Links
Links to the following topics are provided below:
Journals
Mass Spectrometry
Organizations
Proteomics
Research Databases
Software and Tools
Glossaries
Journals
- Electrophoresis
- Journal of Mass Spectrometry
- Journal of Proteome Research
- Mass Spectrometry Reviews
- Molecular and Cellular Proteomics
- Protein Science
- Proteomics
- Rapid Communications in Mass Spectrometry
Mass Spectrometry
- High Performance Mass Spectrometry Facility
- sci.techniques.mass-spec - Mass spectrometry discussion group
- MS People
- spectroscopyNOW.com
Organizations
- DOE Genomes to Life Program
- DOE Office of Biological and Environmental Research (OBER)
- Gene Ontology (GO) Consortium - Developing a dynamic controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing.
- Institute for Systems Biology
- National Science Foundation (NSF) Directorate for Biological Sciences
- PNNL Advanced Mass Spectrometry and Proteomics Group
- PNNL Biomolecular Systems
- PNNL Center for Molecular and Cellular Analysis
- PNNL Instrument Development Laboratory (IDL)
- PNNL Macromolecular Structure and Dynamics (MS&D)
- Shewanella Federation
Proteomics
- NCRR Proteomics Research Resource for Integrative Biology at PNNL
- High Throughput Proteomics Measurements
- Human Proteome Organisation (HUPO)
- nature's genome gateway: proteomics in action
- Pep Talk - CHI's Protein Information Week Conference
- Protein Information Resource
- ProteinScience.com - News and information web portal devoted to proteomics and protein science
- Proteo Monitor - Newsweekly of proteomics technology
- Proteome Society
- Proteomics from Google
- HUPO-PSI (Proteomics Standards Initiative)
- ProteomicsSURF - A research pointer to proteomics and scientific IT Resources
Research Databases
- ExPASy Molecular Biology Server - EBI server dedicated to the analysis of protein sequences and structure as well as 2-D PAGE
- GenBank - NCBI - National Center for Biotechnology Information
- Proteome ISB's Peptide Atlas database
- The GPM DB
- SWISS-PROT - Protein knowledgebase
- TIGR - The Institute for Genomic Research
Software and Tools
- PNNL Software at the OMICS Distribution Center
- Biodas.org - Open Source system for exchanging annotations on genomic sequence data. Distributed Annotation System (DAS) allows a single machine to gather up genome annotation information from multiple distant web sites, collate the information, and display it to the user in a single view.
- Bioinformatics.org - Provides information on free tools being developed for bioinformatics research
- BioJAVA - Open-source project dedicated to providing Java tools for processing biological data
- BLAST (PNNL hosted) - Sequence similarity search tool supports analysis of nucleotide and protein databases
- EMBOSS - The European Molecular Biology Open Software Suite
- Ensembl - A software system which produces and maintains automatic annotation on eukaryotic genomes
- ExPASy Proteomics Tools
- ICR-2LS - FTICR data acquisition and control software package
- Mascot - Protein identification
- Open Bioinformatics Foundation - Protein families database of alignments and HMMs
- Pfam - Protein families database of alignments and HMMs
- PRIMER3 (PNNL hosted)
- Protein Prospector - A collection of tools to assist with MS data analysis
- Proteomics Tools and Related Information - Margie Romine's links
- PSort (PNNL hosted) - Prediction of protein sorting signals and localization sites in amino acid sequences
- SignalP V2.0.b2 - Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms
- Sequest - Correlates uninterpreted tandem mass spectra of peptides with amino acid sequences from protein and nucleotide databases. SEQUEST will determine the amino acid sequence and thus the protein(s) and organism(s) that correspond to the mass spectrum being analyzed.
- TMpred (PNNL hosted) - Prediction of transmembrane regions and orientation
- Tools for Data Mining - NCBI provides access to BLAST, Clusters of Orthologous Groups (COGs), ORF finder, Electronic PCR, UniGene, GeneMap99, VecScreen, Cancer Genome Anatomy Project CGAP, Cancer Chromosome Aberration Project cCAP, Human-Mouse Homology Maps, LocusLink, and VAST search
- XML for Molecular Biology - Paul Gordon's links
Glossaries
- PNNL's PRISMWiki glossary
- CHI's Expression, Genes & More Glossary
- CHI's Informatics Glossary
- CHI's Mass Spectrometry Glossary
- CHI's Proteomics Glossary
- Human Genome Project Information Genome Glossary