Removes reporter ion tag peaks

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

Laurent Gatto <lg390@cam.ac.uk>

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]
#>  [1] 114.0956 114.0975 114.0993 114.1012 114.1030 114.1049 114.1067 114.1085
#>  [9] 114.1104 114.1122 114.1141 114.1159 114.1178 114.1196 114.1214 114.1233
#> [17] 114.1251
intensity(sp1)[sel]
#>  [1]      0.0000      0.0000      0.0000      0.0000   1640.2427  25143.0898
#>  [7]  87905.3906 164363.5156 197455.8125 158061.2812  79058.3672  17596.0898
#> [13]    346.5309      0.0000      0.0000      0.0000      0.0000
plot(sp1,full=TRUE,reporters=iTRAQ4)
intensity(sp2)[sel]
#>  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plot(sp2,full=TRUE,reporters=iTRAQ4)