Pep2Graph: A standalone tool to analyse proteolytic cleavages by proteases from gel-based mass spectrometry data

Proteomics. 2022 Nov;22(22):e2200147. doi: 10.1002/pmic.202200147. Epub 2022 Aug 21.


Proteases are enzymes that regulate substrates via proteolytic activation and coordinate essential cellular functions including DNA replication, DNA transcription, cell proliferation, differentiation, migration and apoptosis. However, techniques to identify proteolytic events in a high-throughput manner is limited. PROtein TOpography and Migration Analysis Platform (PROTOMAP) is a technique that relies on mass spectrometry-based proteomics to globally identify the shifts in the in-gel migration of proteins and their corresponding fragments that are obtained by proteolysis. However, user-friendly software tool to analyse the proteomic data to identify proteolytic events is needed. Here, we report Pep2Graph, a user-friendly standalone tool that integrates peptide sequence information from in-gel proteomics and presents the data as two-dimensional peptographs with in-gel migration, sequence coverage and MS/MS spectra counts. Pep2Graph ( allows users to utilize in-gel proteomics data to study proteolytic events that may play a significant role in normal physiology and pathology.

Keywords: PROTOMAP; peptides; peptograph; proteases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Endopeptidases / metabolism
  • Peptide Hydrolases* / metabolism
  • Proteins / metabolism
  • Proteolysis
  • Proteomics* / methods
  • Tandem Mass Spectrometry / methods


  • Peptide Hydrolases
  • Proteins
  • Endopeptidases