should I Use To Connect PAL3 to an Agilent Pump when Using Analyst® Device Driver?

A sync cable, called the PAL connecting cable APG Remote, should be used to connect the PAL3 autosampler to an Agilent pump when both the devices are configured through the Analyst® Device Driver (ADD).


Can Regular Expressions (Regexes) Used for Data Filtering in SCIEX OS Software Be Saved?

To export and import filter settings so they can be used across multiple results tables and projects in SCIEX OS software, a regular expression (regex) can be created using a custom filter in an existing results table. The custom settings can be exported as a .cset file using the Table Display Settings export feature and reapplied to another table using the Import feature.

10/22/2020    SCIEX OS

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.

10/22/2020    Academia Omics | Pharma CRO | iTRAQ Reagent

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.

10/22/2020    SCIEX OS

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.


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.

10/22/2020    SCIEX OS

How to Change the Font in a Report Template?

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

10/22/2020    Software

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.

10/22/2020    SCIEX OS

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.


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.

10/20/2020    SCIEX OS

Is the Impurity Feature Available in BPV Flex Software?

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


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.


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.


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.


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.


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 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.

06/11/2020    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.

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.

05/14/2020    Academia Omics | Software

How to Extract Multiple XICs in Separate Windows in Analyst® Software Explore Mode

Sometimes in the Analyst® software Explore mode, it's optimal to view individual extracted ion chromatograms (XICs) in separate panes instead of in the same windows when extracting multiple ions from a total ion chromatogram (TIC). To prevent multiple XICs from appearing in the same window, the Appearance Option settings in Analyst software will need to be adjusted.

05/14/2020    Analyst Software

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.

05/14/2020    MultiQuant Software

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.

05/14/2020    Analyst Software

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.

05/14/2020    MultiQuant Software

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.

05/14/2020    Academia Omics | Software

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.

05/14/2020    SCIEX OS

Obtaining Intensity Information from an IDA-EPI MS/MS Spectra

To obtain the intensity information from an IDA-EPI MS/MS spectra, the ProteoWizard data conversion tool, MSConvert, can convert SCIEX data files (.wiff and .wiff.scan) to other formats using MSConvert besides mzML, such as MGF or txt formats. These non-mzML formats create larger files but provide the spectral data in simple mass/intensity text.

05/13/2020    Software

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.

05/13/2020    ProteinPilot Software

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.

05/13/2020    Mass Spectrometers

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.

05/13/2020    DiscoveryQuant Software

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.

05/13/2020    SCIEX OS | MultiQuant 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.

04/30/2020    Analyst Software

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)

04/29/2020    LibraryView Software

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

04/28/2020    Software

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.

04/28/2020    LibraryView Software

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.

04/28/2020    SCIEX OS

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.

04/17/2020    Analyst Software

Accessing ProteinPilot™ Software Searching in the SCIEX Cloud Workspace

To log into the SCIEX Cloud workspace and access the ProteinPilot™ software searching features with just your CloudConnect license, follow the instructions below.

How to Determine if the Acquisition PC Has a Bad Ethernet Card?

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

04/16/2020    Mass Spectrometers

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.

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.

04/16/2020    Software

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.

04/16/2020    Cliquid Software | MPX Software

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 SE (64-bit) and (32-bit).

04/16/2020    SCIEX OS

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.

SCIEX OS 1-5 Software

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


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.

04/16/2020    Cliquid Software

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.

04/16/2020    Analyst Software

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.

04/13/2020    SCIEX OS

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.

04/13/2020    MultiQuant Software

Location of the Event Logs for the MPX 2.0 Driver Software System

The event logs for the MPX 2.0 driver software system are saved under C:\Program Data\SCIEX\MPX Driver\Log\.

03/20/2020    MPX Software

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.

03/20/2020    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.

03/20/2020    SCIEX OS

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:

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.

03/20/2020    Analyst 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 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.

03/20/2020    Software

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.

03/20/2020    Academia Omics | NanoLC 400

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".

03/20/2020    SCIEX OS

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.

03/20/2020    SCIEX OS

Which Folders Should Be Backed Up Before Upgrading the SCIEX OS Software?

Prior to upgrading or removing SCIEX OS software, back up the SCIEX OS Data folder and the SCIEX folder in the Program Data folder.

03/20/2020    SCIEX OS

Is the MPX™ Driver Software System Compatible with Analyst® MD software?

The MPX™ driver software system is not supported with Analyst® MD software. Compatible LC systems are listed in the installation guide for Analyst MD software.

03/20/2020    Clinical | Forensics | Analyst Software

Using an External Calibration Curve in SCIEX OS-MQ Software

To use an external calibration curve with a results table created in SCIEX OS-MQ software, use the Export calibration (and save results...) feature in the Options menu after the calibration curve has been generated.

03/17/2020    SCIEX OS

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.

03/17/2020    Academia Omics | Pharma CRO | SCIEX OS

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.

03/06/2020    SCIEX OS

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.

02/21/2020    Software

Upgrading SCIEX Software Licenses

How to upgrade self-upgrade registered software licenses

01/27/2020    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.

12/26/2019    Software

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

12/18/2019    iTRAQ Reagent

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.

12/17/2019    Analyst Software

Reporter 3.2: How To Report Calculated Concentrations of "<0" or "N/A"

If a MultiQuant™ or Analyst® software results table contains values of "<0" and "N/A" for some calculated concentration values, these text values must be converted to a numerical zero value first using an Excel query. These calculated concentration values cannot be filtered into a Reporter Template Suite 3.2 results template using an if statement that selects for calculated concentration values that are less than or equal to zero.

