removeReporters-methods: Removes reporter ion tag peaks

In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Description

This methods sets all the reporter tag ion peaks from one MS2 spectrum or all the MS2 spectra of an experiment to 0. Reporter data is specified using an "ReporterIons" instance. The peaks are selected around the expected reporter ion m/z value +/- the reporter width. Optionally, the spectrum/spectra can be cleaned to remove successive 0 intensity data points (see the clean function for details).

Note that this method only works for MS2 spectra or experiments that contain MS2 spectra. It will fail for MS1 spectrum.

Methods

signature(object = "MSnExp", reporters = "ReporterIons", clean = "logical", verbose = "logical" )

The reporter ion peaks defined in the reporters instance of all the MS2 spectra of the "MSnExp" instance are set to 0 and, if clean is set to TRUE, cleaned. The default value of reporters is NULL, which leaves the spectra as unchanged. The verbose parameter (default is TRUE) defines whether a progress bar should be showed.

signature(object = "Spectrum", reporters = "ReporterIons", clean = "FALSE")

The reporter ion peaks defined in the reporters instance of MS2 "Spectrum" instance are set to 0 and, if clean is set to TRUE, cleaned. The default value of reporters is NULL, which leaves the spectrum as unchanged.

Author(s)

Laurent Gatto <[e-mail]>

See Also

clean and removePeaks for other spectra processing methods.

Examples

sp1 <- itraqdata[[1]]
sp2 <- removeReporters(sp1,reporters=iTRAQ4)
sel <- mz(sp1) > 114 & mz(sp1) < 114.2
mz(sp1)[sel]
intensity(sp1)[sel]
plot(sp1,full=TRUE,reporters=iTRAQ4)
intensity(sp2)[sel]
plot(sp2,full=TRUE,reporters=iTRAQ4)

MSnbase documentation built on Jan. 23, 2021, 2 a.m.