LipidMS (version 2.1.2)

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,
  acquisitionmode,
  polarity,
  dmzagglom = 10,
  drtagglom = 500,
  drtclust = 100,
  minpeak = c(5, 3),
  drtgap = 10,
  drtminpeak = 20,
  drtmaxpeak = 100,
  recurs = 5,
  sb = c(3, 2),
  sn = 2,
  minint = c(1000, 100),
  weight = c(2, 3),
  dmzIso = 10,
  drtIso = 5
)

Arguments

file

path of the mzXML input file.

acquisitionmode

character value: DIA or DDA (acquisition mode).

polarity

character value: negative or positive.

dmzagglom

m/z tolerance (in ppm) used for partitioning and clustering. 10 by default.

drtagglom

rt window used for partitioning (in seconds). 500 by default.

drtclust

rt window used for clustering (in seconds). 100 by default.

minpeak

minimum number of measurements required for a peak. By default, 5 for MS1 and 4 for MS2.

drtgap

maximum RT gap length to be filled (in seconds). 5 by default.

drtminpeak

minimum RT width of a peak (in seconds). 20 by default. At least minpeak within the drtminpeak window are required to define a peak.

drtmaxpeak

maximum RT width of a single peak (in seconds). 100 by default.

recurs

maximum number of peaks within one EIC. 5 by default.

sb

signal-to-base ratio. By default, 3 for MS1 and 2 for MS2.

sn

signal-to-noise ratio. 2 by default.

minint

minimum intensity of a peak. By default, 1000 for MS1 and 100 for MS2.

weight

weight for assigning measurements to a peak. Optional. By default, 2 for MS1 and 3 for MS2.

dmzIso

numeric. Mass tolerance for isotope matching. 10 by default.

drtIso

numeric. Time windows for isotope matching. 5 by default.

Value

a msobject that contains metadata of the mzXML file, raw data and extracted peaks.

Details

This function executes 2 steps: 1) peak-picking based on enviPick package and 2) isotope annotation.

References

Peak-picking algorithm has been imported from enviPick R-package: https://cran.r-project.org/web/packages/enviPick/index.html

Examples

# NOT RUN {
msobject <- dataProcessing("input_file.mzXML", acquisitionmode="DIA", polarity,
dmzagglom = 25, drtagglom = 500, drtclust = 60, minpeak = c(5, 3),
drtgap = 5, drtminpeak = 20, drtmaxpeak = 100, recurs = 5, sb = c(3, 2),
sn = 2, minint = c(1000, 100), weight = 2, dmzIso = 10, drtIso = 5)
# }
# NOT RUN {
# }