12/16/2019    Software

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.

12/16/2019    SCIEX OS | MultiQuant Software

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.

Does the XCMSPlus Software Use MS/MS Data Matching to Identify Metabolites?

XCMSplus software does not use MS/MS matching to identify features. Instead, this software identifies features based on the precursor m/z.

Causes of the taglet.exe Error in ProteinPilot™ Software

The taglet.exe error in ProteinPilot™ software is due to a wide range of issues including incorrect language settings, installation of the software on the incorrect operating system, and the incorrect addition of modifications — to name a few.

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.

Does My Acquisition PC Have a Bad Ethernet Card?

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

11/13/2019    Software

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.

11/13/2019    Academia Omics

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.

11/11/2019    Academia Omics | SimGlycan Software

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.

11/11/2019    Academia Omics | SimGlycan Software

What is SimGlycan Software?

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

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

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

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.

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.

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.

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.

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.

11/09/2019    Academia Omics | Pharma CRO | iTRAQ Reagent

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.

11/09/2019    Mass Spectrometers

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.

11/09/2019    SCIEX OS

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.

11/09/2019    SCIEX OS

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.

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.

11/08/2019    SCIEX OS

Adding Custom Columns In a Batch in Analyst® Software

To add a custom column(s) to a batch in Analyst® software, right click within the batch table on the Sample tab, and select Add Custom Column.

11/07/2019    Analyst Software

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.

11/06/2019    SCIEX OS

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.

11/06/2019    Analyst Software

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.

11/06/2019    Analyst Software

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.

11/01/2019    SCIEX OS

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.

10/28/2019    MultiQuant Software

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.

10/28/2019    SCIEX OS

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.

10/25/2019    Analyst Software

How to Update or Link a Query File to a Report Template

If the name of a query is ever changed or updated or if a new query needs to be attached to a report template, the query must be relinked to the template used for reports created in MultiQuant™, Analyst® or SCIEX OS software.

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.

10/21/2019    SCIEX OS

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.

10/21/2019    SCIEX OS

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.

10/21/2019    SCIEX OS

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.

10/21/2019    Software

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.

10/17/2019    SCIEX OS

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.

Absence of Calibration Curve in Analyst® or MultiQuant™ Software Due to Omitted Standard Concentration Values

If actual concentration values for standards are omitted from a MultiQuant™ or Analyst® software results table, then the data points for standard concentration versus peak area will all be aligned with zero on the x-axis in the calibration curve, looking nothing like the expected diagonal line. Adding the actual concentration information for the standards spreads the points across the x-axis and restores the expected diagonal linear regression line.

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.

10/15/2019    SCIEX OS

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.

10/15/2019    Cliquid Software

Ensuring the Positive Hits Report Includes Only Positive Hits from a Results Table Generated in SCIEX OS Software

To ensure that only the positive hits appear in a report generated using the Positive Hits template rather than all visible results in a results table, the results table itself first needs to be filtered to show only positives prior to running the report.

10/15/2019    SCIEX OS

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.

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.

10/10/2019    SCIEX OS

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.

10/09/2019    ChemoView Software

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.

10/09/2019    Cliquid Software

To Make Reporter Tags Visible in a Report Template Unblock Them

If a report template is emailed or transferred to another computer and then opened, the xml tags may not be visible because they were blocked for security reasons.

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

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

10/08/2019    MultiQuant Software

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.

10/08/2019    MultiQuant Software

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.

10/07/2019    Analyst Software

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.

10/04/2019    Analyst Software

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.

10/04/2019    Analyst Software

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.

10/04/2019    Pharma CRO | DiscoveryQuant Software

Unlocking the Secure PDF Files Created by SCIEX OS Software

To unlock a secure PDF file created using SCIEX OS software reporter, open the document in a web browser and then print the newly opened document using either Microsoft Print to PDF or Save As PDF.

10/03/2019    SCIEX OS

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.

10/03/2019    Analyst Software

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.

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.

10/02/2019    SCIEX OS

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.

10/02/2019    MPX Software

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.

10/02/2019    SCIEX OS

Entering the Formula for a Stable Isotope Labeled Compound in SCIEX OS Software

To enter the formula for a stable-isotope-labeled compound in the Components tab of a processing method in SCIEX OS software, some specific rules must be followed. When entering the formula, the atomic mass of the isotope is added before the single letter chemical abbreviation of the element, and then the total number of atoms of each isotope follows the chemical symbol.

10/01/2019    SCIEX OS

Resolving Analyst® 1.6.3 Software Launch Error: Cannot Find the File Usernameanalyst.exe

To resolve the error "Cannot find the file usernameanalyst.exe" when opening Analyst® 1.6.3 software, the format of the Windows username on the computer where Analyst software was installed could not contain a period or a space in the middle of the user name. Reformatting the text of the Windows usernames resolved the issue.

10/01/2019    Analyst Software

After Upgrading Analyst® Software, Why Do Data Files Include xx.wiff.scan Files?

After upgrading Analyst® software, some data files now include xx.wiff.scan files. In the Configure mode in Analyst software, navigate to the Tools and Queue Options menu. Deselect the Use flat files for scan data button to prevent the xx.wiff.scan files from being created.

09/30/2019    Analyst Software

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.

