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Mass Spectrometry and Proteomics

Collection of Proteomics Tools
i-mass Guides: Mass Spectrometry's Information Resource
Mass Spectrometry and Biotechnology Resource
IonSource - An extensive collection of Proteomics and Mass Spectrometry Resources
Proteomics Tools: from MUSC
University of Washington YRC Mass Spectrometry
Dr. John Yates's Lab home page
Vanderbilt University Mass Spectrometry Research Center
Samuel Lunenfeld Research Institute Proteomics
European Molecular Biology Laboratory (EMBL) Proteomics Visitor Facility
Mass Spectrometry and Protein Analysis Lab in University of New South Wales
Dr. A. Emili's Lab home page
Dr. R. Aebersold's Lab home page
Dr. B. Chait's Lab home page
Dr. M. Mann's Lab home page
Dr. S. P. Gygi's Lab home page
UCSF Mass Spectrometry Facility
PTCF
Dr. David Muddiman's Laboratory (North Carolina State University)
 

Search Engines for Protein Identification

PEAKS including de-novo sequencing and database search, from Bioinformatics Solutions Inc.
MASCOT from Matrix Science, including: Peptide Mass Fingerprint, Sequence Query, and MS/MS Ion Search.
PROSPECTOR MS-fit
EMBL PeptideSearch
PepMAPPER
ProFound from Gemomic Solution for Mass Fingerprint
MS-Fit &
MS-Isotope		 from the UCSF Mass Spectrometry Facility
 
MOWSE will search the owl protein sequence database with protein fragment information, and return the protein(s) which most likely correspond to your peptide-data.
PeptideSearch from European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany.
FindMod Tool is a tool that can predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides.
CBS Prediction Servers NetNGlyc
NetOGlyc
NetPhos
TGPMO The Global Proteome Machine Organization
Positive Probability PPL website
 
SPIDER SPIDER



Protocols

Protocols for the preparation of samples from NCRR Yeast Resource Center
User Guidelines For Sample Preparation from SLRI Proteomics Database



Protein Databases

UniProt a curated protein sequence database that provides a high level of annotation, a minimal level of redundancy and high level of integration with other databases.
SwissProt fasta format database ftp site
OWL Composite Protein Sequence Database
NCBI A collection of protein sequence entries compiled from a variety of sources including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
NCBI fasta format database ftp site



Mass Spectrum Deconvolution

Maximum Entropy for ESI Mass Spectrometry. QPeaks
ReSpect Home Page



 Bioinformatics Organizations

Genomic Solutions Proteometrics USA
Bioinformatics Solutions Inc PEAKS, Pattern Hunter, and PROSPECT
Micromass Home



 Others

Outline of proteomics by 2D Gels
BLAST
PubMed/MEDLINE
Heuristic Methods for Fast Database Searches FastA & BLAST (questions/ answers)

Sequence Formats introduction to different protein or DNA sequence formats and converting programs
ExPASy Molecular Biology Server
NCBI Taxonomy Browser
Translate Tool translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
Expasy Molecular Biology Server
Proteomics Tools
Prowl
Spectroscopy Now (General Tools and Links)
Pedro's Biomolecular Research Tools
MARS (Toronto)
Genome Canada
Ontario Genomics Institute



 Useful Links from UWO

UWO Taylor Library
UWO Taylor Library Chemistry Links
UWO Taylor Library Biochemistry Links
CRC Handbook of Chemistry and Physics


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Last modified on January 7, 2008 by Jonathan Meyer