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Related Concept Videos

Proteomics01:33

Proteomics

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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: Jan 9, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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ProteoformDB: A Built-In Application to Generate Proteoform Database.

Trung Hoàng1, Yingwei Hu1, Hui Zhang1

  • 1Department of Pathology, Oncology, Urology, and Chemical and Biomolecule Engineering, Johns Hopkins University, Baltimore, Maryland 21231, United States.

Journal of Proteome Research
|December 3, 2025
PubMed
Summary
This summary is machine-generated.

Researchers developed ProteoformDB to catalog over one million human proteoforms. This database aids in understanding protein functions and disease mechanisms by documenting experimentally identified proteoforms.

Keywords:
MS database search strategiescombinatorial PTMsjoint quantificationmass spectrometry-based proteomicsmultisite proteoformsproteoform annotationproteoform biologyproteoform characterizationproteoformDBquantitative proteomics

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Area of Science:

  • Molecular Biology
  • Proteomics
  • Bioinformatics

Background:

  • Proteins are crucial for cellular functions, with complexity arising from diverse proteoforms generated via various biological processes.
  • Understanding proteoforms is key to deciphering protein roles in biological pathways and disease pathogenesis.

Purpose of the Study:

  • To develop an application tool, ProteoformDB, for generating comprehensive proteoform databases.
  • To catalog a significant number of unique human proteoforms for research use.

Main Methods:

  • Development of the ProteoformDB application for database generation.
  • Cataloging of over one million unique single-site human proteoforms.

Main Results:

  • Successful creation and population of ProteoformDB with over one million human proteoforms.
  • Demonstration of ProteoformDB's utility as a resource for documenting experimentally identified proteoforms.

Conclusions:

  • ProteoformDB serves as a valuable resource for protein characterization in quantitative proteomics.
  • The database supports the analysis of both total protein abundances and modified protein forms, advancing proteomic research.