A parser for raw and identification mass-spectrometry data (original) (raw)
Introduction
The mzR package aims at providing a common, low-level interface to several mass spectrometry data formats, namely,mzXML (Pedrioli et al. 2004), mzML (Martens et al. 2010) for raw data, andmzIdentML (Jones et al. 2012), somewhat similar to the Bioconductor package affyio for affymetrix raw data. No processing is done in r BiocStyle::Biocpkg("mzR"), which is left to packages such as r BiocStyle::Biocpkg("xcms") (Smith et al. 2006, Tautenhahn:2008) or r BiocStyle::Biocpkg("MSnbase") (Gatto and Lilley 2012). These packages also provide more convenient, high-level interfaces to raw and identification. data
Most importantly, access to the data should be fast and memory efficient. This is made possible by allowing on-disk random file access, i.e. retrieving specific data of interest without having to sequentially browser the full content nor loading the entire data into memory.
The actual work of reading and parsing the data files is handled by the included C/C++ libraries or backends. The C++ reference implementation for the mzMLis the proteowizard library (Kessner et al. 2008) (pwiz in short), which in turn makes use of the boost C++ (http://www.boost.org/) library. More recently, the proteowizard (http://proteowizard.sourceforge.net/) (Chambers et al. 2012) has been fully integrated using the mzRpwiz backend for raw data, and is not the default option. The mzRnetCDF backend provides support to CDF-based formats. Finally, the mzRident backend is available to access identification data (mzIdentML) through pwiz.
The mzR package is in essence a collection of wrappers to the C++ code, and benefits from the C++ interface provided through the Rcpp package (Eddelbuettel and François 2011).
IMPORTANT New developers that need to access and manipulate raw mass spectrometry data are advised against using this infrastucture directly. They are invited to use the corresponding MSnExp (with on disk mode) from the_MSnbase_ package instead. The latter supports reading multiple files at once and offers access to the spectra data (m/z and intensity) as well as all the spectra metadata using a coherent interface. The MSnbase infrastructure itself used the low level classes in mzR, thus offering fast and efficient access.
All the mass spectrometry file formats are organized similarly, where a set of metadata nodes about the run is followed by a list of spectra with the actual masses and intensities. In addition, each of these spectra has its own set of metadata, such as the retention time and acquisition parameters.
Spectral data access
Access to the spectral data is done via the peaks function. The return value is a list of two-column mass-to-charge and intensity matrices or a single matrix if one spectrum is queried.
Chromatogram access
Access to the chromatogram(s) is done using the chromatogram (orchromatograms) function, that return one (or a list of) data.frames. See ?chromatogram for details. Chromatogram header information is available via the chromatogramHeader function that returns one (or a list of) data.frames. See ?chromatogramHeader for details. This functionality is only available with the pwiz backend.
Identification result access
The main access to identification result is done via psms, scoreand modifications. psms and score will return the detailed information on each psm and scores. modifications will return the details on each modification found in peptide.
Example
mzXML/mzML files
A short example sequence to read data from a mass spectrometer. First open the file.
library(mzR)## Loading required package: Rcpplibrary(msdata)
mzxml <- system.file("threonine/threonine_i2_e35_pH_tree.mzXML",
package = "msdata")
aa <- openMSfile(mzxml)We can obtain different kind of header information.
