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Proteomics

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.
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Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...

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Updated: Jan 1, 2026

Phosphopeptide Enrichment Coupled with Label-free Quantitative Mass Spectrometry to Investigate the Phosphoproteome in Prostate Cancer

Phosphopeptide Enrichment Coupled with Label-free Quantitative Mass Spectrometry to Investigate the Phosphoproteome in Prostate Cancer

Published on: August 2, 2018

Targeting proline in (phospho)proteomics.

Saar A M van der Laarse^1,2, Charlotte A G H van Gelder^1,2, Marshall Bern³

¹Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.

The FEBS Journal

|December 22, 2019

Summary

This summary is machine-generated.

EndoPro protease enhances proteome and phosphoproteome coverage in mass spectrometry experiments. This novel protease offers distinct and complementary results to trypsin, improving peptide identification and post-translational modification site detection.

Keywords:

(phospho)proteomics EndoPro mass spectrometry proline effect protease

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Published on: February 22, 2014

Area of Science:

Proteomics and Phosphoproteomics
Mass Spectrometry
Enzymology

Background:

Trypsin is the standard protease in mass spectrometry-based proteomics but has limitations in covering the full proteome.
Alternative proteases increase detectable proteome and phosphoproteome coverage.
Proline-directed phosphorylations are common in mammals, suggesting a need for proteases active at proline residues.

Purpose of the Study:

To evaluate the performance of the protease EndoPro for mass spectrometry-based proteomics and phosphoproteomics.
To compare EndoPro's proteome and phosphoproteome coverage with trypsin.
To explore EndoPro's activity and specificity across different pH conditions.

Main Methods:

Proteolytic digestion using EndoPro at pH 2 and 5.5.
Peptide identification using multiple fragmentation techniques (HCD, ETD, EThcD) and Byonic search algorithm.
Analysis of phosphoproteome coverage to assess performance in phosphoproteomics.

Main Results:

EndoPro achieves approximately 40% MS2 spectra identification, complementary to trypsin's 66%.
EndoPro exhibits high specificity for C-terminal Pro and Ala residues and broad pH activity.
EndoPro significantly extends phosphoproteome coverage, with distinct and complementary results at different pH values compared to trypsin.

Conclusions:

EndoPro is a valuable tool for expanding proteome and phosphoproteome coverage in mass spectrometry.
Using EndoPro alongside trypsin provides more comprehensive proteomic data.
EndoPro's distinct cleavage specificity and pH activity profile make it a powerful addition to proteomics workflows.