pCleanGear: Preprocess high-resolution tandem mass spectra prior to...

In AimeeD90/pClean_release: Preprocess high-resolution tandem mass spectra prior to database searching

Preprocess high-resolution tandem mass spectra prior to database searching

Description

This package is designed to preprocess high-resolution MS/MS Data, which integrated three modules, removal of label-associated ions, isotope peak reduction and charge deconvolution, and a graph-based network approach and aimed at filtering out extraneous peaks with/without specific-feature. pClean is supportive to a wide array of instruments with all types of MS data, and incorporative into most data analysis pipelines.

Usage

pCleanGear(mgf = NULL, itol = 0.05, outdir = "./", mem = 1,
  cpu = 0, plot = FALSE, aa2 = TRUE, mionFilter = FALSE,
  labelMethod = NULL, repFilter = FALSE, labelFilter = FALSE,
  low = FALSE, high = FALSE, isoReduction = FALSE,
  chargeDeconv = FALSE, largerThanPrecursor = FALSE,
  ionsMerge = FALSE, network = TRUE, idres = NULL,
  ms2tolfilter = 1.2, debug = FALSE)

Arguments

mgf	Input MS/MS data in MGF format.
itol	Fragment tolerance, default 0.05Da.
outdir	Output directory, default current directory.
mem	The maximun memeroy to be used, default 1GB.
cpu	The number of cpu to be used, default 0 (all).
aa2	Consider gap masses of two amino acid, default is TRUE.
mionFilter	Filter immonium ions, default FALSE.
labelMethod	Peptide labeling method, iTRAQ4plex, iTRAQ8plex, TMT6plex, TMT10plex or NULL.
repFilter	Remove reporter ions, default FALSE.
labelFilter	Remove label-associated ions, default FALSE.
low	Remove ions in low b-/y-free window for label-based MS/MS data, default FALSE.
high	Remove ions in high b-/y-free window for label-based MS/MS data, default FALSE.
isoReduction	Reduction of heavy isotopic peaks, default FALSE.
chargeDeconv	Charge deconvolution, default FALSE.
largerThanPrecursor	Remove ions larger than precursor, default FALSE.
ionsMerge	Merge two adjecent ions with similar m/z, default FALSE.
network	Graph-based network filtration.
idres	Use MSGF identification result to annotate peaks (.mzid), default NULL.
ms2tolfilter	Default 1.2.
debug	Whether to export edge file and peak file.

Value

A much cleaner MS/MS data.

AimeeD90/pClean_release documentation built on May 20, 2023, 10:56 p.m.