plotSpectraPTM: Function to plot MS/MS spectra with PTMs

In rformassspectrometry/PSMatch: Handling and Managing Peptide Spectrum Matches

Function to plot MS/MS spectra with PTMs

Description

plotSpectraPTM() creates annotated visualisations of MS/MS spectra, designed to explore fragment identifications and post-translational modifications (PTMs).

plotSpectraPTM() plots a spectrum's m/z values on the x-axis and corresponding intensities on the y-axis, labeling the peaks according to theoretical fragment ions (e.g., b, y, a, c, x, z) computed using labelFragments() and calculateFragments().

Usage

plotSpectraPTM(
  x,
  deltaMz = TRUE,
  ppm = 20,
  xlab = "m/z",
  ylab = "intensity [%]",
  xlim = numeric(),
  ylim = numeric(),
  main = character(),
  col = c(y = "darkred", b = "darkblue", acxy = "darkgreen", other = "grey40"),
  labelCex = 1,
  labelSrt = 0,
  labelAdj = NULL,
  labelPos = 3,
  labelOffset = 0.5,
  asp = 1,
  minorTicks = TRUE,
  ...
)

Arguments

x	a Spectra() object.
deltaMz	logical(1L) If TRUE, adds an additional plot showing the difference of mass over charge between matched oberved and theoretical fragments in parts per million. Does not yet support modifications. The matching is based on calculateFragments() and needs a 'sequence' variable in spectraVariables(x). Default is set to TRUE.
ppm	integer(1L) Sets the limits of the delta m/z plot and is passed to labelFragments().
xlab	character(1) with the label for the x-axis (by default xlab = "m/z").
ylab	character(1) with the label for the y-axis (by default ylab = "intensity").
xlim	numeric(2) defining the x-axis limits. The range of m/z values are used by default.
ylim	numeric(2) defining the y-axis limits. The range of intensity values are used by default.
main	character(1) with the title for the plot. By default the spectrum's MS level and retention time (in seconds) is used.
col	Named character(4L). Colors for the labels, the character names need to be "b", "y", "acxz" and "other", respectively for the b-ions, y-ions, a,c,x,z-ions and the unidentified fragments.
labelCex	numeric(1) giving the amount by which the text should be magnified relative to the default. See parameter cex in par().
labelSrt	numeric(1) defining the rotation of the label. See parameter srt in text().
labelAdj	see parameter adj in text().
labelPos	see parameter pos in text().
labelOffset	see parameter offset in text().
asp	for plotSpectraPTM(), the target ratio (columns / rows) when plotting mutliple spectra (e.g. for 20 spectra use asp = 4/5 for 4 columns and 5 rows or asp = 5/4 for 5 columns and 4 rows; see grDevices::n2mfrow() for details). If deltaMz is TRUE, asp is ignored.
minorTicks	logical(1L). If TRUE, minor ticks are added to the plots. Default is set to TRUE.
...	additional parameters to be passed to the labelFragments() function.

Value

Creates a plot depicting an MS/MS-MS spectrum.

Author(s)

Johannes Rainer, Sebastian Gibb, Guillaume Deflandre, Laurent Gatto

See Also

Spectra::plotSpectra()

Examples

library("Spectra")

sp <- DataFrame(msLevel = 2L, rtime = 2345, sequence = "SIGFEGDSIGR")
sp$mz <- list(c(75.048614501953, 81.069030761719, 86.085876464844,
                88.039, 158.089569091797, 163.114898681641,
                173.128, 177.098587036133, 214.127075195312,
                232.137542724609, 233.140335083008, 259.938415527344,
                260.084167480469, 277.111572265625, 282.680786132812,
                284.079437255859, 291.208282470703, 315.422576904297,
                317.22509765625, 327.2060546875, 362.211944580078,
                402.235290527344, 433.255004882812, 534.258783,
                549.305236816406, 593.217041015625, 594.595092773438,
                609.848327636719, 631.819702148438, 632.324035644531,
                632.804931640625, 640.8193359375, 641.309936523438,
                641.82568359375, 678.357238769531, 679.346252441406,
                706.309623, 735.358947753906, 851.384033203125,
                880.414001464844, 881.40185546875, 906.396433105469,
                938.445861816406, 1022.56658935547, 1050.50415039062,
                1059.82800292969, 1107.52734375, 1138.521484375,
                1147.51538085938, 1226.056640625))
sp$intensity <- list(c(83143.03, 65473.8, 192735.53, 3649178.5,
                       379537.81, 89117.58, 922802.69, 61190.44,
                       281353.22, 2984798.75, 111935.03, 42512.57,
                       117443.59, 60773.67, 39108.15, 55350.43,
                       209952.97, 37001.18, 439515.53, 139584.47,
                       46842.71, 1015457.44, 419382.31, 63378.77,
                       444406.66, 58426.91, 46007.71, 58711.72,
                       80675.59, 312799.97, 134451.72, 151969.72,
                       1961975, 69405.76, 395735.62, 71002.98,
                       3215457.75, 136619.47, 166158.69, 682329.75,
                       239964.69, 242025.44, 1338597.62, 50118.02,
                       1708093.12, 43119.03, 97048.02, 2668231.75,
                       83310.2, 40705.72))
sp <- Spectra(sp)

## Annotate the spectum with the fragment labels
plotSpectraPTM(sp, main = "An example of an annotated plot")

## Annotate the spectrum without the delta m/z plot
plotSpectraPTM(sp, deltaMz = FALSE)

## Annotate the spectrum with different ion types
plotSpectraPTM(sp, type = c("a", "b", "x", "y"))

## Annotate the spectrum with variable modifications
plotSpectraPTM(sp, variable_modifications = c(R = 49.469))

## Annotate multiple spectra at a time
plotSpectraPTM(c(sp,sp), variable_modifications = c(R = 49.469))

## Color the peaks with different colors
plotSpectraPTM(sp, col = c(y = "red", b = "blue", acxy = "chartreuse3", other = "black"))

rformassspectrometry/PSMatch documentation built on June 1, 2025, 2:47 p.m.