Section 2 Isobaric Quantification: Phosphoproteomics

This pipeline shows how to process phosphoproteomics TMT data with PlexedPiper, though it can be used for any type of post-translational modification (PTM) TMT data. We will use data package 3626, which is “PlexedPiperTestData phospho”. In addition to PlexedPiper, we will also need MSnID (the basis for PlexedPiper), PNNL.DMS.utils to interface with PNNL’s DMS, and Biostrings to create an AAStringSet object from a FASTA file. Since a lot of these steps are the same as in Section 1, a lot of the details will be omitted.

## Install missing packages
if (!require("remotes", quietly = T)) install.packages("remotes")
git_packages <- c("MSnID@pnnl-master", "PlexedPiper", "PNNL.DMS.utils")
for (pkg_i in git_packages) {
  if (!require(sub("@.*", "", pkg_i), quietly = T, character.only = T))
    remotes::install_github(file.path("PNNL-Comp-Mass-Spec", pkg_i))
}
if (!requireNamespace("BiocManager", quietly = T))
  install.packages("BiocManager")
if (!require("Biostrings", quietly = T))
  BiocManager::install("Biostrings")
## ------------------------

library(MSnID)
library(PlexedPiper)
library(PNNL.DMS.utils)
library(Biostrings)