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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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Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: Jun 2, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

The proteogenomic mapping tool.

William S Sanders¹, Nan Wang, Susan M Bridges

¹Department of Computer Science & Engineering, Mississippi State University, MS, USA.

BMC Bioinformatics

|April 26, 2011

Summary

This summary is machine-generated.

The Proteogenomic Mapping Tool rapidly maps experimentally observed peptides to their genome locations for structural genome annotation. This standalone application scales for large genomes and offers cross-platform functionality for proteomics researchers.

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Area of Science:

Proteomics
Genomics
Bioinformatics

Background:

High-throughput mass spectrometry (MS) proteomics data complements traditional genome annotation.
Efficiently mapping observed peptides to their source genome is crucial for structural annotation.
Existing tools are often custom scripts, not widely available, and do not scale for large eukaryotic genomes.

Purpose of the Study:

To develop a rapid and scalable tool for mapping experimentally observed peptides to their source genome locations.
To provide a widely accessible and cross-platform solution for proteogenomic mapping.

Main Methods:

Implementation of the Aho-Corasick string searching algorithm in Java.
Processing standardized file types for input.
Searching experimentally observed peptides against a genome translated in all 6 reading frames.

Main Results:

The Proteogenomic Mapping Tool enables rapid and exact mapping of peptides to genomes.
The Java implementation ensures scalability for large eukaryotic genomes.
The application provides cross-platform functionality and runs on standard hardware.

Conclusions:

The Proteogenomic Mapping Tool is a standalone, rapid, and scalable solution for mapping peptides to genomes.
Customizable genetic codes enhance its utility for diverse organisms.
Recommended for researchers using MS-derived proteomics data for structural genome annotation.