Thermo FAIMS to mzML Converter

Overview

The Thermo FAIMS to MzML converts a Thermo .raw file with FAIMS scans into a series of .mzML files, creating one .mzML file for each FAIMS compensation voltage (CV) value in the .raw file. This is similar to the FAIMS-MzXML-Generator but that program creates .mzXML files instead of .mzML files.

Background

MaxQuant currently does not process FAIMS data correctly if multiple compensation voltages are used through the experiment's duration. Both this program and the FAIMS-MzXML-Generator split a FAIMS-based Thermo .raw file into a set of files, each containing only scans collected using a single compensation voltage. However, as of March 2020, MaxQuant does not support reading .mzML files. Still, the output files created by this program are still valid .mzML files and other downstream processing tools may benefit from the availability of these files.

Syntax

ThermoFAIMStoMzML.exe
 InputFilePath [/O:OutputDirectoryPath]
 [/Centroid] [/Renumber]
 [/ScanStart:StartScan] [/ScanEnd:EndScan]
 [/S] [/R:Levels] [/Timeout:Minutes] [/IE]
 [/L] [/LogFile:LogFilePath] [/Preview]
 [/ParamFile:ParamFileName.conf] [/CreateParamFile]

The first argument specifies the input .raw file

• Either just enter the name, or use /I:DatasetName.raw or -I:DatasetName.raw
• Can contain the wildcard character, for example -I:*.raw

Optionally use /O to specify the output directory path

• If omitted, the output files will

Use /Centroid or /CentroidSpectra to use a peak picking algorithm to centroid the mass spectra

Use /Renumber or /RenumberScans to renumber the scans in the output files so that the first scan is always scan 1 and there are no scan gaps

• This is helpful when processing the data with DIA-NN, since it apparently requires that the first scan be scan 1 and that the scan numbers be contiguous

Optionally use /ScanStart and /ScanEnd to limit the scan range to include in the output files (filtering on scan number in the input file)

• For example, /ScanStart:1 /ScanEnd:1000 would only include scans 1 through 1000 in the output files

Use /Timeout to specify the maximum runtime (in minutes) for each call to MSConvert.exe

• The default is /Timeout:5
  • Use a larger value for large .Raw files with a large number of scans and/or dense mass spectra
• This parameter is necessary because if MSConvert.exe encounters an error, the program freezes, waiting for the user to press Ctrl+C
  • By specifying a timeout, this software will terminate MSConvert.exe if it runs too long

Use /S (or /Recurse) to process files in the current directory and in its subdirectories

• Optionally specify the maximum depth using /R, for example /R:2
• The default is /R:0 which means to recurse infinitely
• /R:1 effectively disables recursing
• /R:2 means to process the current directory and files in just this directory's subdirectories

Use /IE or /IgnoreErrors to ignore errors while recursively processing files

• This also applies when when processing files with a wildcard

Use /L to enable logging messages to a file.

• Optionally use /LogFile:FilePath to specify the log file path

Use /Preview to preview the commands that would be run

The processing options can be specified in a parameter file using /ParamFile:Options.conf or /Conf:Options.conf

• Define options using the format ArgumentName=Value
• Lines starting with # or ; will be treated as comments
• Additional arguments on the command line can supplement or override the arguments in the parameter file

Use /CreateParamFile to create an example parameter file

• By default, the example parameter file content is shown at the console
• To create a file named Options.conf, use /CreateParamFile:Options.conf

Contacts

Written by Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: [email protected] or [email protected]
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics
Source code: https://github.com/PNNL-Comp-Mass-Spec/Thermo-FAIMS-to-MzML

License

The Thermo FAIMS to mzML Converter is licensed under the 2-Clause BSD License; you may not use this program except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause

Copyright 2020 Battelle Memorial Institute

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.