知识库文章

ZenoTOF 7600 系统的故障排查：调谐和校准

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

ZenoTOF 7600 系统的故障排查：运行中的校准不通过

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

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

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

Where to find Signal-to-Noise in SCIEX OS Explore mode

This article explains how you can manually evaluate the Signal-to-Noise within a chromatogram in the SCIEX OS Explore mode.

SCIEX Triple Quad™ 和 QTRAP™ 系统常见 LC 问题处理

在SCIEX Triple Quad和QTRAP系统上运行LC-MS方法时，LC系统的压力问题、保留时间变化和峰丢失是常见的问题。请参阅分步说明以解决这些常见问题。

Change CAD Gas Settings from Simplified (Low, Medium, High) to Operator (0-12) in Analyst® Software

The default setting of CAD gas in Analyst® software is “Simplified” and only allows to adjust CAD gas in three steps (low, medium, high). Switching to “Operator” allows to use values from 0 to 12 which enables a more efficient optimization of this parameter for MS/MS and LIT experiments.

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.

How to increase the virtual memory size with Win 10 PC

Windows sets the initial minimum size of the paging file equal to the amount of random access memory (RAM) installed on your computer, and the maximum size equal to three times the amount of RAM installed on your computer. If you see warnings at these recommended levels, then increase the minimum and maximum sizes. This procedure is applicable for PC with Windows 10. For PC with Windows 7 you can follow this procedure: https://sciex.com/support/knowledge-base-articles/low-virtual-memory-warning-1481143909352_en_us

Adding a new ADC linker to Biologics Explorer software

There are two options for adding an antibody-drug conjugate (ADC) linker in Biologics Explorer software for use in intact protein and peptide mapping workflows: 1) as a custom modification using the Modification Editor or 2) as direct additions into the Conjugates tab in the Protein Mapping - Settings window.

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.

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.

Can I obtain statistics information for internal standards in SCIEX OS software 3.4?

In SCIEX OS software 3.4, users can generate statistics for internal standards samples. To display the Statistics pane for internal standards in a results table, highlight the section All Internal Standards in the Components and Groups tab, and then select the option Statistics pane in the Views drop-down menu to display statistics, such as mean, standard deviation, and percent CV for internal standards values (area, peak height, and retention time).

sMRM Calculator in Analyst® shows error 'unable to load method'

sMRM calculator does not work in mixed and integrated mode and displays error 'unable to load method. Check if the method is for the active hardware profile'.

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.

Can the sample information in a data file be exported from SCIEX OS 3.4 software?

Users can now export sample information as a text file from the Explorer module in SCIEX OS 3.4 software. Open a data file, select the Show menu, and select Sample Information. Once the Sample Information pane is open, select the Export option and select Sample Information as Text.

Denoting a GPL result file as reviewed and approved in SCIEX OS software

GLP users need to be able to demonstrate that a results file has been reviewed and approved. A new workflow has been introduced in SCIEX OS software 3.4 to accommodate this requirement. Users can now mark the results file as reviewed or approved from the Results drop-down menu.

Printing sample information in SCIEX OS software creates an audit trail event

In Explore mode, SCIEX OS software allows users to display and print sample information for a data set. In previous versions, printing the sample information was not recorded in the audit trail. Now, with SCIEX OS software 3.4, an event is created in the audit trail record, allowing users to track the output of these records.

Processing oligonucleotides using Bio Tool Kit software

The Bio Tool Kit software can deconvolute oligonucleotides in negative mode using the Reconstruct Protein option. The Bio Tool Kit microApp is embedded in the PeakView™ or SCIEX OS software and requires an additional license to activate these features.

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.

Can the order of the components in a results table be changed in SCIEX OS software?

Users can change the order of the components in a results table in SCIEX OS software by adding a new row and copying and pasting a row from elsewhere in the Components tab of a processing method.

Disable the User Account Control settings before installing Acquity driver for SCIEX OS software

To prevent driver installation issues, it is recommended that you disable the User Account Control (UAC) settings in Windows before installing the Acquity Driver that interfaces with SCIEX OS software.

How to use Bio Tool Kit for interpreting peptide MS/MS data acquired with CID and EAD fragmentation?

The Bio Tool Kit and its Peptide Fragments feature is tremendously helpful when trying to interpret MS/MS peptide data. This can be adjusted to either CID (collision-induced dissociation) or EAD (electron activated dissociation). A glycopeptide example for EAD and CID is described.

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.

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.

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.

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 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.

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.

Bio Tool Kit microapp cannot manually sequence peptide MS/MS data from EAD-derived fragments

The Bio Tool Kit microapp embedded in PeakView® or SCIEX OS software cannot perform de novo manual sequencing or MS/MS fragment matching for peptides fragmented using electron activated dissociation (EAD) on a ZenoTOF 7600 system. The MS/MS data obtained by EAD is too complex and fragment-rich, presenting the software with too many options for potential fragment ions; however, the Bio Tool Kit app can process MS/MS data acquired by CID (collision-induced dissociation).

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.

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.

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.

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.

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).

Restoring and using the script - Manually Integrate - in Analyst® software versions 1.7.2 and 1.7.3

The script - Manually Integrate - is missing in Analyst® software versions 1.7.2 and 1.7.3, although it was previously supported in versions 1.7 and 1.7.1. This articles describes how to restore the script to these later versions of Analyst software. Instructions are provided for integrating peaks of interest with the script that were missed or only partially integrated.

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.

