In rformassspectrometry/PSM: Handling and Managing Peptide Spectrum Matches

BiocStyle::markdown()

Package: r Biocpkg("PSMatch")
Authors: r packageDescription("PSMatch")[["Author"]]
Last modified: r file.info("Fragments.Rmd")$mtime
Compiled: r date()

library("PSMatch")

Introduction

This vignette is one among several illustrating how to use the PSMatch package, focusing on the calculation and visualisation of MS2 fragment ions. For a general overview of the package, see the PSMatch package manual page (?PSMatch) and references therein.

To illustrate this vignette, we will import and merge raw and identification data from the r Biocpkg("msdata"). For details about this section, please visit the Spectra package webpage.

Load the raw MS data:

(spf <- msdata::proteomics(pattern = "2014", full.names = TRUE))
library(Spectra)
sp <- Spectra(spf)

Load the identification data:

(idf <- msdata::ident(pattern = "2014", full.names = TRUE))
id <- PSM(idf) |> filterPSMs()
id

Merge both:

sp <- joinSpectraData(sp, id, by.x = "spectrumId", by.y = "spectrumID")
sp

In this example, we are going to focus the MS2 scan with index 5449 and its parent MS1 scan (index 5447, selected automatically with the filterPrecursorScan() function).

sp5449 <- filterPrecursorScan(sp, 5449)

plotSpectra(sp5449[1], xlim = c(550, 1200))
abline(v = precursorMz(sp5449)[2], col = "red", lty = "dotted")

Calculating fragment ions

The MS2 scan was matched to SQILQQAGTSVLSQANQVPQTVLSLLR (there was obviously no match the the MS1 scan):

sp5449$sequence

The calculateFragments() simply takes a peptide sequence as input and returns a data.frame with the fragment sequences, M/Z, ion type, charge and position.

calculateFragments(sp5449$sequence[2])

Visualising fragment ions

We can now visualise these fragments directly on the MS spectrum. Let's first visualise the spectrum as is:

plotSpectra(sp5449[2])

plotSpectra(sp5449[2], labels = addFragments, labelPos = 3)

Session information

sessionInfo()

rformassspectrometry/PSM documentation built on March 20, 2024, 9:16 a.m.