Section 1 Isobaric Quantification: Proteomics

This pipeline shows how to process global proteomics TMT data with PlexedPiper. We will use data package 3442, which is “PlexedPiperTestData global”. In addition to PlexedPiper, we will also need MSnID (the basis for PlexedPiper) and PNNL.DMS.utils to interface with PNNL’s DMS.

## 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))
}
## ------------------------

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

The pipeline can be broken up into four major parts: prepare MS/MS identifications, prepare reporter ion intensities, create study design tables, and create a quantitative cross-tab. There is another step that is required for statistical testing, which is to create an MSnSet.