知识库文章

How to calibrate MS3 in negative mode in Analyst® software

In PPG calibration there isn’t a solution to calibrate MS3 in negative mode. Moreover, there isn’t a solution to verify MS3 in negative mode (like Reserpine for MS3 in positive mode). Agilent Tuning Mix must be used to calibrate MS3 in positive mode and then “MS3 calibration” must be copied from positive mode to negative mode.

MultiQuant™ MD software error: Missing active project folder

Description on how an Analyst error causes MultiQuant™ companion software within Analyst® software to not function correctly.

How to export the Sample type in automatic reports generated by ChemoView™

The automatic reports that are generated by ChemoView™ are not capable of using all the tags that are also used by Analyst® software. The tag which allows to export the Sample type does not work. The procedure described in this article explains how to work around this issue.

How to create a hardware profile in "read only" mode in Analyst®

In Analyst®, if you use hardware profiles with AAO system it is recomended to put the hardware profile in "read only" mode to prevent file corruption issue.

How To Report Out Regression Types in Reporter Template Suite 3.2

To report out the regression type used in a curve fit, a combination of IF, ELSEIF, and ELSE tags are required in the report template in Reporter Template Suite 3.2.

What Are the Different Data File Types in Analyst® and SCIEX OS Software?

In the data sub-project within a project folder in Analyst® or SCIEX OS Software, there can be a multitude of file types associated with one set of raw data. The file types and the software they are associated with are listed in this article.

What are the suggested time intervals when using a diverter valve?

Efficient use of diverter valve will keep the mass spectrometer source and ion optics from unnecessary and excessive contamination. This article provides guidance on how to set an appropriate time range for use of a diverter valve during an acquisition method.

Calibration peak list is missing during instrument optimization in Analyst® software

During instrument tuning and calibration in Analyst® software, the calibration peak list can be obtained by right clicking on the final spectrum and selecting the List Data option. This will open a new pane that contains the calibration peak list. In this tab, the exact expected masses of the calibration components (e.g., PPG positive) are listed.

How to change source, gas and other default acquisition method parameters in Analyst® software?

When a new method is opened in Analyst® software, the source and gas parameters, including the declustering potential (DP), the collision energy (CE) and the collision cell exit potential (CXP), are populated based on the software's default parameters. Automatic compound optimization method also uses these default values.

Restoring Missing Toolbars and Menus in Analyst® Software

If the toolbars in Analyst® software disappear, leaving a blank, grey area. they can be restored using the command ALT T.

How To Create Personalized Toolbars in Analyst® Software

To create custom toolbars In Analyst® software and have more personalized access to shortcuts and icons, select the View menu and click on Toolbars. Selecting the New or Customize options will allow for new new toolbars to be created or for customized icons to be added to the toolbars.

Reporter 3.2 Error In Analyst® Software: Unable To Cast COM Object

When attempting to generate a report in Analyst® software with Reporter 3.2, an error appears immediately after clicking on create report: Unable to cast COM objectnof type System_ComObject' to interface.

Error when Opening Analyst® Software: Error 1067

After installing Analyst® software 1.7 alone or with Hotfix 1, attempting to open the software results in an error: Error 1067: The process terminated unexpectedly.

Where is the file for the hardware profile used in Analyst® or Analyst TF software located?

The file corresponding to the hardware profile used in a Analyst® or Analyst TF software is located in the API Instrument project in the Analyst Data folder.

Purpose of a Lockfile Alongside a Results Table File in Analyst® Software

In Analyst® Software, when opening a results table, an additional file - the lockfile - appears in the Quantitation Results folder for a particular project. The purpose of the lockfile is to prevent a second user from opening the same results table simultaneously and trying to modify it.

Calculating Mass Properties using a Compound's Formula In Analyst® Software

The mass properties of a compound (e.g., average mass, exact mass, nominal mass) can be calculated from its chemical formula using the calculators found in the Tools menu in Analyst® software.

Changing the Y-Axis Scale from Relative Intensity Percent in Analyst® Software,

When opening raw data in Analyst® software, the Y-axis label reads Rel Int. % with values from 0-100% instead of showing the true intensity value. In the Appearance Options window, select Other Graph Options. Under Percent Y Axis, change the value under the Chromatogram column from Yes to No to set the Y-axis scale back to intensity.

How Can I Transfer an Acquisition Method from Analyst® to SCIEX OS Software?

To transfer or import an acquisition method (*.dam file) created in Analyst® software into SCIEX OS software, open the MS Method tile and then select Convert File. Only the MS experiment will be imported into SCIEX OS software. The LC method from Analyst software will need to be entered manually.

