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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: Sep 9, 2025

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

MRMAssayDB: a comprehensive integrated resource for targeted proteomics assays.

Yassene Mohammed^1,2,3, Pallab Bhowmick³, Christoph H Borchers^1,3,4,5,6

¹Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.

Expert Review of Proteomics

|September 3, 2025

Summary

MRMAssayDB consolidates targeted proteomics assay data, simplifying protein quantification. This integrated platform enhances access to validated peptides and transition data for researchers, streamlining assay selection and panel building.

Keywords:

Absolute quantitation FDA assays assay design data repository knowledgebase multiplexing proteotypic peptide suitability targeted assays

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Quantitative Proteomics Workflow using Multiple Reaction Monitoring Based Detection of Proteins from Human Brain Tissue

Quantitative Proteomics Workflow using Multiple Reaction Monitoring Based Detection of Proteins from Human Brain Tissue

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Last Updated: Sep 9, 2025

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

An HS-MRM Assay for the Quantification of Host-cell Proteins in Protein Biopharmaceuticals by Liquid Chromatography Ion Mobility QTOF Mass Spectrometry

An HS-MRM Assay for the Quantification of Host-cell Proteins in Protein Biopharmaceuticals by Liquid Chromatography Ion Mobility QTOF Mass Spectrometry

Published on: April 17, 2018

Quantitative Proteomics Workflow using Multiple Reaction Monitoring Based Detection of Proteins from Human Brain Tissue

Quantitative Proteomics Workflow using Multiple Reaction Monitoring Based Detection of Proteins from Human Brain Tissue

Published on: August 28, 2021

Area of Science:

Proteomics
Bioinformatics
Biotechnology

Background:

Targeted quantitative proteomics, using methods like Multiple Reaction Monitoring (MRM) and Parallel Reaction Monitoring (PRM), is crucial for precise protein measurement.
Developing and validating assays for targeted proteomics is time-consuming, despite existing data repositories.
MRMAssayDB integrates curated targeted proteomics assay data from multiple sources.

Purpose of the Study:

To create a comprehensive, integrated platform for targeted proteomics assay data.
To improve accessibility and usability of validated proteotypic peptides and transition data.
To facilitate efficient assay selection and quantitative panel development for researchers.

Main Methods:

The MRMAssayDB platform aggregates and annotates targeted proteomics assay data.
The latest release (2021) includes over 1.1 million assays for 939,000 peptides, covering 61,000 proteins across 146 organisms.
A new visualization module maps peptide assays to Alphafold-predicted 3D protein structures and Protein Data Bank (PDB) structures.

Main Results:

MRMAssayDB provides access to over 1.1 million targeted proteomics assays.
The database links proteins to 19,000 Gene Ontology terms and 4,000 biological pathways.
Integrated visualization tools allow examination of peptide locations, modifications, and mutations on 3D protein structures.

Conclusions:

MRMAssayDB significantly enhances access to validated targeted proteomics assays.
The platform streamlines the process of selecting assays and building quantitative panels.
This resource supports researchers in advancing quantitative proteomics studies.