PeptideSpectrum: Plot Annotated Peptide Fragmentation Mass Spectrum

Description

Identify the b- and y-ions or c- and z-ions in a peptide fragmentation mass spectrum given the sequence. Generate a plot and table identifying the fragment ions.

Usage

PeptideSpectrum(expt, theory, t = 0.4, b = 5, label = "", xlim = c(100, 1500), 
                supress = FALSE)

Arguments

expt

data frame containing the experimental MS/MS peak list with the m/z values in the first column and corresponding intensities in the second

theory

data frame of theoretical fragment ions generated by FragmentPeptide

numeric value specifying the m/z tolerance for matching theoretical fragment ions to experimental peaks

numeric value specifying the baseline threshold for peak identification. Expressed as a percent of the maximum intensity.

label

character string to label the spectrum.

xlim

numeric vector of length 2, defining the beginning and ending values of the x-axis.

supress

logical specifying whether or not to supress the peak annotations.

Value

Generates an annotated spectrum and a data frame showing the matches between the experimental peaks and the theoretical fragment ions. The column names refer to the experimental m/z value (expt_mz), the experimental peak intensity (expt_int) and the error between the experimental and theoretical m/z values (error). The other column names are the same as for FragmentPeptide.

Details

A graphics window of width = 10 and height = 5.5 seems to work well. A crude attempt is made to prevent overlapping peak annotations. If this is unsuccessful, use supress = TRUE and then add the annotations using the text function. If two or more peak identifications are made within the set tolerance, all identifications will be printed, overlapping, on the plot.

Examples

Run this code

## plot spectrum of peptide NIDALSGMEGR
t <- FragmentPeptide("NIDALSGMEGR")   # generate theoretical fragment ions
dev.new(width = 10, height = 5.5)
PeptideSpectrum(example.spectrum.peptide, t, label = "CID", xlim = c(100, 1200))
mtext("Peptide fragmentation mass spectrum", line = 1)