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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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Related Experiment Video

Updated: Jun 30, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Accentuate the negative: proteome comparisons using the negative proteome database.

Lawrence T Reiter¹, Long H Do, Michael S Fischer

¹Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093-0349, USA.

|September 30, 2008

Summary

This summary is machine-generated.

The Negative Proteome Database (NPD) identifies unique proteins across species. This tool aids in understanding organism-specific protein functions and discovering novel biological insights.

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Last Updated: Jun 30, 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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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

Area of Science:

Comparative genomics
Proteomics
Bioinformatics

Background:

Complete genome sequences enable large-scale protein comparisons.
Focus has been on shared proteins, neglecting unique proteomes.
Understanding unique proteins is crucial for organism-specific biology.

Purpose of the Study:

To develop a searchable database for identifying proteins unique to specific proteomes.
To facilitate the exploration of organism-specific protein sets.

Main Methods:

Constructed the Negative Proteome Database (NPD).
Performed pair-wise protein sequence comparisons across ten diverse proteomes (including human, fly, worm, yeast, and bacteria).
Utilized Basic Local Alignment Search Tool (BLAST) for sequence alignment.

Main Results:

Identified 107 human proteins potentially involved in motile cilia function.
Discovered 1628 potential pesticide target proteins in Drosophila melanogaster (flies).
Found 659 proteins shared by humans and flies but absent in Caenorhabditis elegans (worms).
Located 180 nuclear-encoded human disease-associated proteins absent in flies.

Conclusions:

The NPD is a unique resource for complex proteome comparisons.
The database and its adaptable algorithm will aid in investigating organism-specific protein sets.
Facilitates discovery of novel gene functions and potential therapeutic targets.