Function to plot MS/MS spectra with PTMs

Source: R/plotSpectra-PTM.R

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,
  USI = TRUE,
  fixedModifications = NULL,
  variableModifications = NULL,
  addCarbamidomethyl = 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.

USI

logical(1L). If TRUE, the universal spectrum identifier is displayed.

fixedModifications

Named numeric or character, passed to PTMods::addFixedModifications(). Applied to all sequences before plotting. NULL by default (no fixed modifications applied).

variableModifications

Named numeric or character, passed to PTMods::addVariableModifications(). Each unique combination of variable modifications generates a separate copy of the corresponding spectrum. NULL by default (no variable modifications applied).

addCarbamidomethyl

logical(1L) set to TRUE by default. Applies carbamidomethylation as a fixed modification unless carbamidomethyl is already present in the given sequences. If carbamidomethylation should be applied as a variable modification, do set addCarbamidomethylation = FALSE. For more details on this, see the appropriate vignette by running `vignette("Fragments", package = "PSMatch")

...

additional parameters to be passed to the labelFragments() and calculateFragments() functions.

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 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 modifications using PTMods
sp_mod <- sp
sp_mod$sequence <- PTMods::addFixedModifications("SIGFEGDSIGR", fixedModifications = c(Nterm = "Acetyl"))
plotSpectraPTM(sp_mod)


## Or call them within the function directly:
plotSpectraPTM(sp, fixedModifications = NULL,
variableModifications = c(R = "Methyl"))
#> Warning: Dropping rownames: duplicated rownames present or rownames not available for all data.frames


## Annotate multiple spectra at a time
plotSpectraPTM(c(sp, sp))


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