知识库文章

Is it necessary to have .wiff, .wiff.scan and wiff2 files together in one folder in order to open data in SCIEX OS software ?

This article describes what can be done with SCIEX OS software if the .wiff file is available but the .wiff and/or .wiff.scan file is missing.

Why are there differences in Points Across Peak between Analyst® software and SCIEX OS software?

The number of data points collected across a chromatographic peak, or "Points Across Peak," can differ between SCIEX OS software and Analyst® software due to differences in the implementation of the sMRM dwell time calculation algorithm. This article explains the factors contributing to these differences and how SCIEX OS software optimizes data acquisition.

Is enabling Checksum necessary for wiff2 Files in SCIEX OS Software?

- Wiff2 files do not require checksums as they have built-in integrity checks. - Wiff1 files require checksum verification. - If the customer is using Analytics, enabling checksum is unnecessary.

Standard Addition Feature in SCIEX OS: Should the sample with the actual concentration of “0” be set to unused?

By design it is not recommended for the Standard Addition workflow in SCIEX OS to set the sample with an actual concentration of “0” to unused.

Why can the ejection time in the results table in Analytics (Sciex OS Software) differ to the ejection time displayed in the auto exported .txt files?

When performing analyses with an Echo-MS and Sciex OS, the ejection time displayed in results tables can differ to the time displayed in the auto exported .txt files.

How to disable the optimize ejection sequence of batch sample to have full control over the ejection order in ECHO® MS in SCIEX OS ?

This article explain how to disable the optimize ejection sequence of batch sample to have full control over the ejection order in ECHO® MS in SCIEX OS.

How the "Intensity Threshold" feature works for screening analyses reprocessing with SCIEX OS ?

This article details SCIEX OS's "Intensity Threshold" feature when reprocessing screening data. This helps understand how the Library score (Identification Confidence Indicator) of an identified compound varies depending on the Threshold value applied by the user.

Enabling electron-activated dissociation (EAD) fragmentation mode in SCIEX OS software

To enable electron-activated dissociation (EAD) fragmentation mode in SCIEX OS software, users must select the Show EAD parameters option from the Options menu in the MS Method workspace. When creating a new MS Method for TOF instruments, the only fragmentation mode available by default is collision-induced dissociation (CID), and the ability to change this is greyed out.

How to avoid column splitting in CSV report output with Reporter 3.2

When using a tag for outlier reasons in a CSV report, the tag is placed inside double quotes to prevent the creation of extra columns.

Changing column temperature on the Optiflow® ion source in SCIEX OS software

Typically, column temperature is changed in the LC method. However, the OptiFlow® ion source has the column compartment directly above the probe on the source itself, so the column temperature parameter is located in the MS method and can only be adjusted there.

Setting up a single-injection CID/EAD data-dependent acquisition (DDA) method for the ZenoTOF 7600 system

In SCIEX OS software versions 3.0 and greater, two information-dependent acquisition (IDA) methods can be created in the same acquisition method: one for electron-activated dissociation (EAD) and one for collision-induced dissociation (CID) fragmentation.

Opening the Queue workspace causes OFX.Core error in SCIEX OS software in versions prior to 3.3.1

Opening the queue workspace can give an error in versions of SCIEX OS software prior to version 3.3.1. The error was a "OFX.Core.Contracts.Exceptions.OFXException" type error, and was resolved by upgrading the software to version 3.3.1 or higher.

Is there a limitation for the number of custom columns in SCIEX OS Analytics results tables?

In SCIEX OS you can add custom columns via different options. Customized results by using the calculated columns and flagging rules features, normal custom columns added in the results table or the ones added already in a batch. All these are displayed in additional columns.

How does the trailing factor in SCIEX OS 3.3.1 and earlier versions choose the ‘common prefix’ in a sample name?

Up to SCIEX OS v3.3.1 the software offers the option to ‘Remove Trailing Index from Sample Name’ in the statistics pane. It can be controlled via the blue button right to the ‘Group by’ functionality.

