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Related Concept Videos

Proteomics01:33

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 2, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

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

Published on: November 15, 2017

Combining quantitative proteomics data processing workflows for greater sensitivity.

Niklaas Colaert1, Christophe Van Huele, Sven Degroeve

  • 1Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium.

Nature Methods
|May 10, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new method for combining quantitative proteomics data, increasing the number of identified human proteins by 20% without compromising data quality. The Rover software offers a user-friendly, open-source solution for this integrative workflow.

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Related Experiment Videos

Last Updated: Jun 2, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

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

Published on: November 15, 2017

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Quantitative proteomics is crucial for understanding cellular processes.
  • Combining data from different software can be challenging.
  • Existing methods may not fully leverage available data.

Purpose of the Study:

  • To develop a normalization method for integrating quantitative proteomics data.
  • To enhance the number of quantified human proteins.
  • To ensure data quality is maintained during data integration.

Main Methods:

  • Developed an integrative workflow to merge outputs from two popular quantification software packages.
  • Implemented a normalization strategy for combining datasets.
  • Utilized the open-source Rover software for workflow implementation.

Main Results:

  • Achieved an average 20% increase in quantified human proteins.
  • Demonstrated no loss of data quality after merging datasets.
  • Successfully integrated data from multiple sources.

Conclusions:

  • The developed normalization method effectively increases protein quantification coverage.
  • The Rover software provides an accessible and efficient tool for data integration.
  • This approach enhances the utility of quantitative proteomics studies.