Canned Calculation for ICH Guideline M10 – 3.2.3 Matrix Effect Available for SCIEX OS Software

This article provides information on the custom calculations required for processing data according to the guidance found in ICH guideline M10 – 3.2.3. The guidance requires that the matrix effect is evaluated by analysing at least 3 replicates of low and high QCs, each prepared using matrix from at least 6 different sources/lots. For each individual matrix sources/lots evaluated, the accuracy should be within ±15% of the nominal concentration and the precision (per cent coefficient of variation (%CV)) should not be greater than 15%. These calculations were created to provide a ready-made solution for flagging in case of detected matrix effects.

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 select exported and saved table settings for a quantitation table in Analyst® Software?

This article provides information on how exported and saved table settings can be selected for new results tables in Analyst® Software.

How to perform quantification by standard additions with MultiQuant® software ?

The quantification of compounds by standard addition in MultiQuant® software requires the use of a query. This article explains how to use this query.

How to change company name in the MultiQuant software audit trail report ?

MultiQuant software users who have a CFR license have the ability to view and print a report of the Audit trails associated with the software. This report automatically displays the company name. This article indicates how to change the company name that is displayed in this report.

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.

How to backup mass spectrum databases with LibraryView when it is impossible to export as an lbp file due to a software issue ?

Software issues may prevent libraries from being backed up in LibraryView. This can be problematic in cases where custom databases have been created and the LibraryView needs to be reinstalled since uninstalling this software deletes all the libraries it contains. It is therefore essential to be able to make backups of these libraries in all circumstances.

How to implement the Maximum Allowed Accuracy Variation for Quality Controls (%) and Standards (%) in Analyst® Software?

This article provides information on how to implement the Maximum Allowed Accuracy Variation for Quality Controls (QCs, %) and Standards (STDs, %) in Analyst® Software. This is possible within the Quantitation Wizard process.

How can I process MS1-level oligonucleotides in Molecule Profiler software?

Molecule Profiler software includes workflows for oligonucleotide impurity studies conducted on an MS1-level. To start using these workflows for oligonucleotide studies, launch the software and select Processing Parameters from the Workflow menu on the left panel.

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 use a CTC PAL 3 within Analyst® software?

A short introduction on how to create a hardware profile including CTC PAL 3 in the Analyst® software, importing Scripts to the Analyst Device Driver Software, managing Racks and creating an Acquisition Method.

Adding workflow templates to Biologics Explorer software without the template manager

Biological Explorer software uses workflow templates that are typically packaged into the software using a built-in template manager. If the template manager is not working, then templates can be added to the Biologics Explorer software by transferring them to a specific file path on the C drive: C:\ProgramData\SCIEX\BiologicsExplorer\templates.

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.

Mastering ExionLC AE & Shimadzu LC 40 Plate Calibration

Discover how to calibrate autosampler plates by watching this step-by-step video guide. Proper needle alignment is critical for EXION AE and Shimadzu LC-40 autosamplers that are commonly used with SCIEX LC-MS systems to prevent a needle from striking the vial cap or missing the vial completely, causing a bent needle. Plate calibration – or plate teaching – is also essential when using a new sample plate for the first time with your autosampler or as part of routine LC maintenance.

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.

Canned Calculation to check the ‘Sum of PFAS’ according to EU directive 2020-2184 using SCIEX OS Software

This article provides information on the SCIEX OS custom calculations required for evaluating PFAS data according to the EU directive 2020-2184. The guidance requires that 'Sum of PFASs', which means the sum of per- and polyfluoroalkyl substances considered a concern for water intended for human consumption, shall not be above 0.1 µg/l. These calculations were created to provide a ready-made solution for flagging outliers.

Importing a .txt or .csv file into a batch in SCIEX OS software

Users can import batch information into the Batch Workspace in SCIEX OS software using the Import from File option under the Open menu.

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.

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.

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.

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.

Plate and Well Types for Waters™ Autosampler

Description of plate setup with common ANSI format plates and considerations for needle placement

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.

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.

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.

Turning off the Dynamic Window Extension when using the Scheduled MRM™ algorithm in Analyst® software

The Scheduled MRM™ algorithm is a feature in Analyst® software that includes a dynamic window extension option. This option allows the scan window to be automatically extended up to the duration of the scan window. Using this feature could result in lower dwell time for some analytes and inconsistent scan times between analytes, requiring it to be disabled.

Purpose of PTD files in project folders in Analyst® software

Files with the PTD (.ptd) extension are database event logs in Analyst® software located within the event log folders in the Analyst Data sub-projects. The event log folders where the PTD files are saved contain the same name as the quantitation methods or results tables from which the event logs are generated. Users can open these files with Notepad, but the information is used internally by the software and is not helpful for end-user purposes.

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.

How to fix common waste drain line issues on ExionLC AE and Shimadzu LC-40 systems

For the ExionLC AE and Shimadzu LC-40 systems, all waste liquid is collected in the drain port at the front of the instrument and discharged using the waste drain line. If this drain line is not installed correctly, this can cause a leak, or the system will show a leak sensor or gas sensor error.

Managing Files and Attachments to SCIEX Now Support Cases Using Large File Exchange

SCIEX Now Large File Exchange enables simple upload and download of files or attachments to all kinds of SCIEX Now support cases.

How to fix a blocked capillary on the PA 800 Plus system

Crystallized reagents on the capillary tip can cause a blocked capillary on the PA 800 Plus system, resulting in no peaks or low signal. This article explains how to clean the cartridge, capillary tips, and cartridge seal and how to perform a manual pressure rinse if the cartridge is blocked.

SCIEX OS 1-5 Software

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