How To Create a Metric Plot in Analyst® Software

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

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

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

Diverter Valve Would Not Work While Using Delay Time in Analyst® Software

The diverter valve will not work properly when using Delay Time in the acquisition method of Analyst® Software due to a mismatch between diverter valve timing and MS acquisition timing. This results in the diverter valve timing not aligning with the MS acquisition time.

Device Driver Error During Acquisition with Analyst® Software While Using a Shimadzu LC-40 System

While acquiring data with Analyst® 1.7.3 Software while using a Shimadzu LC-40 system, the run will intermittently fail and the following error will appear: "Integrated System Shimadzu LC-40 Controller 0: ERROR: Operation failed. device driver exception." To resolve this error, Hotfix1 for Analyst 1.7.3 will need to be installed when it becomes available. Alternatively, change the LC method so that it is 0.1 min longer than the MS method.

What Is the Minimum Accumulation Time in Analyst® TF Software for TripleTOF® Systems?

This article provides guidance on the minimum accumulation time that can be entered in Analyst® TF software for TripleTOF® Systems.

How To Review Statistics for Standards and QCs in Analyst® Software

To review the statistical information for standard and QC samples after creating a results table in Analyst® software, select the statistics button in the software's toolbar. This will open a new window with statistics for the standards and QCs that can be copy and pasted to a spreadsheet.

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

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

Unable To Connect to Shimadzu LC In Hardware Configuration in Analyst® Software

When trying to activate a newly installed Shimadzu LC in a hardware configuration in Analyst® Software, an error will appear stating that the LC could not be connected.

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

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

Clearing an Integrated Syringe Pump Error in Analyst® Software

Different approaches are provided here to resolve an error message that appears in Analyst® software while using the integrated syringe in manual tune mode: "The current sample cannot be run because the syringe pump has reached the end of its travel. To solve this problem please refill the syringe, press "Clear Error" and resubmit the sample".

Resolving the Error "Unexpected Error Has Occurred" when opening Reporter In Analyst® Software

When opening Reporter in Analyst® software, an error message appears reading "Unexpected error has occurred."

Special Acquisition Account (SAA) - a must have for Network Acquisition with Analyst in a regulated environment

This article explain what a Special Acquisition Account is, when to use and how to set it up properly for Analyst Software. This is valid for all Analyst versions from 1.0 up to latest 1.7.3. Also in a non regulated environment, it is recommended to use SAA if Acquiring into a Network.

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

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

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

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

How to Generate a Service Package in Analyst® Software

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

When Does Analyst® Software Start Generating the Archive for Audit Trail Records?

Once the instrument audit trail or a project audit trail contains 1000 audit records, the Analyst® software automatically archives the records and begins a new audit trail.

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

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

How to Create an Ion Ratio Flag in a Report Template

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

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

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

Returning the Results Table Settings to Defaults in Analyst® Software

If custom settings are applied to a results table in Analyst® software, they can be reversed by selecting the default settings option. To do so, right click within the results table to generate a secondary menu. Select the Table Settings option and then select Default.

Extra Backslashes Added when Using Network Location for Root Directory in Analyst® Software

If extra backslashes are added to a network location for a root directory for Analyst® software, a registry edit will be needed to prevent this issue from continuing to occur. The extra backslashes in the data file name can cause errors when trying to create a new project or save files (including results tables).

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

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

Analyst® TF Software Error: Instrument Optimization Parameters Are Not Available

If the error message "Instrument optimization parameters are not available" appears when running Analyst® TF software, check the region and language settings and ensure that English (United States) is set as the default language in the Windows operating system settings.

Why is Scheduled Ionization in Analyst® TF Software 1.8 Not Working with the OptiFlow® Turbo V Ion Source for Nano Flow?

Scheduled ionization in Analyst® TF software 1.8 is not configured to work optimally with the OptiFlow® Turbo V ion source ion source for nano flow. When using the OptiFlow® Turbo V ion source, scheduled ionization is always on, except when the start time in Analyst software is set to zero during pre- and post-run times. This is an issue for the nano spray users, because they will be unable to have the voltage stay on between runs for perpetual spray.

Chromatograms Are Not Appearing in Reports Created with Reporter Template Suite

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

Reporter Template Suite Software: How Do I Get Rid of "No Data" in Report if Sample Comment Is Empty?

