mzdeisotope - Tools for deisotoping and charge deconvolution for mass spectra

Components

• mzdeisotope - A Rust library with tools for deconvolution of peak lists
• mzdeisotoper - An executable tool for applying the deconvolution process whole mass spectrometry data files

Library Usage

TODO

Tool Usage

$ mzdeisotoper --help
Deisotoping and charge state deconvolution of mass spectrometry files.

Read a file or stream, transform the spectra, and write out a processed mzML file or stream.

Usage: mzdeisotoper [OPTIONS] <INPUT_FILE>

Arguments:
  <INPUT_FILE>
          The path to read the input spectra from, or if '-' is passed, read from STDIN

Options:
  -o, --output-file <OUTPUT_FILE>
          The path to write the output file to, or if '-' is passed, write to STDOUT

          [default: -]

  -t, --threads <THREADS>
          The number of threads to use, passing a value < 1 to use all available threads

          [default: -1]

  -r, --time-range <BEGIN-END>
          The time range to process, denoted [start?]-[stop?]

          If a start is not specified, processing begins from the start of the run.
          If a stop is not specified, processing stops at the end of the run.


  -g, --ms1-averaging-range <MS1_AVERAGING_RANGE>
          The number of MS1 spectra before and after to average with prior to peak picking

          [default: 0]

  -b, --ms1-background-reduction <MS1_DENOISING>
          The magnitude of background noise reduction to use on MS1 spectra prior to peak picking

          [default: 0]

  -a, --ms1-isotopic-model <MS1_ISOTOPIC_MODEL>
          The isotopic model to use for MS1 spectra

          [default: peptide]
          [possible values: peptide, glycan, glycopeptide, permethylated-glycan, heparin, heparan-sulfate]

  -s, --ms1-score-threshold <MS1_SCORE_THRESHOLD>
          The minimum isotopic pattern fit score for MS1 spectra

          [default: 20]

  -A, --msn-isotopic-model <MSN_ISOTOPIC_MODEL>
          The isotopic model to use for MSn spectra

          [default: peptide]
          [possible values: peptide, glycan, glycopeptide, permethylated-glycan, heparin, heparan-sulfate]

  -S, --msn-score-threshold <MSN_SCORE_THRESHOLD>
          The minimum isotopic pattern fit score for MSn spectra

          [default: 10]

  -v, --precursor-processing <PRECURSOR_PROCESSING>
          How to treat precursor ranges

          [default: selected-precursors]

          Possible values:
          - full:                Process the entire MS1 mass range and all MSn spectra
          - selected-precursors: Process only the MS1 regions that are selected for MSn and all MSn spectra
          - tandem-only:         Process only MSn spectra without examining MS1 spectra
          - ms1-only:            Process only the MS1 spectra without examining MSn spectra

  -z, --charge-range <CHARGE_RANGE>
          The range of charge states to consider for each peak denoted [low]-[high] or [high]

          [default: 1-8]

  -m, --max-missed-peaks <MS1_MISSED_PEAKS>
          The maximum number of missed peaks for MS1 spectra

          [default: 1]

  -M, --msn-max-missed-peaks <MSN_MISSED_PEAKS>
          The maximum number of missed peaks for MSn spectra

          [default: 1]

  -h, --help
          Print help (see a summary with '-h')

  -V, --version
          Print version

mzdeisotoper can read mzML, MGF, and if built with the mzmlb feature, mzMLb from the file system. The program can also receive mzML or MGF over STDIN, letting you pipe the output of a tool like msconvert or curl into it.