MZ delta Quality Control

The M/Z delta plot illustrates the suitability of MS2 spectra for identification by plotting the M/Z differences of the most intense peaks. The resulting histogram should optimally show modes at amino acid residu masses. The plots have been described in Foster et al. 2011.

Only a certain percentage of most intense MS2 peaks are taken into account to use the most significant signal. Default value is 20% (see percentage argument). The difference between peaks is then computed for all individual spectra and their distribution is plotted as a histogram. Delta M/Z between 40 and 200 are plotted by default, to encompass the residue masses of all amino acids and several common contaminants, although this can be changes with the mzRange argument.

In addition to the processing described above, isobaric reporter tag peaks and the precursor peak can also be removed from the MS2 spectrum, to avoid interence with the fragment peaks.

Note that figures in Foster et al. 2011 have been produced and optimised for centroided data. While running the function on profile mode is likely fine, it is recommended to use centroided data.

A ggplot2 based function called ggMzDeltaPlot() to visualise the M/Z delta distributions is available at https://gist.github.com/lgatto/c72b1ff5a4116118dbb34d9d2bc3470a.

Usage

computeMzDeltas(
  object,
  percentage = 0.2,
  mzRange = c(40, 200),
  BPPARAM = BiocParallel::bpparam()
)

plotMzDelta(x, aaLabels = TRUE)

Arguments

object

An instance of class Spectra().

percentage

numeric(1) between 0 and 1 indicating the percentage of the most intense peaks in each MS2 spectrum to include in the calculation. Default is 0.2.

mzRange

numeric(2) with the upper and lower M/Z to be used to the MZ deltas. Default is c(40, 200).

BPPARAM

An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation. Default is to use BiocParallel::bpparam(). See ?BiocParallel::bpparam for details.

x

A list of M/Z delta values, as returned by computeMzDeltas().

aaLabels

logical(1) defining whether the amino acids should be labelled on the histogram. Default is TRUE.

Value

computeMzDeltas() returns a list of numeric vectors. plotMzDelta() is used to visualise of M/Z delta distributions.

References

Foster JM, Degroeve S, Gatto L, Visser M, Wang R, Griss J, et al. A posteriori quality control for the curation and reuse of public proteomics data. Proteomics. 2011;11: 2182-2194. http://dx.doi.org/10.1002/pmic.201000602

Author

Laurent Gatto with contributions (to MSnbase) of Guangchuang Yu.

Examples

library(msdata)
f <- proteomics(pattern = "TMT.+20141210.mzML.gz", full.names = TRUE)
sp <- Spectra(f)

d <- computeMzDeltas(sp[1:1000])
plotMzDelta(d)