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TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data.

Miguel Cosenza-Contreras1,2, Adrianna Seredynska1,2, Daniel Vogele1,2,3

  • 1Faculty of Biology, University of Freiburg, Freiburg, Germany.

Proteomics
|August 10, 2024
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Summary
This summary is machine-generated.

TermineR enhances proteomic analysis by annotating peptide cleavage specificities and analyzing N-terminal patterns. This approach aids in understanding protein processing and proteolytic activity from mass spectrometry data.

Keywords:
data processingpolycystic kidney diseaseproteolysisterminomics

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Advanced mass spectrometry and bioinformatics enable identification of variable peptide features, including post-translational modifications, without biochemical enrichment.
  • Semi-specific proteome searches identify native protein termini and those from proteolytic activity (neo-N-termini analysis or N-terminomics).
  • Extracting biological insights from complex proteomic search outputs, particularly N-terminomics data, presents significant data mining and analysis challenges.

Purpose of the Study:

  • Introduce TermineR, a novel data analysis approach designed to address the challenges in mining and analyzing proteomic data, specifically for N-terminomics.
  • Enable comprehensive annotation of peptides based on enzymatic cleavage specificity and known protein processing.
  • Facilitate differential abundance and enrichment analysis of N-terminal sequence patterns and visualize neo-N-termini locations.

Main Methods:

  • TermineR provides annotation of peptides by enzymatic cleavage specificity and protein processing features.
  • The approach includes differential abundance and enrichment analysis of N-terminal sequence patterns.
  • TermineR offers visualization tools for the location of neo-N-termini.

Main Results:

  • TermineR was applied to tandem mass tag (TMT)-based proteomics data from a mouse model of polycystic kidney disease.
  • The study assessed semi-specific searches for biological interpretation of cleavage events.
  • The variable contribution of proteolytic products to overall protein abundance was evaluated.

Conclusions:

  • TermineR offers a robust framework for the analysis and interpretation of N-terminomics data derived from semi-specific proteome searches.
  • The approach facilitates a deeper understanding of protein processing, proteolytic activity, and their impact on protein abundance.
  • The TermineR R package is available for broader application in the research community.