mzdeisotope - Tools for deisotoping and charge deconvolution for mass spectra

Components

• mzdeisotope - A Rust library with tools for deconvolution of peak lists
• mzdeisotope-map - A Rust library that expands mzdeisotope for processing ion mobility frames and LC-MS feature maps
• 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

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: -]
  -w, --write-buffer-size <WRITE_BUFFER_SIZE>
          The size of the buffer for queueing writing of results to the output stream [default: 10000]
  -t, --threads <THREADS>
          The number of threads to use, passing a value < 1 to use all available threads [default: -1]
  -h, --help
          Print help (see more with '--help')
  -V, --version
          Print version

Config:
  -l, --log-file <LOG_FILE>
          The path to write a log file to, in addition to STDERR
      --config-file <CONFIG_FILE>
          A TOML configuration file to read additional parameters from
      --write-config-file <WRITE_CONFIG_FILE>
          Write TOML configuration to this file

Processing:
  -r, --time-range <BEGIN-END>
          The time range to process, denoted (start?)-(stop?)
  -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, selected-precursors, tandem-only, ms1-only, dia]
  -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]
  -e, --ms1-mass-error-tolerance <MS1_ERROR_TOLERANCE>
          The mass error to tolerate for MS1 spectra
  -E, --msn-mass-error-tolerance <MSN_ERROR_TOLERANCE>
          The mass error to tolerate for MSn spectra
  -i, --incremental-truncation
          Use incremental truncation of isotopic patterns instead of a single width

Ion Mobility:
  -q, --ion-mobility-deconvolution
          Whether to use the ion mobility framing algorithm
      --ms1-ion-mobility-gap-size <MS1_ION_MOBILITY_GAP_SIZE>
          The maximum gap size in ion mobility units to tolerate in MS1 IM-MS features [default: 0.025]
      --msn-ion-mobility-gap-size <MSN_ION_MOBILITY_GAP_SIZE>
          The maximum gap size in ion mobility units to tolerate in MSn IM-MS features [default: 0.025]
  -f, --ms1-ion-mobility-feature-min-length <MS1_ION_MOBILITY_FEATURE_MIN_LENGTH>
          The minimum feature size for MS1 IM-MS features [default: 3]
  -F, --msn-ion-mobility-feature-min-length <MSN_ION_MOBILITY_FEATURE_MIN_LENGTH>
          The minimum feature size for MSn IM-MS features [default: 2]

Input Files

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.