Function to plot MS/MS spectra with PTMs

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().

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 each spectrum. By default NULL, if variable modifications are used, the same title is applied on all plots originating from a common spectrum.
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 plotSpectra(), 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

Johannes Rainer, Sebastian Gibb, Guillaume Deflandre, Laurent Gatto

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 a 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 = 490469))


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

Arguments

Value

See also

Author

Examples