runInfo(aa)## $scanCount
## [1] 55
##
## $lowMz
## [1] 50.0036
##
## $highMz
## [1] 298.673
##
## $dStartTime
## [1] 0.3485
##
## $dEndTime
## [1] 390.027
##
## $msLevels
## [1] 1 2 3 4
##
## $startTimeStamp
## [1] NAinstrumentInfo(aa)## $manufacturer
## [1] "Thermo Scientific"
##
## $model
## [1] "LTQ Orbitrap"
##
## $ionisation
## [1] "electrospray ionization"
##
## $analyzer
## [1] "fourier transform ion cyclotron resonance mass spectrometer"
##
## $detector
## [1] "unknown"
##
## $software
## [1] "Xcalibur software 2.2 SP1"
##
## $sample
## [1] ""
##
## $source
## [1] ""header(aa,1)## seqNum acquisitionNum msLevel polarity peaksCount totIonCurrent retentionTime
## 1 1 1 1 1 684 341427000 0.3485
## basePeakMZ basePeakIntensity collisionEnergy ionisationEnergy lowMZ highMZ
## 1 120.066 211860000 NA 0 50.3254 298.673
## precursorScanNum precursorMZ precursorCharge precursorIntensity mergedScan
## 1 NA NA NA NA NA
## mergedResultScanNum mergedResultStartScanNum mergedResultEndScanNum
## 1 NA NA NA
## injectionTime filterString spectrumId
## 1 0 <NA> controllerType=0 controllerNumber=1 scan=1
## centroided ionMobilityDriftTime isolationWindowTargetMZ
## 1 TRUE NA NA
## isolationWindowLowerOffset isolationWindowUpperOffset scanWindowLowerLimit
## 1 NA NA 50.3254
## scanWindowUpperLimit electronBeamEnergy
## 1 298.673 NARead a single spectrum from the file.
pl <- peaks(aa,10)
peaksCount(aa,10)## [1] 317head(pl)## mz intensity
## [1,] 50.08176 6984.858
## [2,] 50.62267 7719.419
## [3,] 50.70530 7185.290
## [4,] 50.73298 7509.140
## [5,] 50.83848 9366.624
## [6,] 50.88303 8012.808plot(pl[,1], pl[,2], type="h", lwd=1)One should always close the file when not needed any more. This will release the memory of cached content.
close(aa)mzIdentML files
You can use openIDfile to read a mzIdentML file (version 1.1), which use the pwiz backend.
library(mzR)
library(msdata)
file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
x <- openIDfile(file)mzidInfo function will return general information about this identification result.
mzidInfo(x)## $FileProvider
## [1] "researcher"
##
## $CreationDate
## [1] "2012-07-25T14:03:16"
##
## $software
## [1] "xtandem x! tandem CYCLONE (2010.06.01.5) "
## [2] "ProteoWizard MzIdentML 3.0.21263 ProteoWizard"
##
## $ModificationSearched
## [1] "Oxidation" "Carbamidomethyl"
##
## $FragmentTolerance
## [1] "0.8 dalton"
##
## $ParentTolerance
## [1] "1.5 dalton"
##
## $enzymes
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>e</mi><mi>n</mi><mi>z</mi><mi>y</mi><mi>m</mi><mi>e</mi><mi>s</mi></mrow><annotation encoding="application/x-tex">enzymes</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.625em;vertical-align:-0.1944em;"></span><span class="mord mathnormal">e</span><span class="mord mathnormal">n</span><span class="mord mathnormal" style="margin-right:0.03588em;">zy</span><span class="mord mathnormal">m</span><span class="mord mathnormal">es</span></span></span></span>name
## [1] "Trypsin"
##
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>e</mi><mi>n</mi><mi>z</mi><mi>y</mi><mi>m</mi><mi>e</mi><mi>s</mi></mrow><annotation encoding="application/x-tex">enzymes</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.625em;vertical-align:-0.1944em;"></span><span class="mord mathnormal">e</span><span class="mord mathnormal">n</span><span class="mord mathnormal" style="margin-right:0.03588em;">zy</span><span class="mord mathnormal">m</span><span class="mord mathnormal">es</span></span></span></span>nTermGain
## [1] "H"
##
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>e</mi><mi>n</mi><mi>z</mi><mi>y</mi><mi>m</mi><mi>e</mi><mi>s</mi></mrow><annotation encoding="application/x-tex">enzymes</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.625em;vertical-align:-0.1944em;"></span><span class="mord mathnormal">e</span><span class="mord mathnormal">n</span><span class="mord mathnormal" style="margin-right:0.03588em;">zy</span><span class="mord mathnormal">m</span><span class="mord mathnormal">es</span></span></span></span>cTermGain
## [1] "OH"
##
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>e</mi><mi>n</mi><mi>z</mi><mi>y</mi><mi>m</mi><mi>e</mi><mi>s</mi></mrow><annotation encoding="application/x-tex">enzymes</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.625em;vertical-align:-0.1944em;"></span><span class="mord mathnormal">e</span><span class="mord mathnormal">n</span><span class="mord mathnormal" style="margin-right:0.03588em;">zy</span><span class="mord mathnormal">m</span><span class="mord mathnormal">es</span></span></span></span>minDistance
## [1] "0"
##
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>e</mi><mi>n</mi><mi>z</mi><mi>y</mi><mi>m</mi><mi>e</mi><mi>s</mi></mrow><annotation encoding="application/x-tex">enzymes</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.625em;vertical-align:-0.1944em;"></span><span class="mord mathnormal">e</span><span class="mord mathnormal">n</span><span class="mord mathnormal" style="margin-right:0.03588em;">zy</span><span class="mord mathnormal">m</span><span class="mord mathnormal">es</span></span></span></span>missedCleavages
## [1] "1"
##
##
## $SpectraSource
## [1] "D:/TestSpace/NeoTestMarch2011/55merge.mgf"psms will return the detailed information on each peptide-spectrum-match, include spectrumID, chargeState,sequence. modNum and others.
p <- psms(x)
colnames(p)## [1] "spectrumID" "chargeState"
## [3] "rank" "passThreshold"
## [5] "experimentalMassToCharge" "calculatedMassToCharge"
## [7] "sequence" "peptideRef"
## [9] "modNum" "isDecoy"
## [11] "post" "pre"
## [13] "start" "end"
## [15] "DatabaseAccess" "DBseqLength"
## [17] "DatabaseSeq" "DatabaseDescription"
## [19] "spectrum.title" "acquisitionNum"The modifications information can be accessed using modifications, which will return the spectrumID, sequence, name, mass andlocation.
