dataProcessing: Process mzXML files individually: peakpicking and isotope...
In LipidMS: Lipid Annotation for LC-MS/MS DDA or DIA Data

dataProcessing

R Documentation

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
)

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.

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.

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

Value

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

Author(s)

M Isabel Alcoriza-Balaguer <maialba@iislafe.es>

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)

## End(Not run)

LipidMS documentation built on March 18, 2022, 7:14 p.m.