09/30/2019    Analyst Software

Longer Power Cycle May Help To Resume Instrument Connectivity after Power Failure

Even after resetting the mass spectrometer (by following the power-cycling procedure), the instrument would not come back online after a power failure. On some occasions, the mass spectrometer must be completely powered down for at least 1 min in order for the circuits to discharge and fully release any faulty information.

09/30/2019    Mass Spectrometers

Exporting and Importing a Flagging Rule in SCIEX OS Software

Flagging rules for IS Recovery can be exported from an existing method in the Analytics workspace of Sciex OS software, and then the exported file can be re-imported into a new processing method using the Export/Import functions in the Flagging Rules screen.

09/29/2019    SCIEX OS

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.

09/29/2019    MPX Software

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 and select the link to the software download.

09/29/2019    Mass Spectrometers

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.

09/26/2019    SCIEX OS

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.

09/26/2019    MPX Software

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.

09/26/2019    Analyst Software

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.

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.

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.

09/26/2019    SCIEX OS

Does BPV Flex Software Support Multiple Period Experiments?

BPV Flex can only open the first period of multiple period experiment runs.

09/26/2019    Pharma CRO | BioPharmaView Software

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.

09/25/2019    Analyst Software

Creating a Processing Method in ChemoView™ Software

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

09/25/2019    ChemoView Software

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.

09/24/2019    ChemoView Software

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.

09/24/2019    MPX Software

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.

09/24/2019    ChemoView Software

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.

09/23/2019    SCIEX OS

Can SCIEX OS and MasterView™ Software Be Installed on the Same Computer?

SCIEX OS and MasterView™ software are not compatible, and they cannot coexist on the same computer.

09/23/2019    SCIEX OS | MasterView Software

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.

09/22/2019    ChemoView Software

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.

09/22/2019    SCIEX OS

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.

09/09/2019    Software

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.

09/09/2019    DiscoveryQuant Software

Where Can I Find My Service Package for SCIEX OS 1.6.1 Software?

Any service package generated for SCIEX OS 1.6.1 software can be found as a zipped (compressed) file at C:\ServicesPackages.

08/09/2019    SCIEX OS

Creating a Custom Enzyme in BPV Flex 1.0 Software

To create a custom restriction enzyme in BPV Flex 1.0 software, locate the digestion agents secction in the BPV Flex DataDictionary.xml file. Type an enzyme definition or Copy/paste a definition for the desired enzyme.

08/09/2019    BioPharmaView Software

Adding a New Flagging Rule in the Analytics Workspace of Sciex OS Software

To add a new flagging rule in the Analytics workspace of SCIEX OS software, open the Analytics workspace. Click Process Method and select New. Then select the Flagging Rules page and click Add Rule.

08/09/2019    SCIEX OS

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

BioPharmaView™ software uses the isotopic masses published by NIST online at: Please note that the results generated will be the same throughout all SCIEX software (e.g., PeakView™ and ProteinPilot™ software).

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.

08/09/2019    LipidView Software

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.

08/09/2019    LibraryView Software

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.

08/09/2019    SCIEX OS

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.

08/08/2019    SCIEX OS

Protocol for Resolving the SCIEX OS Error: SciexLibraryService Rejected the Session-Establishment Request

Use the following protocol to change the port 8081 to resolve the software error that occurs wtih both Sciex OS and MasterView/LibraryView installations: SciexLibraryService rejected the session-establishment request.

07/24/2019    SCIEX OS

What Is the Organic Solvent Used with iTRAQ® Reagents during Shipment?

All iTRAQ®, aTRAQ™ and mTRAQ® reagents are shipped in acetonitrile from the factory.

Does SCIEX OS Software Have an Equivallent Security Configuration to Analyst® Software's Mixed Mode?

In Analyst® software, there are three security configuration modes available: Single User, Integrated and Mixed. Are there functional equivalents of all three available in SCIEX OS software? In short, no, there are not.

07/14/2019    SCIEX OS | Analyst Software

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.

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.

Converting MultiQuant™ Software Qmethods to Sciex OS Software Qmethods

This article contains a step-by-step guide for converting a MultiQuant™ 3.0.3 software quantitation method (.qmethod) file to a Sciex OS 1.5 software quantitation method file (.qmethod).

06/26/2019    SCIEX OS | MultiQuant Software

Can Skyline Version 4.2.1 and Higher Process .wiff2 File Formats?

Yes , Skyline version 4.2.1 can process .wiff2 files generated using SCIEX OS software.

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.

05/24/2019    MultiQuant Software

Verifying if .NET Framework 3.5.1 Is Installed on a Windows 7 Operating System

To verify if .NET Framework 3.5.1 is installed on a PC running a Windows 7 operating system, the .NET Framework Verification Tool may need to be deownprogram in the link provided.

05/24/2019    Software

Upgrading MultiQuant® software to 3.0.3 Version Results in Access is Denied Error

After upgrading MultiQuant® software 3.0.2 to 3.0.3 on Windows 10, the software initially launched. But when the software was accessed later, an error was received: "Access is denied".

05/23/2019    MultiQuant Software

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.

05/23/2019    SCIEX OS | LibraryView Software

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.

05/17/2019    Analyst Software

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 was added.

05/17/2019    Analyst Software

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.

05/13/2019    MasterView Software

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.

05/13/2019    SCIEX OS

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.

05/13/2019    Pharma CRO | DiscoveryQuant Software

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.

05/03/2019    Capillary Electrophoresis

List of CE Capillaries with Pre-burned Detection Windows

CE capillaries with pre-burned detection windows are available for purchase; the dimensions and coating information for these products are listed here.

