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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.
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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Related Experiment Video

Updated: Apr 19, 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

Computational phosphoproteomics: from identification to localization.

Dave C H Lee¹, Andrew R Jones, Simon J Hubbard

¹Faculty of Life Sciences, University of Manchester, Manchester, UK.

|December 6, 2014

Summary

This summary is machine-generated.

Phosphoproteomic analysis using mass spectrometry (MS) is crucial for understanding cell regulation. New bioinformatics tools help identify and pinpoint phosphorylation sites on peptides, overcoming interpretation challenges.

Keywords:

Bioinformatics Data processing and analysis Phosphoproteomics Technology

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Last Updated: Apr 19, 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

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Published on: April 29, 2022

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Area of Science:

Biochemistry
Proteomics
Bioinformatics

Background:

Mass spectrometry (MS)-based phosphoproteomics is vital for studying dynamic cellular regulation.
Kinase and phosphatase activity are central to many biological processes.
Identifying phosphopeptides is challenging due to complex mass spectrometry spectra.

Purpose of the Study:

To review the challenges in phosphoproteomic data analysis.
To highlight available informatics solutions for phosphopeptide identification and localization.
To discuss the difficulties in using these tools and implications for data standards.

Main Methods:

Review of existing literature and software tools for phosphoproteomic analysis.
Discussion of bioinformatics approaches for phosphopeptide identification.
Examination of methods for phosphosite localization.

Main Results:

Phosphorylation analysis presents significant informatic challenges, complicating peptide identification.
Novel software and pipelines have been developed to address these challenges.
Ambiguity in modification site localization remains a key issue.

Conclusions:

Effective bioinformatics tools are essential for advancing phosphoproteomic research.
Standardization of data and methods is needed for reliable phosphoproteomic analysis.
Overcoming analytical hurdles is critical for understanding cellular signaling pathways.