SCIEX instruments

SCIEX instruments for proteomics are currently divided into five families:

• QTOF systems (e.g. ZenoTOF 7600)
• QTRAP systems (e.g. QTRAP 6500+)
• Triple Quad systems (e.g. Triple Quad 7500)
• TripleTOF systems (e.g. TripleTOF 6500+)
• X-Series TOF (e.g. X500B QTOF)

The above instruments all use SCIEX Analyst® acquisition software, producing files with a .wiff or .wiff2 extension.

There are a number of legacy instruments. Data in the T2D format produced by older SCIEX MALDI instruments can be processed with Mascot Distiller and is documented under SCIEX Data Explorer.

Mascot DIA

Mascot DIA is a spectrum-centric solution for DIA analysis. Mascot Server provides protein identification and Mascot Distiller raw data processing and quantitation. These processes can be automated using Mascot Daemon.

Mascot Distiller supports files in wiff format; wiff2 format is not currently supported. SCIEX OS version 2.1 and later produce files in wiff format compatible with Mascot Distiller.

For ZenoTOF instruments, Mascot Server ships with a suitable EAD instrument definition.

Mascot Distiller can process and visualise SWATH runs (Sequential Window Acquisition of all Theoretical Mass Spectra) saved in wiff format (not wiff2). Any SWATH or DIA windowing scheme can be used, but we recommend using narrow isolation windows (2Th to 8Th). If a wider window is desired, use dynamic window widths based on the expected number of precursor per window. Mascot Server uses spectrum-centric identification, which can identify up to 5 peptides per spectrum.

Mascot DDA

Mascot DDA is a spectrum-centric solution for DDA analysis. Mascot Server provides protein identification and Mascot Distiller raw data processing and quantitation. These processes can be automated using Mascot Daemon.

Mascot Distiller makes full use of DDA spectra from all SCIEX instruments, as long as the results are presented in wiff format (not wiff2). Distiller has full support for identification and quantitation from DDA data using MS1 and MS2 quantitation.

SCIEX MS Data Converter (DDA)

SCIEX MS Data Converter is a free download from SCIEX. It supports both wiff files and runs on Windows 10 and later. Output can be a simple MGF peak list or an mzML file containing a fairly complete representation of the raw data.

It may be useful to perform ProteinPilot peak picking using SCIEX MS Data Converter and open it in Mascot Distiller (for example, quantitation or de novo identification). To do this, convert the wiff file to an mzML file. The command line will be similar to this:

AB_SCIEX_MS_Converter.exe WIFF C:\tmp\fraction_42.wiff -proteinpilot MZML C:\tmp\fraction_42.mzml

Remember to use double quotes around the file paths if they include any spaces. When the mzML file is opened in Distiller, you need to choose processing options that uncentroid the survey scans but take the existing centroid values from the MS/MS scans.

The converter also allows profile data to be exported to an mzML file. You can open the exported mzML file in Distiller, but it is usually better to work with the original Wiff file.

SCIEX MS Data Converter can be used as a data import filter in Mascot Daemon. This enables batch automation of peak picking and search submission.

MSConvert (DDA)

MSConvert is a component of ProteoWizard that converts between various file formats. It has a large number of options and can be configured as a data import filter in Mascot Daemon. Note that the input file format is not specified; msconvert auto-detects the format.

Some versions of msconvert, when converting wiff to MGF, are unable to output precursor charge in the MGF file. For these versions, it is important to select a default peptide charge when submitting the search. If the peptide charge control is hidden (Mascot Server 3.0 and later), the default is taken from the SearchSubmitDefaultPeptideCharge option.

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