PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results

Mol Cell Proteomics. 2021:20:100018. doi: 10.1074/mcp.TIR120.002216. Epub 2020 Dec 11.


Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift that may correspond to a single modification or a combination of several modifications. Here we present PTM-Shepherd, a bioinformatics tool that automates characterization of post-translational modification profiles detected in open searches based on attributes, such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates. PTM-Shepherd can also perform multiexperiment comparisons for studying changes in modification profiles, e.g., in data generated in different laboratories or under different conditions. We demonstrate how PTM-Shepherd improves the analysis of data from formalin-fixed and paraffin-embedded samples, detects extreme underalkylation of cysteine in some data sets, discovers an artifactual modification introduced during peptide synthesis, and uncovers site-specific biases in sample preparation artifacts in a multicenter proteomics profiling study.

Keywords: Open searching, PTM, Post-translational modification, Mass-tolerant search, Localization, Spectral similarity, Retention time.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Databases, Protein
  • Humans
  • Mice
  • Peptides / chemistry*
  • Peptides / metabolism*
  • Protein Processing, Post-Translational*
  • Proteomics


  • Peptides