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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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Updated: May 10, 2026

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

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

Published on: August 19, 2025

Sipros/ProRata: a versatile informatics system for quantitative community proteomics.

Yingfeng Wang¹, Tae-Hyuk Ahn, Zhou Li

¹Computer Science and Mathematics Division, Oak Ridge National Laboratory and Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

Bioinformatics (Oxford, England)

|June 25, 2013

Summary

This summary is machine-generated.

Sipros/ProRata is an open-source software package for comprehensive proteomics data analysis. It offers advanced protein identification, quantification, and post-translational modification analysis, scalable from desktops to supercomputers.

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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
Bioinformatics
Computational Biology

Background:

Community proteomics studies require robust and versatile data analysis tools.
Existing software packages may lack comprehensive features for identification and quantification.

Purpose of the Study:

To develop and present Sipros/ProRata, an open-source software package for end-to-end proteomics data analysis.
To enhance protein identification and quantification capabilities for diverse proteomics measurements.

Main Methods:

Development of Sipros 3.0, a database-searching program for protein identification and post-translational modification analysis.
Implementation of hybrid Message Passing Interface/OpenMP parallelism for computational scalability.
Upgrade of ProRata 3.0 to support label-free, isobaric chemical labeling, and metabolic labeling quantification.

Main Results:

Sipros 3.0 enables accurate general-purpose protein identification and broad-range post-translational modification searches.
The new Sipros architecture is scalable from desktops to supercomputers.
ProRata 3.0 provides comprehensive quantification options for various labeling strategies.

Conclusions:

Sipros/ProRata is a versatile informatics system for proteomics research.
The software facilitates identification and quantification of proteins and their variants.
It supports a wide variety of community proteomics studies.