MzMLToMzLiteIonMobility

MzMLToMzLiteIonMobility converts mzML files from ion mobility instruments such as the Bruker timsTOF into mzlite files. In these files every peak carries an ion mobility value next to its m/z and intensity, and the tool keeps that value in the mzlite. It is the ion mobility counterpart of MzMLToMzLite, which also explains how to get mzML from raw files and what mzlite is. The tool reads the same parameter record as MzMLToMzLite. The spectra are written with their m/z, intensity and ion mobility arrays as they are in the mzML, and Compress decides how those arrays are stored.

Inputs and outputs

The reader fails on mzML without ion mobility data. -f rewrites every input file in place and removes the string &quot, for mzML exports where that string breaks the XML reader.

The tool writes one <run>.mzlite per input into the output directory. Spectra with an MS level other than 1 or 2 stop the conversion with an error. Scan times are stored in minutes. The mzlite is read by MsFraggerToPSM and PSMBasedQuantificationTIMs. The output directory also receives MzMLToMzLite_log.txt and one <run>_log.txt per input.

Parameters

The wavelet parameters are explained on the MzMLToMzLite page. The default file is TIMsMzMLtoMzLiteParams.json.

Writing a parameter file

open ProteomIQon
open ProteomIQon.Domain

let ms1Wavelet : WaveletPeakPickingParams =
    {
        NumberOfScales       = 3
        YThreshold           = YThreshold.Fixed 1.0
        Centroid_MzTolerance = 0.1
        SNRS_Percentile      = 95.0
        MinSNR               = 1.0
        RefineMZ             = false
        SumIntensities       = false
        PaddingParams        = None
    }

let ms2Padding : PaddingParams =
    {
        MaximumPaddingPoints = Some 7
        Padding_MzTolerance  = 0.05
        WindowSize           = 150
        SpacingPerc          = 95.0
    }

let ms2Wavelet : WaveletPeakPickingParams =
    {
        NumberOfScales       = 10
        YThreshold           = YThreshold.MinSpectrumIntensity
        Centroid_MzTolerance = 0.1
        SNRS_Percentile      = 95.0
        MinSNR               = 1.0
        RefineMZ             = false
        SumIntensities       = false
        PaddingParams        = Some ms2Padding
    }

let timsMzMLToMzLiteParams : Dto.MzMLtoMzLiteParams =
    {
        Compress           = Compression.NoCompression
        StartRetentionTime = None
        EndRetentionTime   = None
        MS1PeakPicking     = PeakPicking.Centroid (CentroidizationMode.Wavelet ms1Wavelet)
        MS2PeakPicking     = PeakPicking.Centroid (CentroidizationMode.Wavelet ms2Wavelet)
    }

// Replace the temp folder with your project folder.
let outputPath = System.IO.Path.Combine(System.IO.Path.GetTempPath(), "TIMsMzMLtoMzLiteParams.json")

Json.serializeAndWrite outputPath timsMzMLToMzLiteParams

Running the tool

Install the tool with dotnet tool install --global ProteomIQon.MzMLToMzLiteIonMobility, then convert one run:

proteomiqon-mzmltomzliteionmobility -i path/to/run.mzML -o path/to/output -p path/to/TIMsMzMLtoMzLiteParams.json

Several runs, three of them converted at the same time:

proteomiqon-mzmltomzliteionmobility -i path/to/run1.mzML path/to/run2.mzML path/to/run3.mzML -o path/to/output -p path/to/TIMsMzMLtoMzLiteParams.json -c 3

A file that fails to parse because of a stray &quot:

proteomiqon-mzmltomzliteionmobility -i path/to/run.mzML -o path/to/output -p path/to/TIMsMzMLtoMzLiteParams.json -f

All flags:

proteomiqon-mzmltomzliteionmobility --help