generating IBSpectra object

[mdkasoji]

Hi,

I'm having trouble at the first step of reading in data and generating a IBSpectra object. I am using the readIBSpectra() function. From the documentation the id.file parameter can be mzIdentml or .csv. I have both formats which I exported from a mascot search. When I try both mzid or csv, I receive the following error messages:

ib <- readIBSpectra("iTRAQ8plexSpectra",id.file=list.files(pattern=".mzid"), peaklist.file=list.files(pattern=".mgf"))

reading id file F004684_merged.mzid [type: mzid] ...Error in t.default(do.call(cbind, xpathApply(doc, paste0(root,"/x:AnalysisProtocolCollection/x:SpectrumIdentificationProtocol/x:ModificationParams/x:SearchModification"), : argument is not a matrix

ib <- readIBSpectra("iTRAQ8plexSpectra",id.file=list.files(pattern=".csv"), peaklist.file=list.files(pattern=".mgf"))

reading id file Mascot_search_results.csv [type: ibspectra] ... done
Error in [.data.frame(id.data, , .SPECTRUM.COLS["SPECTRUM"]) :
undefined columns selected

I would like some assistance in understanding what the error means? Are there formatting issues? If so, what should the format be?

I have mgf files from proteowizard (for each individual sample) as well as one .mgf (consolidated) file from mascot distiller, that I assume contains information for all samples rolled into one .mgf file. Which is the best to use?

I appreciate you help, thanks!

sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] XML_3.98-1.1 isobar_1.10.0 plyr_1.8.1 Biobase_2.24.0 RColorBrewer_1.1-2
[6] DESeq2_1.4.5 RcppArmadillo_0.4.550.1.0 Rcpp_0.11.3 GenomicRanges_1.16.4 GenomeInfoDb_1.0.2
[11] IRanges_1.22.10 BiocGenerics_0.10.0

loaded via a namespace (and not attached):
[1] annotate_1.42.1 AnnotationDbi_1.26.1 DBI_0.3.1 distr_2.5.3 genefilter_1.46.1
[6] geneplotter_1.42.0 grid_3.1.0 lattice_0.20-29 locfit_1.5-9.1 RSQLite_1.0.0
[11] sfsmisc_1.0-26 splines_3.1.0 startupmsg_0.9 stats4_3.1.0 survival_2.37-7
[16] SweaveListingUtils_0.6.2 tools_3.1.0 xtable_1.7-4 XVector_0.4.0

[mdkasoji]

I wanted to follow up with some information regarding my mzid file. I tried to parse the mzid file using the mzID package. Is isobar perhaps looking for fields that are not found in the mzid file? I hope this helps to understand the error message.

From the mzID package, I was able to parse out the following the fields:

names(flatResults)
[1] "spectrumid" "acquisitionnum" "calculatedmasstocharge"
[4] "chargestate" "experimentalmasstocharge" "rank"
[7] "passthreshold" "mascot:expectation value" "mascot:score"
[10] "peptide shared in multiple proteins" "peptide unique to one protein" "pepseq"
[13] "modified" "modification" "start"
[16] "end" "pre" "post"
[19] "isdecoy" "accession" "description"
[22] "databaseFile"

the mzid parser was able to put this into a data.frame. Here is a snapshot of what the data frame contains:

head(flatResults)
spectrumid acquisitionnum calculatedmasstocharge chargestate experimentalmasstocharge rank passthreshold mascot:expectation value
1 index=389 389 402.2144 4 402.2134 1 TRUE 2.289131e-02
2 index=4971 4971 808.9470 2 809.0088 1 TRUE 4.194366e-02
3 index=1712 1712 829.4001 2 829.4018 1 TRUE 3.372927e-07
4 index=1712 1712 829.4001 2 829.4018 1 TRUE 3.372927e-07
5 index=4345 4345 574.6526 3 574.6991 1 TRUE 3.397108e-02
6 index=4345 4345 574.6698 3 574.6991 4 FALSE 2.748586e+00
mascot:score peptide shared in multiple proteins peptide unique to one protein pepseq modified modification start end pre post
1 26.52 NA NA PQGPPQQGGHPRPPR FALSE NA 108 122 R G
2 27.38 NA NA NQIYRVEILAGNAR FALSE NA 581 594 K K
3 79.96 NA NA SGGGFSSGSAGIINYQR FALSE NA 13 29 R R
4 79.96 NA NA SGGGFSSGSAGIINYQR FALSE NA 13 29 R R
5 29.25 NA NA IDLSFLIDGSTSIGKR FALSE NA 292 307 K R
6 10.17 NA NA EVFAEIVKGKIFSVR FALSE NA 91 105 K A
isdecoy accession description
1 FALSE PRPC_HUMAN Salivary acidic proline-rich phosphoprotein 1/2 OS=Homo sapiens GN=PRH1 PE=1 SV=2
2 FALSE Y3307_ARATH Putative DUF21 domain-containing protein At3g13070, chloroplastic OS=Arabidopsis thaliana GN=CBSDUFCH1 PE=3 SV=1
3 FALSE K2C1_PANTR Keratin, type II cytoskeletal 1 OS=Pan troglodytes GN=KRT1 PE=2 SV=1
4 FALSE K2C1_HUMAN Keratin, type II cytoskeletal 1 OS=Homo sapiens GN=KRT1 PE=1 SV=6
5 FALSE VITRN_HUMAN Vitrin OS=Homo sapiens GN=VIT PE=2 SV=1
6 FALSE THII_SULIK Probable tRNA sulfurtransferase OS=Sulfolobus islandicus (strain M.16.4 / Kamchatka #3) GN=thiI PE=3 SV=1
databaseFile
1 Sprot_2014_11.fasta
2 Sprot_2014_11.fasta
3 Sprot_2014_11.fasta
4 Sprot_2014_11.fasta
5 Sprot_2014_11.fasta
6 Sprot_2014_11.fasta

Thanks