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.

04/23/2019    SCIEX OS

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.

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.

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.

04/19/2019    SCIEX OS

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.

04/19/2019    SCIEX OS

Premium Access

The non-targeted peak searching algorithm determines which peaks are included for further library or formula finder searches in the Analytics mode of SCIEX OS Software, and the parameters that can be modified are described here.

04/17/2019    SCIEX OS

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.

04/15/2019    SCIEX OS

Understanding and optimizing signal-to-noise calculation in the 32Karat software

This document provides an overview of the S/N calculation and optimization in the 32Karat software.

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.

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.

04/05/2019    SCIEX OS

Coolant leak troubleshooting tips

The document provides troubleshooting steps for coolant leak issues (to determine where the leak is coming from).

Exporting PDA data from 32Karat into ASCII or AIA (.CDF) files

Procedure to export CE data files from the 32Karat software.

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

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.

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.

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 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.

04/02/2019    SCIEX OS

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.

03/21/2019    SCIEX OS

Recalibrating TOF MS or TOF MS/MS Spectra in SCIEX OS Software

To recalibrate a TOF MS or TOF MS/MS spectrum or recalibrate samples in SCIEX OS software, open the data file in Explore mode, select process, and then select Recalibrate Spectrum or Recalibrate Sample.

03/21/2019    SCIEX OS

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.

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.

03/01/2019    SCIEX OS

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).

02/28/2019    Analyst Software

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.

02/28/2019    Analyst Software

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.

02/28/2019    PeakView Software

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.

02/28/2019    SCIEX OS

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.

02/28/2019    SCIEX OS

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.

02/28/2019    Analyst Software

Changing the Number of Decimals Displayed in Analyst® Software Calibration and Metric Plots

This is a set of instructions for changing the number of decimals displayed in Analyst® software quantitation metric plots and calibration curves. The default number of decimals leaves the significance so low that you can not reproduce the results shown in the results table. A warning is given to let customers know that Regedit is a dangerous utility.

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.

02/15/2019    SCIEX OS

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.

02/15/2019    SCIEX OS

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.

02/15/2019    SCIEX OS

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.

02/15/2019    SCIEX OS

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.

02/15/2019    SCIEX OS

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.

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.

02/08/2019    SCIEX OS

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.

How To Move SCIEX Software License to a Different Computer

Description of the steps required to move an already activated SCIEX Software License from one computer to another.

01/28/2019    Software

How Is a MultiQuant™ Software Report Created in .CSV Format?

To create a report in MultiQuant™ software in .csv format, open a results table and then select Create Report under the File menu. Choose a comma delimited report template, and choose CSV as an output format.

01/24/2019    MultiQuant Software

How Do I Activate My SCIEX License Key?

To activate a SCIEX license key, log into with your username and password. Navigate to and complete the required fields.

01/24/2019    Software

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.


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).

01/09/2019    Academia Omics | Pharma CRO | iTRAQ Reagent

MetabolitePilot™ 1.5 Software Upgrade License Requires Older 1.0 License as Base

When MetabolitePilot™ 1.5 software is launched, an error is received after reinstalling the software indicating that a demo version of the software license has expired. If the license being installed is a MetabolitePilot 1.5 upgrade license, it will always need to be installed alongside the original MetabolitePilot 1.0 license.

12/28/2018    MetabolitePilot Software

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.

12/28/2018    Analyst Software

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.

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.

12/28/2018    Standards and Reagents

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 . .

12/28/2018    MultiQuant Software

Filtering Library Results for Compounds in MetabolitePilot™ Software

Using the blue funnel icon in MetabolitePilot™ software in the top right of the Result Pane will help narrow the search results provided when evaluating information-dependent acquisition (IDA) data for possible compounds that correspond to potential metabolite.

12/28/2018    LibraryView Software

Compatibility of Standard MutliQuant™ Software Files with MultiQuant MD Software

This article describes the compatibility of standard, non-GLP MutliQuant™ software files with MultiQuant MD software.

12/28/2018    MultiQuant Software

Resetting Root Directory to Analyst® Data Folder Restores Selexion® DMS Functionality

Resetting the root directory to the Analyst® Data folder restores Selexion® Differential Mobility Spectrometer (DMS) functionality and allows the hardware profile to activate in Analyst software.

What Are the Integration Types Used by Analyst® Software?

In Analyst® software, integration types by which the baseline is found and integrated when the peak is found are: baseline-to-baseline, valley, exponential skim, and exponential child.

12/27/2018    Analyst Software

Using Audit Trail and Security Features in MultiQuant™ Software Prevents Browsing to Other Project Folders

When using MultiQuant™ software with the audit trail and security features turned on, users will find that they are unable to browse to other project folder locations.

12/27/2018    MultiQuant Software

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.

12/27/2018    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.

12/27/2018    Analyst Software

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.

12/27/2018    Analyst Software | QTOF Systems

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.

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.

12/27/2018    ProteinPilot Software

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.

12/27/2018    SCIEX OS

Windows Folder Permissions Needed for 32 Karat Software Pperation

A table of the needed security permissions that allow the 32 Karat software to operate correctly in a Windows operating system environment is shown.


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).

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.

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.

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.

12/05/2018    Capillary Electrophoresis

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.

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.

Improving Peak Resolution when Using Capillary Electrophoresis

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

SCIEX Software Activation with Online Workstation

How to activate Analyst, MultiQuant or SCIEX OS software with a computer which is connected to the Internet

11/19/2018    Software

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

11/19/2018    Software

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.

