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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: Feb 27, 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

Efficient Quantitative Comparisons of Plasma Proteomes Using Label-Free Analysis with MaxQuant.

Lynn A Beer¹, Pengyuan Liu¹, Bonnie Ky²

¹The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA.

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

|July 5, 2017

Summary

This summary is machine-generated.

Advanced mass spectrometry methods now allow detailed analysis of complex human plasma proteomes. This study presents an improved label-free quantitation technique using MaxQuant for in-depth plasma proteome profiling.

Keywords:

Label-free quantitation MaxQuant Plasma biomarkers Proteomics

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Last Updated: Feb 27, 2026

Phosphopeptide Enrichment Coupled with Label-free Quantitative Mass Spectrometry to Investigate the Phosphoproteome in Prostate Cancer

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Published on: August 2, 2018

Quantitative Analysis of Chromatin Proteomes in Disease

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Label-Free Quantitative Proteomics Workflow for Discovery-Driven Host-Pathogen Interactions

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Published on: October 20, 2020

Area of Science:

Biochemistry
Analytical Chemistry
Proteomics

Background:

Plasma proteome analysis is complex due to wide dynamic range and heterogeneity.
Technological advancements in mass spectrometry (MS) and bioinformatics are improving quantitative proteomic analyses.
Both label-based and label-free quantitation strategies have advanced for proteome comparisons.

Purpose of the Study:

To present a method for in-depth label-free analysis of human plasma samples.
To leverage recent improvements in MS technology and bioinformatics for plasma proteome quantitation.
To demonstrate the utility of MaxQuant software for complex proteomic datasets.

Main Methods:

Utilized label-free quantitation strategy for human plasma samples.
Employed advanced mass spectrometry instrumentation and techniques.
Applied MaxQuant software for data analysis and in-depth proteome profiling.

Main Results:

Successfully performed in-depth quantitative analysis of human plasma proteomes.
Demonstrated the effectiveness of the label-free approach for complex samples.
Achieved accurate quantitative comparisons of expansive proteome datasets.

Conclusions:

The presented label-free method enables comprehensive analysis of human plasma proteomes.
MaxQuant facilitates accurate and in-depth quantitative proteomic studies.
Advances in MS and bioinformatics continue to enhance the study of complex biological samples.