Canned Calculation for SANTE Guideline 11312/2021v2- D8 Available for SCIEX OS Software

This article provides information on the custom calculations required for processing data according to the guidance found in SANTE 11312/2021v2 – D8. The guidance requires that measurements performed with TripleQuad instruments should show for at least two MRMs per analyte a S/N ≥ 3, and an ion ratio from sample extracts that is within ±30% (relative) of the average of calibration standards from same sequence. In addition, the analyte peaks from both product ions in the extracted ion chromatograms must fully overlap.

MRM results table error in SCIEX OS software: Library not installed. There is no installed library database

When creating a new results table with multiple reaction monitoring (MRM) data in SCIEX OS software, an error message appears after selecting the Process button: “Library not installed; there is no installed library database.” If a library search is not required, users can prevent the error from appearing again by deselecting the Quantitation and targeted identification and/or the Non-targeted screening options in the Workflow tab in the open processing method.

Diagnosing signal instability when processing data in Analyst®, MultiQuant™, or SCIEX OS software

Signal instability typically results in fluctuating responses from samples with the same level of analytes, causing significant variability in measured outcomes. Due to random fluctuations in peak area, signal instability could also affect linearity and recovery. If signal instability is observed while processing data in Analyst®, MultiQuant, or SCIEX OS software, it's possible to diagnose the source of signal instability by evaluating: 1) sample and material preparation, 2) LCMS method instability, and 3) instrument issues.

Errors when closing LC or MS methods in SCIEX OS software caused by file names with special characters

After changing an LC or MS method in SCIEX OS software, if a user attempts to close the method without saving, the software will throw either one of these errors: 1) System.Xml.Xmlexception : ')' is an unexpected token or 2) An error occurred while parsing entity name. To avoid these errors, users must rename their project and/or method and avoid using special characters (e.g., &, #, $) in project and method names.

Why are scan windows longer than detection windows in a scheduled MRM method in Analyst® software?

When setting up a scheduled MRM (sMRM) method in Analyst® software, users must add the time for the detection window (in seconds). However, sometimes, the resulting scan window for some of the analytes is larger than what is set in the method. Here, the reason for this issue and ways to prevent it are explained.

Setting a new reference (representative) sample for a processing method in SCIEX OS software

Each processing method created in the Analytics mode in SCIEX OS software has a reference sample that defines the components and is used to set the integration parameters. Users may need to change this sample to update retention time information or for other reasons.

Custom columns do not automatically appear in new results tables in SCIEX OS software

Custom columns for manually entering data in a results table will not appear automatically in a results table in SCIEX OS software, even if they were in the workspace layout from a previous results table. A custom column added using the More menu in the Analytics module will only be available in the results table to which it was added. It will not be saved in the quantitation method file (.qmethod) or the workspace layout file (.qlayout).

Location of compound optimization data files (wiff2) generated in SCIEX OS software

After performing a guided optimization in SCIEX OS software, the raw data file (wiff2) is automatically stored in the SCIEX OS Data root directory in the TempData folder.

Error in SCIEX OS software: A different user currently has another instance of SCIEX OS open

When launching SCIEX OS software, the error message “A different user currently has another instance of SCIEX OS open” is received, preventing users from accessing SCIEX OS software, even if no other users have accessed the software.

Adding custom columns to a batch in SCIEX OS software

To add a custom column to a batch in SCIEX OS software, right-click within the batch area and select the Add Custom Column option.

Using Metrics Tracker in SCIEX OS software 3.4 with a SCIEX 7500+ system

Metrics Tracker is a new workspace in SCIEX OS software 3.4 that monitors trends in essential performance criteria on the SCIEX 7500+ system. After activating a hardware profile, the Metrics Tracker tile should appear in the Configuration section of the SCIEX OS software's home page.