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).

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.

Exporting ProteinPilot™ Software Data to PRIDE (PRoteomics IDEntifications)

Exporting ProteinPilot™ software data to the PRoteomics IDEntifications (PRIDE) database requires the .group files be converted to XML files. ProteomeXchange fully supports both MS/MS proteomics and SRM data submissions. Other types of proteomics data, including ProteinPilot data, is also possible using the partial submission mechanism.

11/09/2018    Academia Omics | Software

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.

11/09/2018    Analyst Software

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.

11/09/2018    MultiQuant Software

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.

11/07/2018    Analyst Software

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.

11/02/2018    Analyst Software

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.

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.

11/01/2018    Software

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 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.

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.

11/01/2018    Analyst Software

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.

10/22/2018    LibraryView Software

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.

10/19/2018    Analyst Software

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.

10/19/2018    Software

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.

10/19/2018    MultiQuant Software

MultiQuant™ Reporter: System Out of Memory Error

When generating a report in MultiQuant™ software, an error appears: "System out of memory." To resolve this error, more memory can be added to the computer, a 64-bit computer can be used, or one of the two following workarounds can be used.

10/18/2018    MultiQuant Software

Ordering Foam Applicators for Cleaning a IonDrive™ QJet Ion Guide

The IonDrive™ QJet ion guide can be cleaned with an anti-static foam swab (part number 1017396 or 1017398).

10/18/2018    Mass Spectrometers

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.

10/18/2018    Analyst 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.

10/18/2018    MultiQuant Software

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.


Possible Non-Numerical Outcomes for MultiQuant™ Software Results Tables

Instead of a number, sometimes MultiQuant™ software returns a non-numerical result in the results table.

10/18/2018    MultiQuant 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.

10/17/2018    Pharma CRO | ProteinPilot Software

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.

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.

10/17/2018    Software

iTRAQ® Reagents: Can Samples Labeled with Both the 4-Plex and 8-Plex Kits Be Mixed?

The iTRAQ® Reagents chemistry for 4plex versus 8plex kits is described.SCIEX does not recommend mixing samples labeled with the reagents from the two separate iTRAQ® kits, 4plex and 8plex, due to the differences in the reagent chemistry.

10/16/2018    Academia Omics | Pharma CRO | iTRAQ Reagent

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.

10/16/2018    SCIEX OS

Compatibility of ProteinPilot Software 4.5 Beta with Microsoft Office 2016

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

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.

10/16/2018    Analyst Software

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.

10/16/2018    Analyst Software

Where Can I Get a New Registration Key for Analyst® Software?

If the registration key information for Analyst® software 1.6.x has been lost, navigate to to obtain a new one.

10/12/2018    Analyst 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.

10/12/2018    Analyst Software

Which Amino Acids in the PepCalMix Are Labeled?

The PepCal Mix (P/N 5045759) contains 20 heavy-labeled peptides, with the heavy isotopes incorporated in the amino acids, K and R.

Keeping a Nano LC/MS System Running after Sample Acquisition Is Completed

To keep a nano LC/MS system running after sample acquisition has completed, the LC/MS can be configured two different ways, assuming the Nano Eksigent 400 system is used.

Is the Analyst® or Analyst® TF Software Backwards Compatible?

The Analyst® or Analyst® TF software is only forward compatible.

10/08/2018    Analyst Software

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.

10/08/2018    Academia Omics

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

10/08/2018    Software

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.

09/06/2018    Analyst Software

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.

09/06/2018    MultiQuant Software

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.

08/31/2018    LibraryView Software

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.

Where Are the Queries Used with MultiQuant™ Software Stored?

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

08/15/2018    Software

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 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.


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.

07/09/2018    Analyst Software

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.

07/09/2018    LibraryView Software

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

07/09/2018    Academia Omics

Where Can I Find Instructions for the Protein Preparation Kit?

Protein preparation instructions can be found on the SCIEX website at or

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.

07/03/2018    SCIEX OS

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.

07/03/2018    Analyst Software

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.

07/03/2018    SCIEX OS

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.

07/03/2018    Software

Using Ammonium Fluoride (AMF) in an HPLC Solvent

Ammonium fluoride can be used in LC/MS applications as a mobile phase additive. It is recommended that only small concentrations as possible be used (around 0.2 mM).

07/03/2018    Mass Spectrometers

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.

07/02/2018    SCIEX OS

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.

07/02/2018    SCIEX OS

Does SCIEX OS 1.4 Support Queries?

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

07/02/2018    SCIEX OS

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.

07/02/2018    MultiQuant Software

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

06/21/2018    Software

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.

06/04/2018    Analyst Software

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.

06/04/2018    Academia Omics | Pharma CRO

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.

06/04/2018    Software

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.

06/01/2018    Analyst Software

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.


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.

06/01/2018    PeakView Software

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.

06/01/2018    MultiQuant 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.

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.

05/31/2018    Analyst Software

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.

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.

05/31/2018    MultiQuant 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."

05/31/2018    MultiQuant Software

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.


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

05/31/2018    Analyst Software

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.

05/31/2018    Academia Omics | Pharma CRO

Can the Sample Injection Volume Be Displayed in an Analyst® Software Results Table?

Analyst® software results tables do not have the option to display the sample injection volume from the data file.

05/25/2018    Analyst Software

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.

05/25/2018    Clinical | Analyst Software

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.

