Section 1 Isobaric Quantification Pipeline: Global Proteomics

This pipeline shows how to process TMT data that is processed outside of PNNL’s DMS. Section ?? shows how to process data from the DMS. For convenience, the results of MS-GF+ and MASIC processing are provided in a companion PlexedPiperTestData package. In addition, we will need PlexedPiper for isobaric quantification and dplyr to manipulate data frames.

# Setup
library(PlexedPiper)
library(PlexedPiperTestData)
library(dplyr)

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.