Middle-down sMRM HR acquisiton method setup using EAD fragmentation on the ZenoTOF® 7600 system

This article describes the parameters for evaluating subunit proteins using electron-activated dissociation (EAD) fragmentation on the ZenoTOF® 7600 system. Specific values for a successful middle-down, high-resolution sMRM acquisition method using EAD fragmentation are provided. Choosing a low, medium, and high charge state of the protein envelope is critical to get the most diverse fragmentation.

Formula Finder returns NA/NA in Explorer mode in SCIEX OS software

In Explorer mode of SCIEX OS Software, Formula Finder's "Found" column will read NA/NA in the Found elemental compositions table when a ChemSpider license is installed.

Creating a client license for SCIEX software supported by a concurrent license server

When setting up a concurrent license server for either Analyst® or SCIEX OS software, one of the final steps is to create and distribute the client license - the license installed on the PC where the SCIEX software is installed.

How can I restrict permissions for reporter templates?

It is often necessary that reporter templates are not altered—neither intentionally nor unintentionally. Therefore, it is important to restrict access to the template data files—this can be done at the Windows level in the file properties.

Adding compound names with square brackets causes LibraryView™ software error: Duplicate compound name in database

When attempting to add a compound name with square brackets to a library from the Analytics workspace in SCIEX OS software, the error "Duplicate compound name in database" appears. To resolve this issue, open LibraryView™ software and ensure the compound is deleted from the trash before adding the new compound under that name.

Using the auto-processing feature in SCIEX OS software in the Batch workspace

Data under acquisition can be automatically processed and added to a results table on a sample-by-sample basis in the Batch workspace in SCIEX OS software. Entering a processing method and a results file name into the Batch workspace in Analytics triggers the auto-processing feature. Individual samples are processed into a results table that is progressively constructed over the course of data acquisition. The auto-processed samples can be added to an existing results table or an entirely new table.

How to create decision rules in SCIEX OS software in the Batch workspace

Enabling decision rules in the Batch workpace allows SCIEX OS software to evaluate the acquired sample using flagging rules defined in an existing processing method. If the decision rule fails, it is possible to dictate the next action in the queue, such as sample re-injection.

Setting up layouts in SCIEX OS software to customize the Analytics workspace

Layouts preserve the format and design of the Analytics workspace in SCIEX OS software. The Analytics workspace is customizable, and results table columns and panes can be organized according to the user's preference. Instead of reconfiguring the layout each time a new results table is created, users can save a layout to maintain the results table formatting for specific projects. Once saved, the layout can be set as the default, ensuring that a particular workspace is permanent and any new results table retains the features of previous results tables in that project.

New calculated column functionality added to SCIEX OS software starting with version 3.3.1

Version 3.3.1 of SCIEX OS software includes many new calculated column functions that were not available in previous versions. Below is a description of these new functions and how to use them.

Eliminating license notifications in LibraryView™ and SCIEX OS software requires identical regional settings

A license notification screen appears when launching LibraryView due to a language setting mismatch between SCIEX OS and LibraryView™ software. Adjusting the regional language settings for both software packages will eliminate these license popup screens.

The in Sciex OS exported .csv audit trial is empty.

It is possible to receive empty .csv files exported from Sciex OS audit trail, caused by missing one of the csvhelper depend dll, which is Microsoft.Bcl.HashCode.dll. The issue has been resolved in the Sciex OS version 3.4.

How can I apply my settings from an existing processing method to samples with new or different components?

Sometimes it is needed to transfer 'generic' customized settings from an existing *.qmethod to a new application, like custom calculations, library search parameters or flagging rules. In this case new or different components need to be added to the existing method, which can only be done if a new reference sample is attached to the existing method.

Using GETSTAT with unknown sample types in SCIEX OS software 3.4

GETSTAT received additional functionality in SCIEX OS software 3.4. Found in the Calculated Columns section of the processing method, the GETSTAT function can now pull in statistics for unknown samples; previously, GETSTAT only worked with QC and standard samples. The new GETSTAT functionality now permits averaging of the calculated concentrations for replicate unknown samples, among other functions.

