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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

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Data Processing and Analysis in Positional Proteomics.

Aleksander Moldt Haack1, Konstantinos Kalogeropoulos1,2,3

  • 1Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.

Proteomics
|November 3, 2025
PubMed
Summary
This summary is machine-generated.

Positional proteomics reveals proteolytic cleavage sites, crucial for understanding disease biomarkers and therapeutic targets. This review details data analysis strategies for studying protein termini and post-translational modifications.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Proteomics
  • Post-Translational Modifications

Background:

  • Proteolytic cleavage is an irreversible post-translational modification (PTM) vital for cellular function.
  • Dysregulated protease activity is linked to disease, altering protein function and creating biomarkers.
  • Positional proteomics offers tools to study natural and neo-protein termini, but faces experimental and data processing challenges.

Purpose of the Study:

  • To review key data analysis and processing strategies for positional proteomics.
  • To highlight differences between positional proteomics and standard proteomics data analysis.
  • To discuss terminomics workflows, labeling strategies, acquisition methods, and normalization approaches.

Main Methods:

  • Comparative analysis of N-terminomics and C-terminomics workflows.
  • Discussion of various labeling strategies and mass spectrometry acquisition methods.
  • Emphasis on normalization strategies, including relative to protein and protease abundance.

Main Results:

  • Identification and quantification of proteolytic cleavage sites require specialized data analysis pipelines.
  • Normalization of cleavage site abundances relative to protein and protease levels is critical.
  • Integration of structural data, solvent accessibility, and tissue expression enhances biological interpretation.

Conclusions:

  • Positional proteomics provides critical insights into proteolysis and its role in disease.
  • Standard proteomics pipelines are insufficient for analyzing cleavage site data.
  • Advanced data analysis integrating multiple data types is essential for biological significance.