An mzIdentML file

This file has been generated by searching the raw mzXML file of the ProteomeXchange PXD000001 data set against the erwinia_carotovora.fasta using the MSGF+ search engine: java -jar ~/bin/MSGFPlus.20140630/MSGFPlus.jar -s TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML -d erwinia_carotovora.fasta -inst 1 -protocol 2

Examples

## source files to repeat the search
library("rpx")
px <- PXDataset("PXD000001")
#> Loading PXD000001 from cache.
pxfiles(px)
#> Project PXD000001 files (11):
#>  [remote] F063721.dat
#>  [local]  F063721.dat-mztab.txt
#>  [remote] PRIDE_Exp_Complete_Ac_22134.xml.gz
#>  [remote] PRIDE_Exp_mzData_Ac_22134.xml.gz
#>  [remote] PXD000001_mztab.txt
#>  [remote] README.txt
#>  [local]  TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
#>  [remote] TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML
#>  [local]  TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
#>  [remote] TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw
#>  ...

f <- dir(system.file("extdata", package = "RforProteomics"),
         pattern = "mzid", full.names=TRUE)
library("mzID")
id <- mzID(f)
#> reading TMT_Erwinia.mzid.gz...
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#> Warning: 'as.is' should be specified by the caller; using TRUE
#>  DONE!
id
#> An mzID object
#> 
#> Software used:   MS-GF+ (version: Beta (v10072))
#> 
#> Rawfile:         /home/lgatto/dev/00_github/RforProteomics/sandbox/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
#> 
#> Database:        /home/lgatto/dev/00_github/RforProteomics/sandbox/erwinia_carotovora.fasta
#> 
#> Number of scans: 5287
#> Number of PSM's: 5563