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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 3, 2026

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Published on: April 19, 2019

Systematic evaluation of label-free and super-SILAC quantification for proteome expression analysis.

Andreas Tebbe¹, Martin Klammer¹, Stefanie Sighart¹

¹Evotec (München) GmbH, Am Klopferspitz 19a, 82152, Martinsried, Germany.

Rapid Communications in Mass Spectrometry : RCM

|September 18, 2015

Summary

Label-free proteome quantification on advanced mass spectrometry is effective for biomarker discovery. Additional replicate analyses and peptide fractionation enhance its precision and robustness for high-coverage proteome profiling.

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Last Updated: Apr 3, 2026

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Published on: April 19, 2019

Quantitative Analysis of Chromatin Proteomes in Disease

Quantitative Analysis of Chromatin Proteomes in Disease

Published on: December 28, 2012

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

Area of Science:

Proteomics
Mass Spectrometry
Biomarker Discovery

Background:

Mass spectrometry (MS)-based proteomics enables comprehensive proteome profiling.
Accurate quantification is crucial for high-coverage proteome analysis on modern instruments like quadrupole orbitrap mass spectrometers.

Purpose of the Study:

To systematically compare label-free proteome quantification with stable isotope labeling using amino acids in cell culture (super-SILAC).
To evaluate label-free quantification strategies for high-coverage proteome analysis on ultra-high-performance liquid chromatography (UHPLC)/MS.

Main Methods:

UHPLC/MS experiments were performed on a Q Exactive instrument.
Label-free quantification was compared against super-SILAC using six human cancer cell lines.
Peptide fractionation using high pH reversed-phase chromatography was investigated.

Main Results:

Label-free methods identified more proteins (approx. 5000) than super-SILAC (approx. 3500).
Label-free quantification showed slightly lower precision than super-SILAC but was improved by replicate analyses and peptide fractionation.
More significant differences in cell line comparisons were detected using label-free quantification.

Conclusions:

Label-free proteome quantification is a valuable tool for target and biomarker discovery.
State-of-the-art UHPLC/MS workflows benefit from robust label-free quantification strategies.
Optimized label-free approaches enhance proteome coverage and precision.