LipidMS (version 3.0.4)

dataProcessing: Process mzXML files individually: peakpicking and isotope annotation

Description

Process mzXML files individually: peakpicking and isotope anotation

Usage

dataProcessing(
  file,
  acquisitionmode,
  polarity,
  dmzagglom = 15,
  drtagglom = 500,
  drtclust = 100,
  minpeak = c(5, 3),
  drtgap = 10,
  drtminpeak = c(15, 15),
  drtmaxpeak = c(100, 200),
  recurs = 5,
  sb = c(3, 2),
  sn = 2,
  minint = c(1000, 100),
  weight = c(2, 3),
  dmzIso = 5,
  drtIso = 5,
  verbose = TRUE
)

Value

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

Arguments

file

file path.

acquisitionmode

character value: MS, DIA or DDA.

polarity

character value: negative or positive.

dmzagglom

mz tolerance (in ppm) used for partitioning and clustering.

drtagglom

RT window used for partitioning (in seconds).

drtclust

RT window used for clustering (in seconds).

minpeak

minimum number of measurements required for a peak.

drtgap

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

drtminpeak

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

drtmaxpeak

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

recurs

maximum number of peaks within one EIC.

sb

signal-to-base ratio.

sn

signal-to-noise ratio.

minint

minimum intensity of a peak.

weight

weight for assigning measurements to a peak.

dmzIso

mass tolerance for isotope matching.

drtIso

time window for isotope matching.

verbose

print information messages.

Author

M Isabel Alcoriza-Balaguer <[e-mail]>

Details

It is important that mzXML files are centroided.

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

Numeric arguments accept one or two values for MS1 and MS2, respectively.

References

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

Isotope annotation has been adapted from CAMERA algorithm: Kuhl C, Tautenhahn R, Boettcher C, Larson TR, Neumann S (2012). “CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets.” Analytical Chemistry, 84, 283–289. http://pubs.acs.org/doi/abs/10.1021/ac202450g.

See Also

batchdataProcessing and setmsbatch

Examples

if (FALSE) {
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)
}