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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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Updated: Oct 11, 2025

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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Collision Cross Sections for Native Proteomics: Challenges and Opportunities.

Brandon T Ruotolo1

  • 1Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.

Journal of Proteome Research
|November 30, 2021
PubMed
Summary
This summary is machine-generated.

New mass spectrometry (MS) and ion mobility (IM) technologies can help map protein structures and complexes. Collision cross section (CCS) values show promise for identifying intact proteins and their assemblies in native proteomics.

Keywords:
collision induced unfoldingion mobilityion mobility-mass spectrometrymultiprotein complexesnative mass spectrometryprotein identificationproteoformstructural biologystructural mass spectrometrystructural proteomics

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Area of Science:

  • Proteomics
  • Structural Biology
  • Biochemistry

Background:

  • Comprehensive protein analysis requires simultaneous measurement of composition and structure.
  • Mass spectrometry (MS) is a key tool for interrogating the structural proteome.
  • Native proteomics aims to capture endogenous protein assembly states.

Purpose of the Study:

  • To explore the utility of collision cross section (CCS) values for intact protein and complex identification in native proteomics.
  • To examine current evidence and technology trends in this area.
  • To assess the promise and limitations of CCS for multiprotein complex analysis.

Main Methods:

  • Review of current mass spectrometry (MS) and ion mobility (IM) technologies.
  • Analysis of collision cross section (CCS) data for protein identification.
  • Examination of native proteomics workflows and their integration with IM-MS.

Main Results:

  • Ion mobility (IM) separation provides rapid protein size information via collision cross section (CCS) values.
  • CCS values enhance confidence in protein identification from peptide mixtures in liquid chromatography-IM-MS.
  • The potential for CCS to identify intact proteins and complexes in native proteomics is under investigation.

Conclusions:

  • CCS values hold significant promise for advancing native proteomics and the analysis of multiprotein complexes.
  • Further technological development is needed to fully realize the potential of CCS in this field.
  • This approach offers a roadmap towards comprehensive protein catalogs for disease therapies.