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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Proteomics01:33

Proteomics

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 proteomics...

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Related Experiment Video

Updated: May 12, 2026

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin
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CLIPPER 2.0: Peptide-Level Annotation and Data Analysis for Positional Proteomics.

Konstantinos Kalogeropoulos1, Aleksander Moldt Haack1, Elizabeta Madzharova1

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

Molecular & Cellular Proteomics : MCP
|May 4, 2024
PubMed
Summary
This summary is machine-generated.

CLIPPER 2.0 is a new computational tool that streamlines data analysis for positional proteomics, accelerating the study of protease signaling and substrate cleavage. This tool enhances the interpretation of large mass spectrometry datasets.

Keywords:
LC-MScomputational proteomicsdegradomicspositional proteomicspost-translational modification

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Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Positional proteomics, utilizing mass spectrometry (MS)-based degradomics, is crucial for protease research and signaling pathway analysis.
  • Advancements in liquid chromatography (LC)-MS/MS instrumentation generate vast datasets of protein termini and neo-termini.
  • Data analysis and post-processing remain a significant bottleneck in positional proteomics workflows.

Purpose of the Study:

  • To introduce CLIPPER 2.0, a computational tool designed to facilitate peptide-level annotation and data analysis in positional proteomics.
  • To address the bottleneck in analyzing large-scale terminomic datasets generated by MS-based methods.

Main Methods:

  • CLIPPER 2.0 builds upon existing algorithms for MS-based protein termini analysis.
  • The tool supports various sample preparation workflows and proteomics search algorithms.
  • It enables automated database retrieval, statistical analysis, network analysis, and visualization of terminomic data.

Main Results:

  • CLIPPER 2.0 facilitates fast and automated analysis of positional proteomics data.
  • The tool was successfully applied to analyze GluC and MMP9 cleavages in HeLa cell lysates.
  • Demonstrated applicability in analyzing complex terminomic datasets.

Conclusions:

  • CLIPPER 2.0 significantly enhances the data analysis capabilities for positional proteomics.
  • The tool provides a comprehensive solution for processing and interpreting terminomic datasets, advancing protease research.
  • CLIPPER 2.0 is publicly available, promoting wider adoption and further development in the field.