Process mzXML files: peak-picking using enviPick and deisotoping using CAMERA.
dataProcessing(file, mslevel, polarity, dmzgap = 50, drtgap = 25,
ppm = TRUE, minpeak, maxint = 1e+09, dmzdens, drtdens = 20,
merged = FALSE, drtsmall, drtfill = 5, drttotal = 100,
recurs = 4, weight, SB, SN = 2, minint, ended = 2,
removeIsotopes = TRUE)path of the mzXML input file.
numeric value indicating if data belongs to level 1 (fullMS) or level 2 (MS/MS).
character value: negative or positive.
enviPick parameter. 50 by default.
enviPick parameter. 25 by default.
logical value. TRUE if dmzdens was set in ppm and FALSE if it was in as an absolute value. TRUE by default.
minimum number of measurements required within the RT window of drtsmall. Optional. By default, 5 when mslevel = 1 and 4 when mslevel = 2.
EIC cluster with measurements above this intensity are kept, even if they do not fulfill minpeak. 1E9 by default.
maximum measurement deviation (+/-) of m/z from its mean within each EIC. Optional. By default, 15 when mslevel = 1 and 30 when mslevel = 2.
RT tolerance for clustering. Optional. 20 by default.
merge EIC cluster of comparable m/z. Logical. FALSE by default.
peak definition - RT window of a peak. Optional. By default, 100 when mslevel = 1 and 30 when mslevel = 2.
maximum RT gap length to be filled. 5 by default.
maximum RT length of a single peak. 100 by default.
maximum number of peaks within one EIC. 3 by default.
weight for assigning measurements to a peak. Optional. By default, 1 when mslevel = 1 and 2 when mslevel = 2.
signal-to-base ratio. Optional. By default, 3 when mslevel = 1 and 2 when mslevel = 2.
signal-to-noise ratio. 2 by default.
minimum intensity of a peakr. Optional. By default, 1000 when mslevel = 1 and 100 when mslevel = 2.
within the peak detection recursion set by argument recurs, how often can a peak detection fail to end the recursion?. 2 by default.
logical. If TRUE, only isotopes identified as M+0, are kept when mslevel = 1, and M+0 or unknown when mslevel = 2. TRUE by default. If FALSE, an additional column is added to the peak list to inform about isotopes.
List with two data frames: peaklist, with 4 columns (m.z, RT, int, and peakID) and rawScan, with all the scans information in 5 columns (m.z, RT, int, peakID and Scan). PeakID columns links both data frames: extracted peaks and raw data. The Scan column indicates the scan number (order) to which each row of the rawScans data frame belong.
This function executes 2 steps: 1) peak-picking using enviPick package and 2) it seaches isotopes using CAMERA. If mslevel = 1 and remove isotopes is set as TRUE, only ions with more than 1 isotope are kept.
https://cran.r-project.org/web/packages/enviPick/index.html
Kuhl C, Tautenhahn R, Boettcher C, Larson TR ans Neumann S (2012). "CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography-mass spectrometry data sets." Analytical Chemistry, 84, pp. 283-289. htto://pubs.acs.org/doi/abs/10.1021/ac202450g.
# NOT RUN {
dataProcessing("input_file.mzXML", mslevel = 1, polarity = "positive")
# }
# NOT RUN {
# }
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