Generate peak lists with mzR (deprecated) — generateMSPeakListsMzR • patRoon

Uses the mzR package to read the MS data needed for MS peak lists. This function is now deprecated, please use generateMSPeakLists instead.

generateMSPeakListsMzR(fGroups, ...)

# S4 method for class 'featureGroups'
generateMSPeakListsMzR(
  fGroups,
  maxMSRTWindow = 5,
  precursorMzWindow = 4,
  topMost = NULL,
  avgFeatParams = getDefAvgPListParams(clusterMzWindow = 0.005),
  avgFGroupParams = getDefAvgPListParams(clusterMzWindow = 0.005, withPrecursorMS =
    FALSE)
)

# S4 method for class 'featureGroupsSet'
generateMSPeakListsMzR(fGroups, ...)

Arguments

fGroups: The featureGroups object for which MS peak lists should be generated.
...: (sets workflow) Further arguments passed to the non-sets workflow method.
maxMSRTWindow: 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.
precursorMzWindow: 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.
topMost: Only extract MS peak lists from a maximum of topMost analyses with highest intensity. If NULL all analyses will be used.
avgFeatParams: Parameters used for averaging MS peak lists of individual features. Analogous to avgFGroupParams.
avgFGroupParams: A list with parameters used for averaging of peak lists for feature groups. See getDefAvgPListParams for more details.

Value

An MSPeakLists object.

Details

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.

References

Chambers, C. M, Maclean, Brendan, Burke, Robert, Amodei, Dario, Ruderman, L. D, Neumann, Steffen, Gatto, Laurent, Fischer, Bernd, Pratt, Brian, Egertson, Jarrett, Hoff, Katherine, Kessner, Darren, Tasman, Natalie, Shulman, Nicholas, Frewen, Barbara, Baker, A. T, Brusniak, Mi-Youn, Paulse, Christopher, Creasy, David, Flashner, Lisa, Kani, Kian, Moulding, Chris, Seymour, L. S, Nuwaysir, M. L, Lefebvre, Brent, Kuhlmann, Frank, Roark, Joe, Rainer, Paape, Detlev, Suckau, Hemenway, Tina, Huhmer, Andreas, Langridge, James, Connolly, Brian, Chadick, Trey, Holly, Krisztina, Eckels, Josh, Deutsch, W. E, Moritz, L. R, Katz, E. J, Agus, B. D, MacCoss, Michael, Tabb, L. D, Mallick, Parag (2012). “A cross-platform toolkit for mass spectrometry and proteomics.” Nat Biotech, 30(10), 918–920. doi:10.1038/nbt.2377 , http://dx.doi.org/10.1038/nbt.2377.

Keller A, Eng J, Zhang N, Li X, Aebersold R (2005). “A uniform proteomics MS/MS analysis platform utilizing open XML file formats.” Mol Syst Biol.

Kessner D, Chambers M, Burke R, Agus D, Mallick P (2008). “ProteoWizard: open source software for rapid proteomics tools development.” Bioinformatics, 24(21), 2534–2536. doi:10.1093/bioinformatics/btn323 .

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 P, Deutsch EW (2010). “mzML - a Community Standard for Mass Spectrometry Data.” Mol Cell Proteomics. doi:10.1074/mcp.R110.000133 .

Pedrioli PGA, 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 (2004). “A common open representation of mass spectrometry data and its application to proteomics research.” Nat Biotechnol, 22(11), 1459–1466. doi:10.1038/nbt1031 .