Uses the mzR package to read the MS data needed for MS peak lists.
generateMSPeakListsMzR(fGroups, ...)
# S4 method for featureGroups
generateMSPeakListsMzR(
fGroups,
maxMSRtWindow = 5,
precursorMzWindow = 4,
topMost = NULL,
avgFeatParams = getDefAvgPListParams(),
avgFGroupParams = getDefAvgPListParams()
)
# S4 method for featureGroupsSet
generateMSPeakListsMzR(fGroups, ...)The featureGroups object from which MS peak lists should be extracted.
(sets workflow) Further arguments passed to the non-sets workflow method.
Maximum chromatographic peak window used for spectrum averaging (in seconds, +/- retention
time). If NULL all spectra from a feature will be taken into account. Lower to decrease processing time.
The m/z window (in Da) to find MS/MS spectra of a precursor. This is typically used
for Data-Dependent like MS/MS data and should correspond to the isolation m/z window (i.e. +/- the
precursor m/z) that was used to collect the data. For Data-Independent MS/MS experiments, where precursor
ions are not isolated prior to fragmentation (e.g. bbCID, MSe, all-ion, ...) the value should be
NULL.
Only extract MS peak lists from a maximum of topMost analyses with highest intensity. If
NULL all analyses will be used.
Parameters used for averaging MS peak lists of individual features. Analogous to
avgFGroupParams.
A list with parameters used for averaging of peak lists for feature groups. See
getDefAvgPListParams for more details.
A MSPeakLists object.
This function uses mzR to generate MS peak lists. This function is called when calling generateMSPeakLists with
algorithm="mzr".
The MS data files should be either in .mzXML or .mzML format.
The input MS data files need to be centroided. The convertMSFiles function can be used to
centroid data.
A cross-platform toolkit for mass spectrometry and proteomics Chambers, Matthew C. and Maclean, Brendan and Burke, Robert and Amodei,
Dario and Ruderman, Daniel L. and Neumann, Steffen and Gatto, Laurent and
Fischer, Bernd and Pratt, Brian and Egertson, Jarrett and Hoff, Katherine
and Kessner, Darren and Tasman, Natalie and Shulman, Nicholas and Frewen,
Barbara and Baker, Tahmina A. and Brusniak, Mi-Youn and Paulse, Christopher
and Creasy, David and Flashner, Lisa and Kani, Kian and Moulding, Chris and
Seymour, Sean L. and Nuwaysir, Lydia M. and Lefebvre, Brent and Kuhlmann,
Frank and Roark, Joe and Rainer, Paape and Detlev, Suckau and Hemenway,
Tina and Huhmer, Andreas and Langridge, James and Connolly, Brian and Chadick,
Trey and Holly, Krisztina and Eckels, Josh and Deutsch, Eric W. and Moritz,
Robert L. and Katz, Jonathan E. and Agus, David B. and MacCoss, Michael and
Tabb, David L. and Mallick, Parag Nat Biotechnol. 2012 NOct;30(10):918-920.
Mol Cell Proteomics. 2010 Aug 17. mzML - a Community Standard for Mass Spectrometry Data. Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Rompp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW.
Nat Biotechnol. 2004 Nov;22(11):1459-66. A common open representation of mass spectrometry data and its application to proteomics research. Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.
Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Keller A, Eng J, Zhang N, Li XJ, Aebersold R.
Bioinformatics. 2008 Nov 1;24(21):2534-6. Epub 2008 Jul 7. ProteoWizard: open source software for rapid proteomics tools development. Kessner D, Chambers M, Burke R, Agus D, Mallick P.
generateMSPeakLists for more details and other algorithms.