05/25/2018    Analyst Software

The Analyst® Device Driver 1.3 Release Notes

The Analyst® Device Driver 1.3 Release Notes are attached. Please consult this guide for the new features and changes from the previous versions.

05/21/2018    Analyst Software

Unable to Create Project in Analyst® Software

If a project folder is not accessible in Analyst® software, then the root directory must be set to C:\Analyst Data\Projects\. Additional projects and subprojects are set up under this root directory.

05/21/2018    Analyst Software

How to Adjust the Ion Ratio in MultiQuant Software

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

05/21/2018    MultiQuant Software

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.

05/21/2018    Analyst Software

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.

05/21/2018    MPX 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.

05/21/2018    MultiQuant Software

SCIEX Registered Software Webpage Lists All Recently Activated Licenses

The SCIEX Registered Software webpage ( lists all recently activated licenses.

05/21/2018    Software

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)).

05/21/2018    Analyst Software

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.

05/21/2018    LibraryView Software

Analyst® 1.7 Software Launch Error: No Such Feature Exists

If the license error "No such feature exists" appears when launching Analyst® 1.7 software, install the license file to the C:\ProgramData\AB SCIEX\Analyst\License folder resolve the issue.

05/16/2018    Analyst Software

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.

05/16/2018    Analyst Software

Avoiding an Invalid Transition List Format Error when Building a Method in Skyline for Analyst® Software

When building a MRM method in Skyline for use in Analyst® 1.6.1 software, the following error may appear: "Invalid transition list format. Failure parsing numeric value".

05/15/2018    Analyst Software

What Are the Reasons for Hybrid Electrodes Probe Blockage?

Common issue reported with hybrid electrodes probes.

05/15/2018    Academia Omics | Mass Spectrometers

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.

05/15/2018    Analyst Software

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.

05/15/2018    ProteinPilot Software

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.

05/15/2018    Academia Omics

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.

05/15/2018    Bio Tool Kit Software

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?

05/15/2018    Analyst Software

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.

05/14/2018    Analyst Software

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.

05/14/2018    MultiQuant Software

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.

05/14/2018    Software

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.

05/14/2018    Analyst Software

How Are Graph Axis Setting Changed in Analyst® Software?

To change the x- and y- axis settings for a chromatogram in Analyst® software, navigate to the Tools menu, select Settings, and then the Appearance Options menu. The x- and y-axis options are in the Other Graph Options tab.

05/14/2018    Analyst Software

Does the BioTool Kit MicroApp Require a Separate License in PeakView® Software?

The BioTool Kit MicroApp features cannot be accessed in PeakView® software unless a separate license is installed alongside the PeakView® license.

Molecular Ion Not Appearing during Compound Optimization

Adding mobile phase to the analyte or increasing its concentration during compound optimization may help improve ionization.


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.

05/11/2018    Analyst Software

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.

05/11/2018    Analyst Software

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.

05/11/2018    Analyst Software

Downloading Software from the SCIEX Website Requires the Most Current Browser

To successfully download a trial license or software from the SCIEX website, your browser needs to be up-to-date.

05/11/2018    Software

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.

05/08/2018    Analyst Software

High Mass Cooling in Analyst® Software during Full Scans

The High Mass Cooling functionality was introduced to Analyst® software to minimize the negative effects of very high RF voltages on the quadrupole rod arrays. It is used only on certain instruments (5500, and 6500 series in low mass mode only) in order to slightly extend the usable mass range while maintaining optimal ion transmission and sensitivity.

05/04/2018    Analyst Software

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.

05/03/2018    Analyst Software

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.

05/03/2018    Analyst Software

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.

05/03/2018    Analyst Software

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.

05/03/2018    SCIEX OS

Protocols for Protein Precipitation in Samples before Using iTRAQ® Kits

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

05/01/2018    Academia Omics | Pharma CRO | iTRAQ Reagent

Setting Up a Scheduled Ionization Method in Analyst 1.7 Software

The scheduled ionization feature can be used to reduce the mass spectrometer downtime by decreasing the risk of contamination. To set up a scheduled ionization method in Analyst® 1.7 software, follow the instructions below.

05/01/2018    Analyst Software

Does Analyst® 1.7 Software Support the Windows Long-Term Service Channel?

Windows10 and Analyst® software are not supported by the Windows long-term service channel.

04/27/2018    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.

04/12/2018    Analyst Software

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.

04/10/2018    Analyst Software

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.

03/22/2018    Analyst Software

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.

03/22/2018    MultiQuant Software

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.

03/22/2018    SCIEX OS

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.

03/22/2018    MultiQuant Software

ProteinPilot™ 5.x Software: Incorrect Result Output for Instrument Names in the Group File

ProteinPilot™ software uses the incorrect mass spectrometer name in its group file output file. When a TripleTOF® 5600 system was selected, the group file contains the name QSTAR® Elite instead for system information. This causes the wrong results to be output; if the incorrect instrument name is used, then the incorrect tolerance settings are applied.

Where Can I Download SCIEX Software?

Full versions of many our software programs can be downloaded from the SCIEX website at

03/16/2018    Software

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.

03/16/2018    MultiQuant Software

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.

03/16/2018    LibraryView Software

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.

03/16/2018    Software

Restoring Calibration Reference Tables in Analyst® Softare

To restore a calibration reference table in Analyst® software, copy the TuneData.tun file over to the current API instrument folder/Preferences folder.

03/15/2018    Analyst Software

For MS3 Experiments, Why Are Two Peaks Adjacent to the Ion of Interest Also Selected?

