MSstatsWeightedSummary: Weighted Protein-Level Summarization for Protein Clusters

Protein-level summarization of feature (PSM)-level data is an important step in proteomics data analysis methods, including the MSstats workflow. MSstats and MSstatsTMT packages summarize features based on unique peptides. This package implements a statistical method to jointly summarize clusters of proteins that share features using weights specific to peptide-protein matches.

Installation:

if (!require(devtools)) {
    install.packages("devtools")
}
devtools::install_github("Vitek-Lab/MSstatsWeightedSummary")

Getting help:

Vignette online

?getWeightedProteinSummary
?normalizeSharedPeptides
?addClusterMembership
vignette(package = "MSstatsWeightedSummary")

Major functionalities:

• normalizeSharedPeptides: feature-level data MSstatsTMT normalization that accounts for shared peptides
• addClusterMembership: identification of clusters of proteins that share peptides (connected components of peptide-protein graph)
• getWeightedSummary: protein-level summarization of feature-level data. Performed separately for each cluster of proteins and each run. Input and output compatible with MSstatsTMT workflow for analysis of mass spectrometry proteomics data with isobaric labeling.

How to cite

This package implements a statistical model introduced in the article Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach. The bibtex entry can be found by calling:

citation(package = "MSstatsWeightedSummary")