How to calculate statistic values of Unknowns in SCIEX OS v3.3.1

The statistics pane in SCIEX OS displays various statistic values for Standards, Quality Controls and other sample types. The values can be transferred to the results table and used for further calculations via the Custom Calculations Operator ‘GETSTAT’. But as the GETSTAT functions are available only when the Group by Concentration for Standards or Group by Concentration for QCs grouping options are selected, it was not possible to transfer the statistic values for Unknowns in the results table. With new custom calculation operator there is a workaround to calculate statistic values for duplicate injections.

How to Detect Acquisition Method Changes

To detect changes in an acquisition method in Analyst® or Sciex OS, the sample information of two injections can be compared via Microsoft Word to track changes e.g. between runs of separate days.

Is there Quantitative Default Data for Testing Purposes Available from SCIEX?

To test software functionality and familiarize with the quantitation workflow of SCIEX OS, SCIEX provides Triple Quad 7500 raw data and result tables with different evaluation approaches on the homepage for download. The data is stored in a full SCIEX OS project and can be used with SCIEX OS v3.1.6 and higher.

Generating a Service Package in SCIEX OS Software from Version 3.4

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

How to rename a computer without having to reinstall SCIEX OS ?

This article explains how to change the name of a PC without having to reinstall the SCIEX OS software.

How does the SCIEX OS software calculate the IS Quality in the results table ?

This article explains how to interpret the value indicated by IS Quality and how SCIEX OS calculates this value.

Error when adding samples to a results table in lower versions of SCIEX OS software

An error appears when adding samples to an existing results table in SCIEX OS software versions below 3.0: "Collection was modified; enumeration operation may not execute." This is a known bug for processing methods that use combined flagging rules, and the issue was resolved in version 3.0.

Configuring ChemSpider and its databases in SCIEX OS software Explorer mode

To use ChemSpider in the Explorer mode in SCIEX OS software, Formula Finder settings must be configured correctly. After selecting the Show Options icon in Formula Finder, a Formula Finder Settings screen appears. Users must select the ChemSpider Service options in the Dictionaries tab to see the compounds suggested by ChemSpider in the Formula Finder window of the Explorer module. `

Error when adding MS/MS spectra to a library within SCIEX OS software

When trying to add an MS/MS spectum to a compound in a library in SCIEX OS software, an error appears: System.ServiceModel.FaultException`1[System.ServiceModel.ExceptionDetail] : Object reference not set to an instance of an object. Adding MS/MS spectra to other compounds from the same results table does not generate this issue, which is caused by the inclusion of an apostrophe in the compound's name.

Components mismatch error in SCIEX OS software is due to extra space in analyte name

If an extra space is added to the end of an analyte name in the Components column in the Batch workspace, an error message "Components Mismatch: 1 component in the selected processing method is not found in any selected batch samples" is generated in SCIEX OS software. Removing the extra space in the component name will allow the data to be processed.

Calculated column functions in SCIEX OS software in the Analytics processing method

Calculated columns found in the Analytics processing method in SCIEX OS software allow for the automatic calculation of raw data using user-defined functions that are otherwise not available when processing data. This article lists all the functions available in all versions of SCIEX OS for calculated columns.

Secure Network Account (SNA) - Recommended for Network Acquisition with SCIEX OS

This article explains what a Secure Network Account is, when to use it and how to set it up for use with SCIEX OS Software. This is valid for all SCIEX OS versions. It is highly recommended for all systems using Network Acquisition, but especially in Regulated Environments, where restrictions on user permissions are enforced.

How to check that the heaters located in the source of the MS are working ?

This article describes the procedure to follow to check that the heaters located in the source (Turbo V ion source and IonDrive Turbo V ion source) of the mass spectrometer are working. This procedure describes the procedures for both, Analyst® software and SCIEX OS software.

How to configure stacked injection in SCIEX OS or Analyst® with a Shimadz LC 40

SCIEX OS and Analyst® have a feature that allows you to control the injector of a Shimadz LC chain directly in the Sciex software using custom injection programs. This article describes how to write the program to perform stacked injection with LC 40.