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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: May 16, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Aggregation Methods for Quantifying PTM and Structural Changes in Bottom-Up Proteomics.

Erik D VonKaenel¹, Jordan C Rozum¹, Tong Zhang¹

¹Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.

Journal of Proteome Research

|May 15, 2026

Summary

This summary is machine-generated.

We evaluated peptide-to-protein roll-up methods for proteomic analyses. Site-centric roll-up improves quantification for post-translational modifications and structural studies like limited proteolysis-mass spectrometry (LiP-MS).

Keywords:

bottom-up proteomics limited-proteolysis mass spectrometry post-translational modification proteomics quantification

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Published on: October 24, 2018

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Last Updated: May 16, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Published on: October 24, 2018

Area of Science:

Proteomics
Mass Spectrometry
Bioinformatics

Background:

Bottom-up proteomics uses peptide-to-protein aggregation (roll-up) for data reliability.
Standard roll-up may be suboptimal for post-translational modification (PTM) and limited proteolysis-mass spectrometry (LiP-MS) studies.

Purpose of the Study:

Investigate the impact of different roll-up strategies on site-level quantification in PTM differential analysis.
Introduce and evaluate a novel site-centric roll-up approach for LiP-MS.

Main Methods:

Benchmarking various roll-up methods (sum, mean, median) using simulation studies.
Comparing sensitivity and specificity for detecting structural and PTM-driven changes.
Evaluating site-level vs. peptide-level quantification in LiP-MS.

Main Results:

Median and mean roll-up methods demonstrate superior performance over the sum method for both PTM and LiP proteomics.
Site-level quantification in LiP-MS proves more effective than peptide-level quantification.
The novel site-centric approach enhances LiP-MS data interpretation.

Conclusions:

Provides the first systematic, data-driven guidance for selecting roll-up techniques in site-level proteomic analyses.
Highlights the importance of tailored roll-up strategies for PTM and structural proteomics.
Site-centric roll-up offers significant advantages for LiP-MS applications.