readChromatogram: Extracts chromatographic data from a raw file.

In fgcz/rawrr: Direct Access to Orbitrap Data and Beyond

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",
  tmpdir = tempdir()
)

Arguments

rawfile	the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.
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.
tmpdir	defines the directory used to store temporary data generated by the .NET assembly rawrr.exe. The default uses the output of tempdir().

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 <[e-mail]> 2018, 2019, 2020.

References

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

See Also

• The Thermo Fisher Scientific RawFileReader C# code snippets https://planetorbitrap.com/rawfilereader.

• https://CRAN.R-project.org/package=protViz

• https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000086542

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()
}

fgcz/rawrr documentation built on Dec. 8, 2024, 2:10 a.m.