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Related Concept Videos

Proteomics01:33

Proteomics

7.8K
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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Updated: Sep 6, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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urPTMdb/TeaProt: Upstream and Downstream Proteomics Analysis.

Jeffrey Molendijk1, Rui Yip1, Benjamin L Parker1

  • 1Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC 3010, Australia.

Journal of Proteome Research
|June 27, 2022
PubMed
Summary
This summary is machine-generated.

We created the underrepresented post-translational modification database (urPTMdb) to find novel protein modifications in experimental data. This tool, integrated with TeaProt, aids in discovering unexpected PTM regulations and biological insights.

Keywords:
PTMbioinformaticsdatabaseproteomicssoftware

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Post-translational modifications (PTMs) are crucial for protein function but underrepresented PTMs are difficult to study.
  • Existing databases often lack comprehensive data on less-studied PTMs, hindering discovery.
  • Analyzing PTMs in complex biological systems requires integrated computational tools.

Purpose of the Study:

  • To develop a curated database (urPTMdb) for underrepresented protein modification substrates.
  • To create an integrated analysis tool (TeaProt) for PTM and transcription factor enrichment.
  • To demonstrate the utility of urPTMdb and TeaProt in analyzing complex proteomic datasets.

Main Methods:

  • Curated protein lists for underrepresented PTMs were compiled for urPTMdb.
  • TeaProt was developed as a Shiny tool integrating GSEA, transcription factor analysis, and pathway analysis.
  • Proteomic data from Western diet studies and TARG1 interactome were analyzed using urPTMdb and TeaProt.

Main Results:

  • urPTMdb facilitates the discovery of enriched underrepresented PTMs in proteomics data.
  • TeaProt integrates various analyses, including drug-gene interactions, localization, and disease associations.
  • Analysis revealed altered cellular processes in diet-induced proteome remodeling and identified novel ADP-ribosylation substrates.

Conclusions:

  • urPTMdb and TeaProt provide a powerful platform for discovering and analyzing underrepresented PTMs.
  • These tools enhance the understanding of PTMs' roles in biological processes and disease.
  • The integrated approach accelerates PTM discovery and biological interpretation.