Proteomics Resources on the Web

primers and glossaries | groups and initiatives | databases | journals | medline search

Some content reprinted from:
Environ Health Perspect. 2003 Nov;111(15):A816-25
Hood E. Proteomics: characterizing the cogs in the machinery of life.
Link to PubMed: 14630521- Link to PDF
Federal publication - copyright free.

Updated October 2006
Adapted from Bioinformatics Resources: Proteomics
Submitted by Fred Stoss, Arts and Sciences Libraries, University at Buffalo, State University of New York; edited by Patricia M. Weiss
MLA News p. 9.

Primers and Glossaries

Introduction to Proteomics
http://www.childrenshospital.org/cfapps/research/data_admin/Site602/mainpageS602P0.html
This site, compiled by researchers at the Children’s Hospital in Boston, explains the technical aspects of proteomics and provides interactive features, simple animations, and textual explanations in non-technical terms.
Proteomics
http://www.thebiotechclub.org/industry/emerging/proteomics.php
From the GSAS Harvard Biotechnology Club, this is a useful primer about the emerging technology of proteomics, with links to the biotechnology entities.
Functional Genomics Resources: Proteomics
http://www.sciencemag.org/feature/plus/sfg/resources/res_proteomics.dtl
Proteomics is deeply rooted in the biological, chemical, and computational sciences. The American Association for the Advancement of Science, publishers of Science, lists general and cross-disciplinary links related to proteomics.
Pharmaceutical Proteomics Glossary
http://www.genomicglossaries.com/content/proteomics.asp
From the Cambridge Healthtech Institute, this tool provides bioinformatics glossaries that define the terms, words, and concepts of what is sometimes referred to as the “new biology.”
IonSourceProteomeIonSourceProteome Players and Resource Links
http ://www.ionsource.com/links/proteolinks.htm
This site is a comprehensive directories for commercial, nonprofit, and governmental organizations, and links to literature and selected Websites.
Proteomics Interest Group—ProtIG
http://proteome.nih.gov/
This is the Website of the National Institutes of Health special interest group that organizes seminars, discussions, and workshops on proteomics in a wide variety of scientific, technical, and medical settings. Audio and video links to its seminars as well as links to software and external resources are provided.
Clinical Proteomics Research Map—CPRMap
http://www.cprmap.com
CPRMap provides trade news on clinical studies, findings, applications, new products, and conferences dealing with proteomics in medical settings.
Amino Acid Information
http://prowl.rockefeller.edu/aainfo/contents.htm
This Website provides a ready-reference link to many chemical, physical, and biological properties of amino acids.

Groups and Initiatives

Human Proteome Organisation (HUPO)
http://www.hupo.org/
An international research consortium intended to encourage large-scale analysis of the human proteome.
The ExPASy (Expert Protein Analysis System) proteomics server
http://www.expasy.org/
From the Swiss Institute of Bioinformatics (SIB) ExPASy is dedicated to the analysis of protein sequences and structures. It has a useful assortment of tools: Proteomics and sequence analysis tools.
Human Proteomics Initiative
http://www.expasy.org/sprot/hpi/
Joint effort of the Swiss Institute of Bioinformatics and the European Bioinformatics Institute that seeks to comprehensively annotate all known human proteins.
National Heart, Lung, and Blood Institute Proteomics Initiative
http://www.nhlbi.nih.gov/meetings/proteomics.htm
A seven-year, $157 million program to accelerate the development of innovative technologies to characterize healthy and diseased heart, lung,
blood, and sleep processes in 10 special centers of proteomics research across the country.
Protein Structure Initiative
http://www.structuralgenomics.org/
A 10-year project funded by the National Institute of General Medical Sciences to determine the three-dimensional structures of 10,000 unique proteins, while dramatically reducing the time and costs involved in the process.

Databases

Protein Database at NCBI/Entrez at PubMed
Go to PubMed; click on "Protein" in the Black Menu Bar. This way you have access to the NJ Tucker Library Journal access icons.
The protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
Biomolecular Interaction Network Database
http://www.blueprint.org/
A comprehensive, publicly accessible repository administered by blueprint WORLDWIDE for data and software tools related to critical biomolecular functions.
Chemical Effects in Biological Systems Knowledge Base
http://www.niehs.nih.gov/nct/cebs.htm
National Center for Toxicogenomics database that will exhaustively document the toxic effects of chemicals in the environment and be fully searchable by compound, structure, toxicity, pathology, gene, gene group, single-nucleotide polymorphism, pathway, and network
Human Protein Reference Database
http://www.hprd.org/ 
Joint project of The Johns Hopkins University and the Institute of Bioinformatics that is expected to eventually contain comprehensive entries on 10,000 human proteins, including domain architecture, post-translational modifications, interaction networks, and disease associations.
Peri S, et al: Human protein reference database as a discovery resource for proteomics.
Nucleic Acids Res. 2004 Jan 1;32 Database issue:D497-501. Link to free full text: 14681466
Protein Sequence Database
http://pir.georgetown.edu/
A comprehensive annotated protein sequence database in the public domain, maintained by the Protein Information Resource.The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information.
Swiss-Prot
http://us.expasy.org/sprot/
A curated protein sequence database developed by the Swiss Institute of Bioinformatics and the European Bioinformatics Institute that strives to provide a high level of annotation, a minimal level of redundancy, and high level of integration with other databases.
TrEMBL
http://www.ebi.ac.uk/trembl/
A database maintained by the European Bioinformatics Institute that contains the translations of all coding sequences present in the European Molecular Biology Laboratory's Nucleotide Sequence Database that are not yet integrated into Swiss-Prot.
United Protein Database
http://www.uniprot.org/
With $15 million in funding from six NIH institutes and centers, will combine the resources of Swiss-Prot, TrEMBL, and the Protein Sequence Database.

Journals

Molecular and Cellular Proetomics
Link to publisher's site. (NJ paid subscription: All years of full text available campus use only. Free full text archive, vol. 1, 2002 to after 1 year posted every January. Abstracts available for all issues.)
" In Press" articles from this publication appear to be free to all at this site. Proteome Science ( an Open Access journal)
Link to the publisher's site. (vol. 1, 2003 - )
Zabel D. Stankus T. Making sense of next big things in science: The promise of proteomics. Ref User Serv Q 2002 Winter 42(2):110-8.

MEDLINE search on PubMed

Mesh Terms:
Proteomics
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
Year introduced: 2003

Proteome
The protein complement of an organism coded for by its genome.
Year introduced: 2000

Coordinate with the disease you are studying.