I have a proteomics data with format .RAW
then I converted it to mzXML by proteoWizard. Now I want to load it and search for proteins etc
There are few ways which none could help me go through the data
for example
file <- list.files("path to my data", pattern="mydata.mzXML",full.names=TRUE, recursive = TRUE)
raws <- readMSData(file, verbose=FALSE)
raws
this gives me the following
Object of class "MSnExp"
Object size in memory: 1870.38 Mb
- - - Spectra data - - -
MS level(s): 2
Number of MS1 acquisitions: 5428
Number of MSn scans: 25855
Number of precursor ions: 25855
25736 unique MZs
Precursor MZ's: 350.19 - 1549.6
MSn M/Z range: 99 6062.42
MSn retention times: 3:56 - 133:58 minutes
- - - Processing information - - -
Data loaded: Thu Sep 24 15:11:54 2015
MSnbase version: 1.16.2
- - - Meta data - - -
phenoData
rowNames: 1
varLabels: sampleNames
varMetadata: labelDescription
protocolData: none
featureData
featureNames: X1.1 X10.1 ... X9999.1 (25855 total)
fvarLabels: spectrum
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
however when I use another way to import the data I get the following information
mzf <- file.path("path to the data", pattern="my data.mzXML")
> ms <- openMSfile(mzf)
> hd <- header(ms)
> dim(hd)
[1] 42785 21
> names(hd)
[1] "seqNum" "acquisitionNum" "msLevel" "polarity" "peaksCount" "totIonCurrent"
[7] "retentionTime" "basePeakMZ" "basePeakIntensity" "collisionEnergy" "ionisationEnergy" "lowMZ"
[13] "highMZ" "precursorScanNum" "precursorMZ" "precursorCharge" "precursorIntensity" "mergedScan"
[19] "mergedResultScanNum" "mergedResultStartScanNum" "mergedResultEndScanNum"
they are different in dim. WHY?
is there a way to import data directly from .RAW ?
if no, which software is the best to convert the data into a format which I will be sure that i am not losing any information ?
Many thanks
