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Updated: Sep 22, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
MaxQuant Module for the Identification of Genomic Variants Propagated into Peptides
Pavel Sinitcyn1, Maximilian Gerwien1, Jürgen Cox2
1Computational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany.
Abstract:
Standard shotgun proteomics data analysis pipelines usually only identify peptides that are encoded in the reference genome. In many situations, it is desirable to identify peptides resulting from non-synonymous variations as well. Here, we present a new module in the MaxQuant software that takes both DNA and RNA based next-generation sequencing (NGS) data as well as raw proteomics data as input. This allows for the identification of variant peptides that are otherwise missed.

