proteoQC (version 1.8.2)

runTandem: Run X!Tandem

Description

Run X!Tandem

Usage

runTandem(spectra = "", fasta = "", outdir = "./", outprefix = "",
  cpu = 1, enzyme = 1, xmx = 2, varmod = NULL, fixmod = NULL,
  tol = 10, tolu = "ppm", itol = 0.6, itolu = "Daltons", miss = 1)

Arguments

spectra

MS/MS peak list file

fasta

database file

outdir

output directory

outprefix

output file prefix

cpu

The number of CPU used for X!Tandem

enzyme

The ID of enzyme used for database searching. See showEnzyme.

xmx

Set for parameter of "Java -Xmx".

varmod

Variable modifications used for database searching. See showMods.

fixmod

Fixed modifications used for database searching. See showMods.

tol

The error window on experimental peptide mass values

tolu

Units can be selected from: ppm, Daltons.

itol

Error window for MS/MS fragment ion mass values.

itolu

Units can be selected from: Daltons

miss

Max miss clevage

Value

• a file path