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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 proteomics...

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Related Experiment Video

Updated: Jun 17, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Cross species proteomics.

J C Wright¹, R J Beynon, S J Hubbard

¹Department Veterinary Preclinical Sciences, University of Liverpool, Crown Street, Liverpool, UK.

Methods in Molecular Biology (Clifton, N.J.)

|December 17, 2009

Summary

This summary is machine-generated.

Cross-species proteomics identifies proteins without a sequenced genome by searching against related species' genomes. This approach faces challenges due to sequence differences impacting peptide mass matching, affecting protein identification success.

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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

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Last Updated: Jun 17, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Area of Science:

Proteomics
Genomics
Bioinformatics

Background:

Mass spectrometry-based proteomics relies on sequenced genomes for protein identification.
Lack of a sequenced genome necessitates cross-species proteomics, using related species' genomes.
Identifying proteins across species boundaries is challenging due to sequence variations.

Purpose of the Study:

To review the challenges and methods in cross-species proteomics.
To assess the success of various approaches in past studies.
To provide recommendations and predict future developments for cross-species proteomics.

Main Methods:

Review of existing literature on cross-species proteomics.
Analysis of factors influencing protein identification across species, including phylogenetic distance and protein conservation.
Discussion of different strategies employed to overcome identification challenges.

Main Results:

Cross-species proteomics is feasible but limited by sequence divergence, which complicates peptide mass matching.
Phylogenetic distance and protein conservation significantly impact the extent of successful protein identification.
Various approaches have been attempted with varying degrees of success.

Conclusions:

Cross-species proteomics requires careful consideration of sequence homology and phylogenetic distance.
Best practices and future technological advancements are crucial for improving protein identification across species.
This review offers guidance for researchers and predicts future improvements in the field.