If AF2 (a parameter describing the amplitude of the resonant excitation field) is very large, then off-resonant excitation will begin to increase the kinetic energy of neighboring m/z ions.

03/15/2018    QTRAP Systems | Analyst Software

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.

03/15/2018    Analyst Software

Analyst® 1.7 Software Patch for Windows 10 Update 1709 Installation Error

When installing Analyst® 1.7 software with Hotfix 1 and the patch for Analyst 1.7 for Windows 10 Update 1709, the following error message was received, "You must have Analyst 1.7 software installed to install Analyst 1.7 Patch for Windows 10 Update 1709."


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.

03/14/2018    Analyst Software

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.

03/14/2018    Analyst 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.


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.

03/12/2018    MPX Software

Creating Windows User Groups for Analyst® Software Security Configuration

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

03/08/2018    Analyst Software

Adding User Groups to the Analyst® Software Secruity Configuration

The steps below describe how to add user groups into the Analyst® software security configuration.

03/08/2018    Analyst Software

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.

03/07/2018    MultiQuant Software

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.

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.

03/06/2018    Analyst 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.

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.

Premium Access

MarkerView™ 1.2.1 and 1.3 software and PeakView® 2.2 software can import T2D files generated on the TOF/TOF™ series of instruments.

02/26/2018    Academia Omics | MarkerView Software

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.

02/26/2018    Academia Omics | Pharma CRO | iTRAQ Reagent

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.

01/31/2018    QTOF Systems

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.

01/12/2018    Analyst Software

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.

01/12/2018    ChemoView Software

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.

01/11/2018    Analyst Software

Converting Sciex OS WIFF2 Files to the MzML and MzXML Format

The Proteowizard tool ( for MzML and MzXML conversion has been updated to work with the new WIFF2 files that are produced by SCIEX OS 1.2 and 1.3.

12/22/2017    Analyst Software

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.

12/22/2017    MultiQuant Software

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.

12/22/2017    Analyst Software

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.

12/22/2017    Analyst Software

Why Can't I Open Analyst® Software when My Security Role Is Set to Supervisor?

If a user has the security role of supervisor in Analyst® software, then he/she can override a screen lock or logout of the software--but only if the Analyst security configuration is set to Mixed Mode.

12/22/2017    Analyst Software

Clearing a Manual Tune Error Message in Analyst® Software

If the syringe runs dry while doing direct infusion, a manual tune error may disrupt compound optimization in Analyst® software manual tune mode, requiring an LC/MS system reset.

12/21/2017    Analyst Software

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.

12/21/2017    Mass Spectrometers

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.


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.

12/21/2017    Analyst 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.

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.

12/21/2017    LibraryView Software

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.

12/21/2017    SCIEX OS | LibraryView Software

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.

12/21/2017    Software

Configuring Analyst® Software for Email Notification of Audit Trail Events

Users can configure the Analyst® software to send an email message if there are three log on errors within one day. This email notification is available only if the workstation is in Integrated Mode or Mixed Mode.

12/21/2017    Analyst Software

Adding Acquity Plate Definitions into Analyst® Software

To add the definition of the Acquity 96-well, 1-mL plate (using ANSI-96well1mL.plate file) to Analyst® software, a plate definition file must be acquired from Waters.

12/20/2017    Analyst Software

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.

12/20/2017    SCIEX OS

Will SCIEX Have a Windows 10 Compatible Analyst® and Mutiquant™ Software Version?

Analyst 1.7 software and Multiquant 3.0.3 software are now available, and both of these versions are Windows 10 compatible.

12/20/2017    Software

Separating Concatenated .wiff Files in Analyst® Software

To separate concatenated .wiff file sets, a script called Make Subset File is used. This script might have limitations for Analyst® and Analyst TF software because it depends on the experiments in the file (i.e., the script does not work for IDA methods). The script is found on the Analyst TF software CD in the folder \Extras\Scripts\Make Subset File.

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.

12/15/2017    Analyst Software | SWATH Acquisition

Column Name Conflict Error when Running MultiQuant™ Software Reports

The error message "The column name 'ion type' conflicts with an existing column" appears when running MultiQuant™ software reports. This occurs when the report uses a query, but gets interrupted midway through the processing, leaving several additional columns in the MultiQuant results table.

12/14/2017    MultiQuant Software

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.


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.

12/14/2017    Analyst Software

Which Calibration Standards Can Be Used for Intact Protein Analysis on TripleTOF® and X500 Systemss?

An APCI calibrant solution for the SCIEX X500B System and a mAb standard from Waters were compared. Results show that the mass to charge ratio for the calibrant solutions remain constant regardless of the charge state. Secondly, for readings over 500 m/z, the calibration is highly linear for the X500B system.

12/14/2017    Academia Omics | Pharma CRO | QTOF Systems

Injection Error Dectected after Sample Start: Shimadzu LC Controller Device Fault

If an injection error is detected after starting samples in the Analyst® software queue, and everything else seems fine with the LCMS system, check that the Shimadzu autosampler rack is seated correctly in the autosampler housing.

12/14/2017    Analyst Software

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.

12/13/2017    MultiQuant Software

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).

12/13/2017    Analyst Software

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.

12/13/2017    Software

Opening SCIEX OS Results Tables Containing UV and MS Data

To open a SCIEX OS results table created using a data file (.wiff2) with both UV and MS data, both data types must be selected for processing when creating the quantitation method in Sciex OS. Otherwise, an error message is received "Error. Cannot be empty, Parameter name: experiments" when opening Sciex OS results tables after they are created.