When using the Reporter Template Suite Software with MultiQuant™, Analyst® or SCIEX OS software, the report output may indicate "no data" in the sample comment column if there is no text in the corresponding column in the results table. To eliminate "no data" as a response in the report, try using the following IF/ELSE statement: IF EMPTY($Sample_Comment) (Text Field: none) ELSE (Text Field: Sample Comment)

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

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

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

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

Reporter Templates Cannot Be Edited Due to Missing XML Tags

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

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

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

Chromatograms Are Randomly Missing from the Report after Upgrading Microsoft Office

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

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

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

Reporter Error: Template Not in Your Trusted Location

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

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

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

Library Hits Are Missing from the Library Search Reports in Analyst® Software

When using the library search report templates in Analyst® software, the library hits or the name of the compounds that has a library match does not show up in the report. This is due to an IF statement present in the pre-installed, standard, library-search templates that checks if the library hit is greater than zero ($Libs_Max_Hit_Count>0).

Adding a Syringe Pump To a Hardware Profile in Analyst® Software

Adding a syringe pump to a hardware profile in Analyst® software is necessary if the user needs to use the syringe pump to infuse sample during manual tuning. This article provides instructions on how to update a hardware profile to include a syringe pump.

Can Data Files Be Renamed after Acquisition Is Complete?

It's possible to change the name of a raw data file after it has been acquired in Analyst® or SCIEX OS software. Both the .wiff and .wiff.scan files would have to be named in the exact same manner or they may become corrupted.

Analyst® Software: Where Are the Library Search Parameters Set?

In Analyst® software, the library search parameters such as maximum number of hits, minimum purity, hit, etc. are set in the config files that are saved under C:\Program Files (x86)\AB SCIEX\AnalystReporter\Resources\AlgorithmConfigFiles.

Is Installing a SCIEX Software Hotfix on an Unsupported Instrument Problematic?

There are no negative effects caused to software or instruments by installing SCIEX software hotfixes on an instrument model not expressly covered by the hotfix (as indicated in the release notes).

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

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

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

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

Location of the Analyst® Software Configuration Files

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

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

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

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

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

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

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

Delete Rights Are Not Needed to Save or Overwrite a PDF Report in Analyst® Software 1.7.2

In Analyst® software 1.7.2, delete rights are not needed to save or overwrite a PDF file to the folder where the original PDF report is saved.

Status Display Issue for ExionLC 2.0 Systems with UV/Vis Detectors in Analyst® Software

If an Exion LC 2.0 system contains a DAD or multiwavelength detector, then after the LC system and mass spectrometer go to Standby state, the Analyst® software status icon for the ExionLC 2.0 system turns yellow, but the LC system state is shown as Wait.

How Do I Display the Calibration Peak List in Analyst® Software?

This article describes how to apply the appropriate calibration peak list reference table during a tuning procedure in Analyst® software.

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

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

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

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

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

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

How to Simulate a Hardware Profile with a Mass Spectrometer and Shimadzu LC in Analyst® Software

In Analyst® software, creating a simulated hardware profile allows a user to create acquisition methods and batches when using the software on a processing PC that is not connected to an instrument. To create a simulated hardware profile, open the Hardware Configuration Editor and select a hardware profile that you would like to simulate. Then select Edit Profile.

What Type of Analyst® Software Data Is Used with Keystone™ Converter Software?

Keystone™ converter software will convert nominal mass .wiff1 files from Analyst® software 1.4.1 and later versions.

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

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

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".

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.

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.

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.

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.

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.

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.

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.

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. 

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.

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.

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.

How to Set the Parameter Settings in Analyst® Software Back to Original Factory Settings

The parameters settings in Analyst® software can be set back to the original, default factory settings by selecting the Parameter Settings option from the Tools menu and then using the Factory Settings button to reset the parameters of the selected scan type.

Where 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.

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. 

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).

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. 

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

How to 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Resolving a Shimadzu LC Fatal Error: Could Not Activate Profile in Analyst® Software

The LC/MS hardware profile containing a Shimadzu LC could not be activated in Analyst® software. Under the Configuration tab for the Shimadzu system controller (CBM), the serial port filed was selected and changed to TCP/IP. The IP address 192.168.200.99 was added.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

How do I interface SCIEX software to a laboratory information management system (LIMS) or Electronic Laboratory Notebook (ELN).

Description of the options available for interfacing SCIEX software with LIMSELN.

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.

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.

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.

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.

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.

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 https://sciex.com/analyst-and-analyst-tf-key-generator-registration to obtain a new one.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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

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

How 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)).

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.

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.

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".

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.

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?

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

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

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

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

How 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Creating Windows User Groups for Analyst® Software Security Configuration

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

Adding User Groups to the Analyst® Software Secruity Configuration

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

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.

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.

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.

Converting Sciex OS WIFF2 Files to the MzML and MzXML Format

The Proteowizard tool (http://proteowizard.sourceforge.net/downloads.shtml) for MzML and MzXML conversion has been updated to work with the new WIFF2 files that are produced by SCIEX OS 1.2 and 1.3.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

Analyst Regression Equations

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

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?

