LipidMS (version 1.1.0)

dataProcessing: Process mzXML files: peakpicking and deisotoping

Description

Process mzXML files: peak-picking using enviPick and deisotoping using an adaptation of the CAMERA algorithm.

Usage

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, rttolIso = 2, ppmIso = 20)

Arguments

file

path of the mzXML input file.

mslevel

numeric value indicating if data belongs to level 1 (fullMS) or level 2 (MS/MS).

polarity

character value: negative or positive.

dmzgap

enviPick parameter. 50 by default.

drtgap

enviPick parameter. 25 by default.

ppm

logical value. TRUE if dmzdens was set in ppm and FALSE if it was in as an absolute value. TRUE by default.

minpeak

minimum number of measurements required within the RT window of drtsmall. Optional. By default, 5 when mslevel = 1 and 4 when mslevel = 2.

maxint

EIC cluster with measurements above this intensity are kept, even if they do not fulfill minpeak. 1E9 by default.

dmzdens

maximum measurement deviation (+/-) of m/z from its mean within each EIC. Optional. By default, 15 when mslevel = 1 and 30 when mslevel = 2.

drtdens

RT tolerance for clustering. Optional. 20 by default.

merged

merge EIC cluster of comparable m/z. Logical. FALSE by default.

drtsmall

peak definition - RT window of a peak. Optional. By default, 100 when mslevel = 1 and 30 when mslevel = 2.

drtfill

maximum RT gap length to be filled. 5 by default.

drttotal

maximum RT length of a single peak. 100 by default.

recurs

maximum number of peaks within one EIC. 3 by default.

weight

weight for assigning measurements to a peak. Optional. By default, 1 when mslevel = 1 and 2 when mslevel = 2.

SB

signal-to-base ratio. Optional. By default, 3 when mslevel = 1 and 2 when mslevel = 2.

SN

signal-to-noise ratio. 2 by default.

minint

minimum intensity of a peakr. Optional. By default, 1000 when mslevel = 1 and 100 when mslevel = 2.

ended

within the peak detection recursion set by argument recurs, how often can a peak detection fail to end the recursion?. 2 by default.

removeIsotopes

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.

rttolIso

numeric. Time windows for isotope matching.

ppmIso

numeric. Mass tolerance for isotope matching.

Value

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.

Details

This function executes 2 steps: 1) peak-picking using enviPick package and 2) it searches isotopes using an adaptation of the CAMERA algorithm. If mslevel = 1 and remove isotopes is set as TRUE, only ions with more than 1 isotope are kept.

References

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.

Examples

# NOT RUN {
dataProcessing("input_file.mzXML", mslevel = 1, polarity = "positive")
# }
# NOT RUN {
# }