12/13/2017    SCIEX OS

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.

12/11/2017    MultiQuant Software

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.

License Not Supported Error Appears after Installing MultiQuant™ Software

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

12/11/2017    MultiQuant Software

Where Can I find Safety Data Sheets (MSDS) or Certificates of Analysis (CoA)?

To find the Safety Data Sheets and Certificate of Analysis for Sciex reagents, navigate to

12/11/2017    Standards and Reagents

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.

12/11/2017    Analyst Software

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.

12/11/2017    MultiQuant Software

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.

12/11/2017    Software

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.

12/08/2017    Academia Omics | Pharma CRO | iTRAQ Reagent

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.

12/08/2017    Analyst Software

Analyst Regression Equations

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

12/04/2017    Analyst Software

Where can I download MaxQuant software?

MaxQuant software is a quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets. It supports all main labeling techniques like SILAC, di-methyl, TMT and iTRAQ, as well as label-free quantification.

12/01/2017    Academia Omics | Software

Where Can I Find a Column Part Number from Eksigent?

The provided link lists all micro and nano columns including nano chip columns.

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.

Why Doesn't the Recalculated Concentration in Excel Fit the Calculated Concentration in Analyst?

If I check the calculated results from Analyst for calculated concentration in Excel, the results do not match exactly. Why does this happen and how can I avoid this?

MultiQuant™ Software Cannot Launch with an sMRM Extension License Only

Two licenses need to be installed when using an sMRM extension license: One must be the MultiQuant™ software basic license, and the other is the sMRM extension license.

11/22/2017    MultiQuant Software

Can MutliQuant™ 2.x and MultiQuant 3.x Software Be Installed Side-by-Side on the Same PC?

Only one version of MultiQuant™ software can be installed on a PC. Two separate versions of MultiQuant cannot be installed side-by-side.

11/22/2017    MultiQuant Software

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.

11/22/2017    Analyst Software

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.

11/22/2017    Clinical

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?

11/22/2017    Academia Omics | Pharma CRO | Software

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.

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.

11/15/2017    Analyst Software

Activating Markerview Software Requires an Activation Key Code, Not a License File

Installing Markerview requires an activation key code, not a license file. Software activation key codes can be obtained by emailing

11/14/2017    MarkerView Software

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.

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.

Where Can I Download Skyline Software ?

This article includes the link to a free download of Skyline software.

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.

11/08/2017    SCIEX OS

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).

What is the Format of the Login for Analyst Software?

The format of the login for Analyst® software can be in two formats: 1) type in the user name and select the domain from the drop down or 2) log in using or DOMAIN\UserName.

10/31/2017    Analyst Software

How Is a Special Acquisition Account Setup in Analyst® Software?

To select an Acquisition Account Mode, navigate to the Security Configuration menu in Analyst® software and in the Security tab select the type of account, Client or Special Acquisition Administration Account.

10/31/2017    Analyst 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.

10/31/2017    Analyst Software

How Is the Software Protection Service in Windows 7 Disabled?

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

10/31/2017    Software

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.

10/31/2017    Analyst Software

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.

10/31/2017    MPX Software

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.

10/31/2017    Analyst Software

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.

10/30/2017    Analyst Software

Part Number for the Tubing from the Exion/Shimadzu Autosampler to the Column Oven?

The tubing connecting the Exion/Shimadzu autosampler to the column oven is stainless steel with connectors and is coated with flexible plastic (600 mm x 0.1 mm). This part can be obtained can be obtained directly from Shimadzu (PN 228-53184-91) or from the online SCIEX store.

10/23/2017    ExionLC AC | ExionLC AD

How to delete Results Table Settings in Analyst Quantitation Mode

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

10/23/2017    Analyst Software

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.

Explore Mode - Extract Ions - Overlay Multiple Panes Automatically

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

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.

10/20/2017    ChemoView 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.

MultiQuant™ Software Would Not Launch after License Installation

MultiQuant™ software may not launch after installation, and a -1 license installation error may appear. To resolve this issue, the user needs to be logged into Windows as an administrator and have full access to the program files on the C: drive.

10/17/2017    Software

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.

10/13/2017    Mass Spectrometers

Scheduled MRM™ Data with Polarity Switching Not Opening in MultiQuant™ Software

Scheduled MRM™ methods with polarity switching must use the same sMRM mode--either basic or advanced--but not both in the same Analyst® software acquisition method.

10/04/2017    MultiQuant Software

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.

10/03/2017    MultiQuant Software

How Is the SWATH® Acquisition Variable Window Calculator Excel Sheet Used?

This article includes step-by-step instructions on how to calculate variable windows for your SWATH® acquisition experiment and how to generate the input and output list.

Premium Access

A summary of the findings from an investigation into the identity of background Ions found in -ve mode electrospray mass spectrometry with suggestions to help minimize their impact on analysis.

10/02/2017    Mass Spectrometers

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

09/29/2017    QTRAP Systems | Triple Quad Systems

How Do I Obtain a Trial License for SCIEX Software?

To download and obtain a licensed trial for a SCIEX companion software, navigate to and select the software that you would like to try.

09/27/2017    Software

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.

09/26/2017    MultiQuant Software

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.

09/26/2017    Analyst Software

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.

09/26/2017    MasterView Software

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.

09/20/2017    SCIEX OS

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".

09/18/2017    Analyst Software

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.

09/18/2017    Analyst Software