3 Handling raw MS data
The mzR package provides an interface to the proteowizard code base, the legacy RAMP is a non-sequential parser and other C/C++ code to access various raw data files, such as mzML, mzXML, netCDF, and mzData. The data is accessed on-disk, i.e it does not get loaded entirely in memory by default. The three main functions are openMSfile to create a file handle to a raw data file, header to extract metadata about the spectra contained in the file and peaks to extract one or multiple spectra of interest. Other functions such as instrumentInfo, or runInfo can be used to gather general information about a run.
library("mzR")
ms <- openMSfile(mzf)
ms## Mass Spectrometry file handle.
## Filename: TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
## Number of scans: 7534hd <- header(ms)
dim(hd)## [1] 7534 21names(hd)## [1] "seqNum" "acquisitionNum"
## [3] "msLevel" "polarity"
## [5] "peaksCount" "totIonCurrent"
## [7] "retentionTime" "basePeakMZ"
## [9] "basePeakIntensity" "collisionEnergy"
## [11] "ionisationEnergy" "lowMZ"
## [13] "highMZ" "precursorScanNum"
## [15] "precursorMZ" "precursorCharge"
## [17] "precursorIntensity" "mergedScan"
## [19] "mergedResultScanNum" "mergedResultStartScanNum"
## [21] "mergedResultEndScanNum"head(peaks(ms, 234))## [,1] [,2]
## [1,] 100.3852 93.86617
## [2,] 101.6572 83.94572
## [3,] 107.3893 91.63007
## [4,] 112.0505 15697.57129
## [5,] 113.0538 106.47455
## [6,] 113.3050 83.92274str(peaks(ms, 1:5))## List of 5
## $ : num [1:25800, 1:2] 400 400 400 400 400 ...
## $ : num [1:25934, 1:2] 400 400 400 400 400 ...
## $ : num [1:26148, 1:2] 400 400 400 400 400 ...
## $ : num [1:26330, 1:2] 400 400 400 400 400 ...
## $ : num [1:26463, 1:2] 400 400 400 400 400 ...Exercise Extract the index of the MS2 spectrum with the highest base peak intensity and plot its spectrum (we will see more about MS data visualisation in the next section). Is the data centroided or in profile mode?
hd2 <- hd[hd$msLevel == 2, ]
i <- which.max(hd2$basePeakIntensity)
hd2[i, ]## seqNum acquisitionNum msLevel polarity peaksCount totIonCurrent
## 5404 5404 5404 2 -1 275 2283283712
## retentionTime basePeakMZ basePeakIntensity collisionEnergy
## 5404 2751.313 859.5032 354288224 45
## ionisationEnergy lowMZ highMZ precursorScanNum precursorMZ
## 5404 0 100.5031 1995.63 5403 859.1722
## precursorCharge precursorIntensity mergedScan mergedResultScanNum
## 5404 3 627820480 0 0
## mergedResultStartScanNum mergedResultEndScanNum
## 5404 0 0pi <- peaks(ms, hd2[i, 1])
plot(pi, type = "h")
mz <- hd2[i, "basePeakMZ"]
plot(pi, type = "h", xlim = c(mz-0.5, mz+0.5))
Zooming into spectrum 100.
pj <- peaks(ms, 100)
plot(pj, type = "l")
plot(pj, type = "l", xlim = c(536,540))
