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Converting spectral data files with MSConvert

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Robert Millikin edited this page Aug 20, 2019 · 4 revisions

FlashLFQ supports reading .mzML and Thermo .raw file formats. If you are using another vendor's format, you can convert to .mzML using ProteoWizard's MSConvert software. This Wiki page describes the MSConvert settings you should use so that the data can be run through FlashLFQ. Note that .mgf files do not contain MS1-level spectral data and cannot be used for quantification by FlashLFQ.

  1. Add files via the "Browse" button. You may need to click "Add" once you have selected your files.
  2. Under "Filters", select "Peak Picking". This centroids the spectral data. The vendor algorithm is fine, unless you have Waters data. If you have Waters data, select CWT for the algorithm. Make sure MS Levels is set to "1 - ". Click "Add". Make sure peakPicking is the first filter in the list (you can drag and drop to make sure it is the first).
  3. Make sure the "Output Format" is set to mzML.
  4. Click "Start".

Some notes:

  • FlashLFQ cannot read numpress compressed data. Do not select these options.
  • The screenshot below is from MSConvert version 3.0.10922.

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