getPhosphoRSProbabilities {isobar} | R Documentation

## 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.

### 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

[Package isobar version 1.38.0 Index]