The FAIMS MzXML Generator converts a Thermo .raw file with FAIMS scans into a series of .mzXML files, creating one .mzXML file for each FAIMS compensation voltage (CV) value in the .raw file.
MaxQuant currently does not process FAIMS data correctly if multiple compensation voltages are used through the experiment's duration. The FAIMS MzXML Generator was developed as a workaround to this issue by splitting a FAIMS Raw file into a set of MaxQuant compliant .mzXML files, each containing only scans collected using a single compensation voltage. These resulting .mzXML files can then be processed via MaxQuant as usual.
Written in C#, the FAIMS MzXML Generator accepts Thermo .raw files collected from FAIMS experiments. To begin using the application, download the latest release from the FAIMS-MzXML-Generator Release Page on GitHub and decompress the .zip file.
There are two executables available: a GUI and a command line interface. Both use the ThermoFisher.CommonCore DLLs, so you do not need to have MSFileReader or Xcalibur installed.
File FAIMS_MzXML_Generator.exe provides a Graphical User Interface (GUI) for converting .raw files. Select your input files, optionally define the output directory, then click Create MzXMLs
- Status messages are shown while the mzXML files are created
File WriteFaimsXMLFromRawFile.exe provides a command line interface (CLI) console application.
- The CLI works on both Windows and on Linux
- To invoke on Linux, use Mono:
mono WriteFaimsXMLFromRawFile.exe Datafile.raw
WriteFaimsXMLFromRawFile.exe InstrumentFile.raw [/O:Output_Directory_Path]
[/Centroid] [/Profile]
[/QuickCVLookup] [/Preview]
[/ParamFile:ParamFileName.conf] [/CreateParamFile]
The first command line argument specifies the .raw file to convert
- It can be a filename, or a full path to a file
- The name supports wildcards, for example
*.raw - You can also use
/I:FileName.raw
The second command line argument defines the output directory path
- This parameter is optional
- You can also use
/O:OutputDirectory
By default, spectra are centroided
- To disable this and instead write profile mode spectra, use
/Centroid:Falseor/Profileor/Profile:True
Use /QuickCVLookup to speed up the pre-scan of a .raw file to find CV values
- Once each CV values has been seen in 50 scans, the search for additional CV values will be stopped
- This is generally safe since typically machines cycle through a CV list
- However, for safety, this is false by default
Use /Preview to preview the files that would be created
The processing options can be specified in a parameter file using /ParamFile:Options.conf or /Conf:Options.conf or /P: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
This tool was specifically developed to split FAIMS .raw files into MzXMLs.
- If your file doesn't contain compensation voltages, the FAIMS MzXML generator will not create any MzXMLs, by design
- Instead, use MsConvert, which is available with ProteoWizard
Written by Dain Brademan for the Joshua Coon Research Group (University of Wisconsin) in 2018
Converted to use ThermoFisher.CommonCore DLLs by Matthew Monroe for PNNL (Richland, WA) in 2020
E-mail: brademan@wisc.edu or matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/FAIMS-MzXML-Generator/releases or https://github.com/coongroup/FAIMS-MzXML-Generator
The FAIMS MzXML Generator is licensed under the MIT license; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/MIT
Copyright (c) 2018 Coon Group
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.