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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 20, 2025

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

piNET: a versatile web platform for downstream analysis and visualization of proteomics data.

Behrouz Shamsaei¹, Szymon Chojnacki¹, Marcin Pilarczyk¹

¹Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, USA.

Nucleic Acids Research

|May 30, 2020

Summary

The piNET server offers integrated analysis and visualization for quantitative proteomics data, focusing on post-translational modification (PTM) networks and chemical/genetic perturbations for deeper biological insights.

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Related Experiment Videos

Last Updated: Dec 20, 2025

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

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Published on: June 8, 2020

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Area of Science:

Proteomics
Bioinformatics
Systems Biology

Background:

Advancements in proteomics necessitate efficient computational tools for data analysis.
Interpreting large-scale protein profiling data requires integrated approaches.

Purpose of the Study:

To present the piNET server for integrated annotation, analysis, and visualization of quantitative proteomics data.
To emphasize post-translational modification (PTM) networks and integration with perturbation signatures for mechanistic insights.

Main Methods:

Utilizes a Spring-Boot JAVA platform with Apache Lucene indexing for rapid peptide mapping.
Integrates databases like PhosphoSitePlus, iPTMnet, and SIGNOR for PTM-centric network analysis.
Incorporates LINCS (Library of Integrated Network-Based Cellular Signatures) signatures for chemical and genetic perturbations.

Main Results:

Provides interactive graphs and tables for peptide-protein annotation and PTM site mapping.
Generates high-resolution visualizations of enzyme-substrate networks, including kinase-phospho-peptide interactions.
Enables mapping and visualization of LINCS signature connectivity for upstream enzyme modulators.

Conclusions:

piNET is a versatile, user-friendly tool for comprehensive proteomics data interpretation.
Facilitates deeper understanding of PTMs and their regulatory mechanisms through integrated network analysis.
Offers programmatic access via a RESTful API for automated data processing.