compMS2Construct: Constructor for compMS2 class object from a peak table and...

In WMBEdmands/compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

Description

Matches MS1 features to MS2 spectra (.mzXML/.mzML/.mgf) files based on a mass-to-charge and retention time tolerance. Composite spectra and other data can subsequently be visualized during any stage of the compMS2Miner processing workflow. Composite spectra can be denoised, ion signals grouped and summed, substructure groups identified, common Phase II metabolites predicted and features matched to data bases monoisotopic mass data and insilico MS2 fragmentation data. The resulting data can then be readily curated by sending to a local or online couchDB database.

Usage

compMS2Construct(MS1features = NULL, msDataDir = NULL, MS2files = NULL,
  nCores = NULL, argsCorrNetwork = list(obsNames = NULL, corrThresh = 0.6,
  corrMethod = "spearman", delta = 0.05, MTC = "BH"), mode = "pos",
  precursorPpm = 10, ret = 10, TICfilter = 10000, minPeaks = 1,
  isoWid = 4, verbose = TRUE)

Arguments

MS1features	either a data.frame, full file path as a character string to a .csv file of a MS1 feature table in the form observation (samples) in columns and variables (Mass spectral signals) in rows, the first 3 columns must consist of: EIC number or unique peak identifier. mass-to-charge ratio of peak group. median/ peak apex retention time in seconds. optionally the 4th column of the MS1feature table may contain any adducts and isotopes identified by for example the CAMERA R package. If this column is present the adducts will be incorporated in to the compMS2 class object and used to guide the subsequent metID.dbAnnotate function. This can be very useful for narrowing possible annotations in subsequent stages of the compMS2miner workflow and particularly in reduction of false positives annotations. The adduct annotations must consist of the following notation style for example [M-H]-, [2M+2CH3OH]2-, [M-H+C2H4O2+Na]-. Abbreviations such as Hac (CH3COOH) for acetic acid and ACN (i.e. C2H3N) for acetonitrile are not acceptable formulae must be used to determine the correct elemental composition must be included. As is typical of the output of CAMERA for example multiple possible adducts can appear for the same feature where they have shared/similar expected masses. If argument is not supplied a GUI (tcltk) file selection window will open and a .csv file can then be selected.
msDataDir	character full path to a directory containing LC-MS/MS data files in either the open framework .mzXML or newer .mzML file types also mascot generic format files (.mgf). If argument is not supplied a GUI (tcltk) file selection window will open and the directory can be selected.
MS2files	character vector of full paths to ms2 files (either .mzML, .mzXML or .mgf). Alternative to choosing the directory. In this way particular files within a directory or files from multiple directory locations can be specified.
nCores	numeric Number of cores for parallel computation.
mode	character Ionisation polarity must be either 'pos' or 'neg'.
precursorPpm	numeric Parts per million mass accuracy to match MS1 features to MS2 spectra (ppm)
ret	numeric retention time tolerance to match MS1 features to MS2 spectra (+/- seconds).
TICfilter	numeric Minimum Total Ion Current to consider an MS2 spectrum. Any MS2 scan below this threshold will not be considered.
isoWid	numeric isolation width of DDA precursor ions, utilized to identify potentially chimeric spectra.
verbose	logical if TRUE display progress bars.
minPeaks.	minimum number of fragment ions for a spectrum to be considered (default = 1).

Value

A compMS2 object

WMBEdmands/compMS2Miner documentation built on May 9, 2019, 10:04 p.m.