MzMLToMzLite

MzMLToMzLite converts an mzML file into an mzlite file. It is the first tool of the chain, every later tool reads the mzlite it writes. mzlite is the SQLite based storage format of MzIO. It holds the same spectra and metadata as the mzML, in a form that supports random access to single spectra. To get mzML from vendor raw files, use msconvert. Galaxy Europe runs msconvert in the browser without a local install, see their guide. During the conversion the tool can restrict the spectra to a retention time window and can centroid profile spectra with a wavelet peak picker. Centroiding replaces the many points that describe one peak by a single m/z and intensity pair. The algorithm is described in the BioFSharp.Mz documentation.

Inputs and outputs

-f rewrites every input file in place and removes the string &quot from it. Some mzML exports contain that string in places where the XML reader cannot handle it. Leave the flag off unless the conversion fails on such a file.

The tool writes one <run>.mzlite per input <run>.mzML into the output directory. Only spectra with MS level 1 or 2 are copied, and spectra whose peak array is empty after peak picking are skipped. Scan times in the mzlite are stored in minutes, whatever unit the mzML used. The mzlite is read by PeptideSpectrumMatching, PSMBasedQuantification and AlignmentBasedQuantification. The output directory also receives MzMLToMzLite_log.txt and one <run>_log.txt per input.

Parameters

CentroidizationMode.Manufacturer is for vendor raw files. For mzML input use ProfilePeaks or the wavelet centroiding.

When a spectrum type is set to PeakPicking.Centroid (CentroidizationMode.Wavelet w), w is a WaveletPeakPickingParams record. The values below are the MS1 settings from the ion mobility default file and serve as a starting point.

The default file is mzMLToMzLiteParams.json. A file with wavelet centroiding on both levels is TIMsMzMLtoMzLiteParams.json.

Writing a parameter file

open ProteomIQon
open ProteomIQon.Domain

let mzMLToMzLiteParams : Dto.MzMLtoMzLiteParams =
    {
        Compress           = Compression.NoCompression
        StartRetentionTime = None
        EndRetentionTime   = None
        MS1PeakPicking     = PeakPicking.ProfilePeaks
        MS2PeakPicking     = PeakPicking.ProfilePeaks
    }

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

Json.serializeAndWrite outputPath mzMLToMzLiteParams

Running the tool

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

proteomiqon-mzmltomzlite -i path/to/run.mzML -o path/to/output -p path/to/mzMLToMzLiteParams.json

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

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

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

proteomiqon-mzmltomzlite -i path/to/run.mzML -o path/to/output -p path/to/mzMLToMzLiteParams.json -f

All flags:

proteomiqon-mzmltomzlite --help