ms-deisotope¶

Convert raw mass spectra data into deisotoped neutral mass peak lists written to mzML.

ms-deisotope [OPTIONS] MS_FILE OUTFILE_PATH

Options

-a, --averagine <averagine>¶

Averagine model to use for MS1 scans. Either a name or formula. May specify multiple times. (May specify more than once)

-an, --msn-averagine <averagine>¶

Averagine model to use for MS^n scans. Either a name or formula. May specify multiple times. (May specify more than once)

-s, --start-time <float>¶

Scan time to begin processing at in minutes

-e, --end-time <float>¶

Scan time to stop processing at in minutes

-c, --maximum-charge <int>¶

Highest absolute charge state to consider

-n, --name <string>¶

Name for the sample run to be stored. Defaults to the base name of the input data file

-t, --score-threshold <float>¶

Minimum score to accept an isotopic pattern fit in an MS1 scan

-tn, --msn-score-threshold <float>¶

Minimum score to accept an isotopic pattern fit in an MS^n scan

-m, --missed-peaks <int>¶

Number of missing peaks to permit before an isotopic fit is discarded

-mn, --msn-missed-peaks <int>¶

Number of missing peaks to permit before an isotopic fit is discarded in an MSn scan

-p, --processes <int>¶

Number of worker processes to use. Defaults to 4 or the number of CPUs, whichever is lower

-b, --background-reduction <float>¶

Background reduction factor. Larger values more aggresively remove low abundance signal in MS1 scans.

-bn, --msn-background-reduction <float>¶

Background reduction factor. Larger values more aggresively remove low abundance signal in MS^n scans.

-r, --transform <func>¶

Scan transformations to apply to MS1 scans. May specify more than once. (May specify more than once)

-rn, --msn-transform <func>¶

Scan transformations to apply to MS^n scans. May specify more than once. (May specify more than once)

-v, --extract-only-tandem-envelopes¶

Only work on regions that will be chosen for MS/MS

--verbose¶

Log additional diagnostic information for each scan.

-g, --ms1-averaging <int>¶

The number of MS1 scans before and after the current MS1 scan to average when picking peaks.

--ignore-msn¶

Ignore MS^n scans

-i, --isotopic-strictness <float>¶

-in, --msn-isotopic-strictness <float>¶

-snr, --signal-to-noise-threshold <float>¶

Signal-to-noise ratio threshold to apply when filtering peaks

-mo, --mass-offset <float>¶

Shift peak masses by the given amount

-D, --default-precursor-ion-selection-window <float>¶

The isolation window width to assume when it is not specified.

Arguments

MS_FILE¶

Required argument <path>

OUTFILE_PATH¶

Required argument <path>