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Links/Tools
INTEREST GROUPS FOR THE STANFORD METABOLOMICS AND PROTEOMICS COMMUNITY
STANFORD ORGANIZATIONS & LINKS
ONLINE TOOLS & CALCULATORS
- BioVenn - create area-proportional Venn diagrams for biological lists
- Blast - NCBI Basic Local Alignment Search Tool (preset parameters for short, nearly exact protein sequences)
- ChemCal - molecular mass calculator
- Delta Mass - database of protein post-translational modifications
- Entrez - NCBI database search and retrieval system
- ExPASy - proteomics tools
- IonSource - collection of tools and tutorials
- Mascot - online database searching for protein ID
- MS Tools - from SIS; includes graphical periodic table
- MS-Utils - MS software tool
- NEWT - taxonomy database browser
- Peaks Online - online de novo peptide sequencing
- PepNovo - online de novo mass spectrum interpretation
- Proteomics Tools - from the Institute for Systems Biology
- PubChem - database of small molecules and their biological activities; search by compound name, formula, structure
- Scaffold - download free viewer to read Scaffold (.sfd) files
- Tripeptides - tripeptide mass calculator at Colby College REFERENCE DATA
- IUPAC periodic table of the elements, atomic weights 2013
- Unimod - public domain database of protein modifications for mass spectrometry
- List of Elements - exact masses & isotopic abundances
- MS contaminant & detergent info:
o Common background for ions of electrospray - New Objective Technical Note PV-3
o Commonly observed ions in ESI and EI spectra, from the University of Alberta
o EI spectra of common solvents - University of Bristol
o Threshold values for detergents in protein and peptide mass spectrometry - letter to RCM
o Table of common ESI polymer and cluster ions
TUTORIALS & INFORMATION
LINKS TO COMPANIES PROVIDING STANDARDS - STABLE ISOTOPE LABELED AND UNLABELED:
ORGANIZATIONS
- ABRF - Association of Biomolecular Resource Facilities
- ASMS - American Society for Mass Spectrometry
- BAMS - Bay Area Mass Spectrometry
- CACO - California Analytical Chemists Organization (formerly BAACN)
- CASSS - California Separation Science Society
- Shared Proteomics - an online proteomics commmunity
- Sci.techniques.mass-spec newsgroup
OTHER USEFUL INFO - scientific presentations & writing
- Scientifically Speaking - Preparing & delivering scientific talks and using visual aids; brief section on posters. Also available as a .pdf booklet - The Oceanography Society
- Tips for preparing oral presentations - Office of Naval Research
- Advice on preparing posters - C. Purrington, Swarthmore College
- Guidelines for scientific writing - M. Alley, Penn State & co-editors
JUST FOR FUN