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Related Concept Videos

Proteomics01:33

Proteomics

10.0K
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: Mar 7, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Toward an Optimized Workflow for Middle-Down Proteomics.

Alba Cristobal1,2, Fabio Marino1,2, Harm Post1,2

  • 1Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.

Analytical Chemistry
|February 25, 2017
PubMed
Summary
This summary is machine-generated.

Optimizing middle-down proteomics enhances the detection and sequence coverage of middle-range peptides. This refined approach improves proteome analysis, particularly for post-translational modifications.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biochemistry

Background:

  • Mass spectrometry (MS)-based proteomics is typically divided into bottom-up (peptides) and top-down (intact proteins) approaches.
  • Middle-down proteomics analyzes middle-range peptides (3.0–10 kDa) but requires workflow optimization.
  • Existing workflows need targeted improvements for efficient middle-range peptide analysis.

Purpose of the Study:

  • To optimize workflows for middle-down proteomics.
  • To enhance the detection and sequence coverage of middle-range peptides.
  • To improve the analysis of post-translational modifications.

Main Methods:

  • Explored proteases (Asp-N, Glu-C) and acid cleavage for generating middle-range peptides.
  • Utilized strong cation exchange (SCX) and reversed-phase liquid chromatography (RP-LC) with larger pore size columns for enhanced separation.
  • Assessed various MS settings and peptide fragmentation techniques (HCD, ETD, EThcD).

Main Results:

  • Optimized methods significantly improved the detection of middle-range peptides.
  • Enhanced sequence coverage was achieved for middle-range peptides.
  • The refined workflow demonstrated potential for improved proteome coverage.

Conclusions:

  • Targeted optimization of each module in middle-down proteomics is crucial.
  • The developed methods enhance the characterization of middle-range peptides.
  • This approach facilitates deeper proteome coverage and improved analysis of post-translational modifications.