getPhosphoRSProbabilities: Generate input files for PhosphoRS, call it, and get...

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

Get phosphorylation site localization probabilities by calling PhosphoRS and parsing its output. getPhosphoRSProbabilities generates a XML input file for PhosphoRS calling writePhosphoRSInput, then executes phosphoRS.jar with java, and parses the XML result file with readPhosphoRSOutput.

Usage

  getPhosphoRSProbabilities(id.file, mgf.file, massTolerance, activationType,
                 simplify = FALSE, mapping.file = NULL, mapping =
                 c(peaklist = "even", id = "odd"), pepmodif.sep =
                 "##.##", besthit.only = TRUE, phosphors.cmd =
                 paste("java -jar", system.file("phosphors",
                 "phosphoRS.jar", package = "isobar")), file.basename =
                 tempfile("phosphors."))


  writePhosphoRSInput(phosphoRS.infile, id.file, mgf.file, massTolerance,
                 activationType, mapping.file = NULL, mapping =
                 c(peaklist = "even", id = "odd"), pepmodif.sep =
                 "##.##", modif.masses = rbind(c("PHOS", "1",
                 "1:Phospho:Phospho:79.966331:PhosphoLoss:97.976896:STY"),
                 c("Oxidation_M", "2",
                 "2:Oxidation:Oxidation:15.994919:null:0:M"),
                 c("Cys_CAM", "3",
                 "3:Carbamidomethylation:Carbamidomethylation:57.021464:null:0:C"),
                 c("iTRAQ4plex", "4",
                 "4:iTRAQ4:iTRAQ4:144.1544:null:0:KX"), c("iTRAQ8plex",
                 "5", "5:iTRAQ8:iTRAQ8:304.308:null:0:KX"),
                 c("TMT6plex", "7",
                 "7:TMT6:TMT6:229.162932:null:0:KX"), c("TMTsixplex",
                 "6", "6:TMT6:TMT6:229.162932:null:0:KX")))


  readPhosphoRSOutput(phosphoRS.outfile, simplify = FALSE, pepmodif.sep = "##.##", besthit.only = TRUE)

  filterSpectraPhosphoRS(id.file, mgf.file, ..., min.prob = NULL, do.remove=FALSE)

Arguments

id.file	Database search results file in ibspectra.csv or mzIdentML format. See IBSpectra and isobar vignette for information on converting Mascot dat and Phenyx pidres files into ibspectra format.
mgf.file	Peaklist file
massTolerance	Fragment ion mass tolerance (in Da)
activationType	Activation types of spectra. CID, HCD, or ETD.
simplify	If TRUE, returns a data.frame instead of a list.
mapping.file	Mapping file. See also readIBSpectra.
mapping	Mapping columns.
besthit.only	Only show best hit, simplifies result to data.frame instead of list.
phosphors.cmd	PhosphoRS script.
file.basename	Base name for creating phosphoRS input and output files.
phosphoRS.infile	PhosphoRS input XML file name.
phosphoRS.outfile	PhosphoRS output XML file name.
pepmodif.sep	separator of peptide and modification in XML id
modif.masses	masses and ID used for PhosphoRS
min.prob	Threshold for PhosphoRS peptide probability to consider it for quantification
...	Further arguments to getPhosphoRSProbabilities
do.remove	If TRUE, spectra below the min.prob threshold are not just set as 'use.for.quant=FALSE' but removed.

Details

PhosphoRS is described in Taus et al., 2011. It can be downloaded from http://cores.imp.ac.at/protein-chemistry/download/ and used as Freeware. Java is required at runtime.

Value

If simplify=TRUE, a data.frame with the following columns: spectrum, peptide, modif, PepScore, PepProb, seqpos

If simplify=FALSE, a list (of spectra) of lists (of peptide identifications) of lists (with information about identification and localization). spectrum -> peptide 1, peptides 2, ... -> peptide. First level: - spectrum Second level: - peptide identifications for spectrum (might be more than one) Third level: - peptide: vector with peptide sequence and modification stirng - site.probs: matrix with site probabilities for each phospho site - isoforms: peptide score and probabilities for each isoform

Author(s)

Florian P Breitwieser

References

Taus et al., 2011

isobar documentation built on Nov. 8, 2020, 7:48 p.m.