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.

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.

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 user@domain.org or DOMAIN\UserName.

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.

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.

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.

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.

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.

How to delete Results Table Settings in Analyst Quantitation Mode

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

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.

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.

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.

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".

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.

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

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

How Are SWATH™ Acquisition Files Recalibrated?

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

How to deal with the Analyst User Registration Pop-Up-Window

When freshly installed and not yet registered Analyst asks in a pop-up-window for a Registration Key. Here is shown where to get it.

Recommendations for Computer Maintenance for Analyst® Software

What types of computer maintenance can be done to ensure that Analyst® software runs smoothly?

Intact protein script for TripleTOF™ instruments

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

LC Pumps Continue to Run after a Batch Ends in Analyst 1.6.3

If a batch completes, but the LC pumps never turn off, the Max Idle Time may need to be adjusted in Queue Options.

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

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

How Are Submitted Batches Rearranged in the Analyst Queue?

Batches can be rearranged in the Analyst software queue using the Move Batch option. In the Move Batch window, drag the batch to be moved to the desired location to rearrange.

How can you edit a query file extension?

Editing a query file extension requires renaming of the file name.

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

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

Analyst: How is the limit on the number of samples in the queue increased?

The limit on the number of samples added to the queue for a run can be adjusted using the Max. Num. Waiting Samples setting in the Queue Options menu.

Where is the method found that is created during automatic compound optimization?

When several compounds are optimized in Analyst 1.6.3, one method is created with all the MRM transitions included. The final MRM method created contains all compounds and is present at the bottom of the compound optimization report.

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

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

How do I avoid creating an Invalid transition list format error when building a method in Skyline for Analyst

Description of the Cause of Invalid transition list format error

Converting a report template from Reporter 3.0.1 to Reporter 3.2 fails if the template contains information in the footer of the document.

The conversion of xml Reporter 3.0.1 to docx Reporter 3.2 fails.

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

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

Analyst Projects dropdown is not in alphanumeric order

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

I am running Analyst 1.5.1 with or without June 2010 hotfixes and I am having failed acquisitions with my batches I generate using a HPLC utilising an AAO Analyst Access Objects driver.

Details of the requirements to run AAO HPLC Device with Analyst 1.5.1 and 150 Transitions.

Analyst Software Batch Editor Could not open the batch data DAB Sever Error

When importing a Analyst batch from a file the import fails and the Error Could not open the batch data DAB Sever Error is displayed

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

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

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

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

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

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

How Do I Configure Analyst® Software for Network Acquisition

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

Reporter gives an error on Analyst 1.6.x workstation Unexpected error has occurred

Reporter gives an error on Analyst 1.6.x workstation Unexpected error has occurred

Reporter 3.0 or 3.2 Cannot see tags for formatting.

Word does not show the tags content controls used for creating reports.

Multi-Page Printing Subsequent pages identical to the first.

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

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

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

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

Description how to activate the pressure trace in the hardware profile

Unhandled exception has occurred Waters Acquity Method Editor v1.4 & 1.5

When saving or opening a method with the Waters Acquity Method Editor an unhandled exception occurs System.NullReferenceException Object reference not set to an instance of an object

Setup of Diverter Valve

How to setup a diverter valve, including plumbing and Analyst software setup.

Submitting and Starting Sample Batch in Analyst® Software

How to start acquiring data using Analyst software

Create Acquisition Method with Agilent HPLC in Analyst® Software

Walk Through of Analyst acquisition method (.dam) creation when a Agilent HPLC is employed.

Create Acquisition Method with Shimadzu HPLC in Analyst® Software

Walk through of creating an Analyst acquisition method (.dam) when a Shimadzu HPLC is employed.

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

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

How can I convert .wiff to NetCDF format

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

How do I measure Peak Signal to Noise in Analyst Software

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

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

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

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

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

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

When opening a reporter 3.0.1 XML Template in Microsoft Word 2007 SP1 then the error message The file contains custom XML elements which are no longer supported by Word. If you save this file these custom XML elements will be removed permanently

How Do I Change the Significant Figures of Regression Equation in Analyst

Description of how to change the display of the regression equation in Analyst

Analyst.exe Unable To Locate Component pt95FKn71.dll

When Launching Analyst or Activating a Hardware Profile you receive the message Analyst.exe Unable To Locate Component with message body This application has failed to start because pt95Fkn71.dll was not found. Reinstalling the application may fix this problem.

Unspecified error when using Quantitate in Analyst Software

This article describes how to resolve the Unspecified error message encountered when trying to quantitate a new batch with Analyst Software