Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

Proceedings of the National Academy of Sciences of the United States of America·2014

Same author

Defining functional DNA elements in the human genome.

Proceedings of the National Academy of Sciences of the United States of America·2014

Same author

Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome.

Journal of proteome research·2013

Same author

A peptide-spectrum scoring system based on ion alignment, intensity, and pair probabilities.

Journal of proteome research·2013

Same author

Comparative genome analysis of ciprofloxacin-resistant Pseudomonas aeruginosa reveals genes within newly identified high variability regions associated with drug resistance development.

Microbial drug resistance (Larchmont, N.Y.)·2013

Same author

Agent-based modeling of competence phenotype switching in Bacillus subtilis.

Theoretical biology & medical modelling·2013

Search research articles

Related Experiment Video

Updated: May 12, 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

Peppy: proteogenomic search software.

Brian A Risk¹, Wendy J Spitzer, Morgan C Giddings

¹Department of Biochemistry & Biophysics, UNC School of Medicine, Chapel Hill, North Carolina 27599, United States. brian@geneffects.com

Journal of Proteome Research

|April 26, 2013

Summary

This summary is machine-generated.

Peppy software automates proteogenomic searches for novel protein identification and gene annotation. This tool efficiently processes large genomes on standard computers, making proteogenomics accessible to more researchers.

More Related Videos

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Related Experiment Videos

Last Updated: May 12, 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 Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Area of Science:

Proteomics
Genomics
Bioinformatics

Background:

Proteogenomic searching aids in novel protein identification, gene annotation, and detecting individual-specific peptides.
Current methods are often labor-intensive, requiring segmented searches and multiple unintegrated tools.
Large genome analysis is computationally demanding, limiting accessibility.

Purpose of the Study:

To introduce Peppy, a software tool for efficient and automated proteogenomic searches.
To overcome limitations of existing proteogenomic analysis methods, particularly for large genomes.
To enhance the accessibility of proteogenomic research for a broader scientific community.

Main Methods:

Peppy generates peptide databases from genomes and performs automated decoy generation, search, and analysis.
It tracks peptide loci, matches peptides to MS/MS spectra, and assigns confidence scores.
The software is written in Java for cross-platform compatibility and is fully multithreaded for speed.

Main Results:

Peppy enables rapid and accurate proteogenomic searches.
The software successfully handles large genomes efficiently, overcoming memory and computation time constraints.
Identifications are reported at a user-defined false discovery rate threshold.

Conclusions:

Peppy streamlines the proteogenomic workflow, making it faster, more accurate, and automated.
The software's efficiency and accessibility on standard hardware democratize proteogenomic research.
Peppy facilitates novel protein discovery and gene annotation across diverse genomic scales.