getPhosphoRSProbabilities: Generate input files for PhosphoRS, call it, and get modification site probabilities

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.

Value

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

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.

References

Taus et al., 2011