readChromatogram {rawrr}R Documentation

Extracts chromatographic data from a raw file.

Description

Extracts chromatographic data from a raw file.

Usage

readChromatogram(rawfile, mass = NULL, tol = 10, filter = "ms", type = "xic")

Arguments

rawfile

the file name.

mass

a vector of mass values iff type = 'xic'.

tol

mass tolerance in ppm iff type = 'xic'.

filter

defines the scan filter, default is filter="ms" if a wrong filter is set the function will return NULL and draws a warning.

type

c(xic, bpc, tic) for extracted ion , base peak or total ion chromatogram.

Details

Chromatograms come in different flavors but are always signal intensity values as a function of time. Signal intensities can be point estimates from scanning detectors or plain intensities from non-scanning detectors, e.g., UV trace. Scanning detector (mass analyzers) point estimates can be defined in different ways by, for instance, summing all signals of a given spectrum (total ion chromatogram or TIC), or by extracting signal around an expected value (extracted ion chromatogram = XIC), or by using the maximum signal contained in a spectrum (base peak chromatogram = BPC). On top, chromatograms can be computed from pre-filtered lists of scans. A total ion chromatogram (TIC), for instance, is typically generated by iterating over all MS1-level scans.

Value

chromatogram object(s) containing of a vector of times and a corresponding vector of intensities.

Author(s)

Christian Trachsel, Tobias Kockmann and Christian Panse <cp@fgz.ethz.ch> 2018, 2019, 2020.

References

Automated quality control sample 1 (autoQC01) analyzed across different Thermo Scientific mass spectrometers, MSV000086542.

See Also

Examples


# Example 1: not meaningful but proof-of-concept
(rawfile <- rawrr::sampleFilePath())

rawrr::readChromatogram(rawfile, mass=c(669.8381, 726.8357), tol=1000) |> plot()
rawrr::readChromatogram(rawfile, type='bpc') |> plot()
rawrr::readChromatogram(rawfile, type='tic') |> plot()

# Example 2: extract iRT peptides
 if (require(ExperimentHub) & require(protViz)){
iRTpeptide <- c("LGGNEQVTR", "YILAGVENSK", "GTFIIDPGGVIR", "GTFIIDPAAVIR",
  "GAGSSEPVTGLDAK", "TPVISGGPYEYR", "VEATFGVDESNAK",
  "TPVITGAPYEYR", "DGLDAASYYAPVR", "ADVTPADFSEWSK",
  "LFLQFGAQGSPFLK")


# fetch via ExperimentHub
library(ExperimentHub)
eh <- ExperimentHub::ExperimentHub()
EH4547 <- normalizePath(eh[["EH4547"]])

(rawfile <- paste0(EH4547, ".raw"))
if (!file.exists(rawfile)){
    file.link(EH4547, rawfile)
}
op <- par(mfrow=c(2,1))
readChromatogram(rawfile, type='bpc') |> plot()
readChromatogram(rawfile, type='tic') |> plot()
par(op)

# derive [2H+] ions
((protViz::parentIonMass(iRTpeptide) + 1.008) / 2) |>
   readChromatogram(rawfile=rawfile) |>
   plot()
}

[Package rawrr version 1.2.0 Index]