m <- modifications(x)
head(m)## spectrumID sequence
## 1 index=12 LCYIALDFDEEMKAAEDSSDIEK
## 2 index=12 LCYIALDFDEEMKAAEDSSDIEK
## 3 index=285 KDLYGNVVLSGGTTMYEGIGER
## 4 index=83 KDLYGNVVLSGGTTMYEGIGER
## 5 index=21 VIDENFGLVEGLMTTVHAATGTQK
## 6 index=198 GVGGAIVLVLYDEMK
## peptideRef name mass
## 1 LCYIALDFDEEMKAAEDSSDIEK_15.9949@M$12;_57.0215@C$2;_ Carbamidomethyl 57.0215
## 2 LCYIALDFDEEMKAAEDSSDIEK_15.9949@M$12;_57.0215@C$2;_ Oxidation 15.9949
## 3 KDLYGNVVLSGGTTMYEGIGER_15.9949@M$15;__ Oxidation 15.9949
## 4 KDLYGNVVLSGGTTMYEGIGER_15.9949@M$15;__ Oxidation 15.9949
## 5 VIDENFGLVEGLMTTVHAATGTQK_15.9949@M$13;__ Oxidation 15.9949
## 6 GVGGAIVLVLYDEMK_15.9949@M$14;__ Oxidation 15.9949
## location
## 1 2
## 2 12
## 3 15
## 4 15
## 5 13
## 6 14Since different software will use different scoring function, we provide a score to extract the scores for each psm. It will return a data.frame with different columns depending on software generating this file.
scr <- score(x)
colnames(scr)## [1] "spectrumID" "X.Tandem.expect" "X.Tandem.hyperscore"Future plans
Other file formats provided by HUPO, such as mzQuantML for quantitative data (Walzer et al. 2013) are also possible in the future.
Session information
Chambers, Matthew C., Brendan Maclean, Robert Burke, Dario Amodei, Daniel L. Ruderman, Steffen Neumann, Laurent Gatto, et al. 2012. “A cross-platform toolkit for mass spectrometry and proteomics.” Nat Biotech 30 (10): 918–20. https://doi.org/10.1038/nbt.2377.
Eddelbuettel, Dirk, and Romain François. 2011. “Rcpp: Seamless R and C++ Integration.” Journal of Statistical Software 40 (8): 1–18. http://www.jstatsoft.org/v40/i08/.
Gatto, L, and K S Lilley. 2012. “MSnbase – an R/Bioconductor Package for Isobaric Tagged Mass Spectrometry Data Visualization, Processing and Quantitation.” Bioinformatics 28 (2): 288–9. https://doi.org/10.1093/bioinformatics/btr645.
Jones, A R, M Eisenacher, G Mayer, O Kohlbacher, J Siepen, S J Hubbard, J N Selley, et al. 2012. “The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results.” Mol Cell Proteomics 11 (7): M111.014381. https://doi.org/10.1074/mcp.M111.014381.
Kessner, Darren, Matt Chambers, Robert Burke, David Agus, and Parag Mallick. 2008. “ProteoWizard: Open Source Software for Rapid Proteomics Tools Development.” Bioinformatics 24 (21): 2534–6. https://doi.org/10.1093/bioinformatics/btn323.
Martens, Lennart, Matthew Chambers, Marc Sturm, Darren Kessner, Fredrik Levander, Jim Shofstahl, Wilfred H Tang, et al. 2010. “MzML - a Community Standard for Mass Spectrometry Data.” Molecular and Cellular Proteomics : MCP. https://doi.org/10.1074/mcp.R110.000133.
Pedrioli, Patrick G A, Jimmy K Eng, Robert Hubley, Mathijs Vogelzang, Eric W Deutsch, Brian Raught, Brian Pratt, et al. 2004. “A Common Open Representation of Mass Spectrometry Data and Its Application to Proteomics Research.” Nat. Biotechnol. 22 (11): 1459–66. https://doi.org/10.1038/nbt1031.
Smith, C A, E J Want, G O’Maille, R Abagyan, and G Siuzdak. 2006. “XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification.” Anal Chem 78 (3): 779–87. https://doi.org/10.1021/ac051437y.
Walzer, M, D Qi, G Mayer, J Uszkoreit, M Eisenacher, T Sachsenberg, F F Gonzalez-Galarza, et al. 2013. “The mzQuantML Data Standard for Mass Spectrometry-Based Quantitative Studies in Proteomics.” Mol Cell Proteomics 12 (8): 2332–40. https://doi.org/10.1074/mcp.O113.028506.