Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Proteomics01:33

Proteomics

10.1K
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...
10.1K

You might also read

Related Articles

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

Sort by
Same author

Diversity Oriented Clicking for Modular Synthesis.

Nature reviews. Methods primers·2026
Same author

Genetic and pharmacological inactivation of peptidoglycan remodeling increases antibiotic susceptibility of vancomycin-resistant Enterococcus faecium.

Nature communications·2026
Same author

Genetic and pharmacological inactivation of peptidoglycan remodeling increases antibiotic susceptibility of vancomycin-resistant <i>Enterococcus faecium</i>.

bioRxiv : the preprint server for biology·2026
Same author

Desiderata for a biomedical knowledge network: opportunities, challenges and future directions.

Bioinformatics advances·2026
Same author

Federated knowledge retrieval elevates large language model performance on biomedical benchmarks.

GigaScience·2026
Same author

A case-based explainable graph neural network framework for mechanistic drug repositioning.

Bioinformatics (Oxford, England)·2026

Related Experiment Video

Updated: Mar 16, 2026

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
09:52

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

1.5K

A comprehensive and scalable database search system for metaproteomics.

Sandip Chatterjee1, Gregory S Stupp1, Sung Kyu Robin Park2

  • 1Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.

BMC Genomics
|August 17, 2016
PubMed
Summary

We developed ComPIL, a metaproteomic analysis method, to overcome database size limitations in shotgun proteomics. This approach enables deeper proteomic sequencing and functional analysis of complex samples like the human gut microbiome.

Keywords:
DatabaseMetaproteomicsMicrobiomeMongoDBProteomic search engineProteomics

More Related Videos

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

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

Published on: November 2, 2021

2.6K
Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

6.3K

Related Experiment Videos

Last Updated: Mar 16, 2026

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
09:52

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

1.5K
The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

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

Published on: November 2, 2021

2.6K
Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

6.3K

Area of Science:

  • Proteomics
  • Bioinformatics
  • Metagenomics

Background:

  • Shotgun proteomics requires matching experimental spectra to protein databases.
  • Current methods face limitations with large sequence databases, hindering analysis of complex samples.
  • Increasing public sequencing data exacerbates database size challenges.

Purpose of the Study:

  • To address protein database size limitations in metaproteomic analysis.
  • To enable deeper proteomic sequencing and functional characterization of complex biological samples.
  • To develop a broadly applicable metaproteomic analysis method.

Main Methods:

  • Designed ComPIL (a scalable set of sequence databases for optimal querying).
  • Integrated ComPIL with a modified ProLuCID search engine (Blazmass) for rapid spectral matching.
  • Applied the method to human cell lysate and human gut microbiome samples.

Main Results:

  • ComPIL detected nearly all peptides from human HEK293 lysate using a ~500x smaller database than standard human databases.
  • Identified proteins from adenovirus in HEK293 lysate.
  • Significantly increased peptide and protein identifications in human gut microbiome samples compared to previous methods, with high accuracy.

Conclusions:

  • ComPIL combined with Blazmass enables proteomic searches with significantly larger databases.
  • This approach is suitable for complex samples with unknown composition and identifying unexpected proteins.
  • The ComPIL database, Blazmass search engine, and microbiome data are open source.