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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: Dec 27, 2025

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

Proline: an efficient and user-friendly software suite for large-scale proteomics.

David Bouyssié¹, Anne-Marie Hesse², Emmanuelle Mouton-Barbosa¹

¹Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.

Bioinformatics (Oxford, England)

|February 26, 2020

Summary

This summary is machine-generated.

Proline is a new software suite for mass spectrometry (MS)-based proteomics data analysis. It efficiently processes, curates, and visualizes large datasets, ensuring reliable identification and quantification results for proteomics studies.

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Area of Science:

Proteomics
Mass Spectrometry
Bioinformatics

Background:

Reliable identification and quantification of mass spectrometry-based proteomics data is crucial.
Existing tools often lack integrated data management and efficient processing for large-scale studies.

Purpose of the Study:

To introduce Proline, a comprehensive software suite for MS-based proteomics data analysis.
To demonstrate Proline's capabilities in data processing, curation, visualization, and publication.

Main Methods:

Development of the Proline software suite integrating processing algorithms and data management.
Assessment of label-free quantification workflow efficiency using a spiked-in sample.
Comparison of Proline's quantification accuracy against a widely used software.

Main Results:

Proline offers a user-friendly interface for collecting, processing, and visualizing proteomics datasets.
The software demonstrates computational efficiency and robust data curation capabilities.
Proline achieved high quantification accuracy in label-free quantification, comparable to existing tools, for datasets of any size.

Conclusions:

Proline is a robust and efficient software suite for MS-based proteomics data analysis.
It facilitates reliable data processing, curation, and publication, addressing limitations of existing tools.
The software is available for Windows and Linux under an open-source license.