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COVID-19 status: SUMS is safely supporting research under current physical distancing and occupancy rules.  Meetings and seminars continue to be held via Zoom.  Email us at spectrometry@stanford.eduMore info

SUMS Weekly Office Hours
 
Have a question about a potential mass spec project?
Not sure exactly who to talk with at SUMS?
Drop in to our open virtual office on Tuesday afternoons between 4:15 and 4:45 pm Pacific Time and get answers!
 

 

 

Thank you to all those involved to make SUMS-RAS 2021 a success!

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Links/Tools

INTEREST GROUPS FOR THE STANFORD METABOLOMICS AND PROTEOMICS COMMUNITY

STANFORD ORGANIZATIONS & LINKS

ONLINE RESOURCES, 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)
  • ChemCalc - 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
  • Mass Spectrometry Methods - Reviewed methods for improved intra- and inter- lab reproducibility
  • MS Tools - from SIS; includes graphical periodic table
  • NEWT - taxonomy database browser
  • 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; 2016 interactive periodic table
  • Unimod - public domain database of protein modifications for mass spectrometry
  • List of Elements - exact masses & isotopic abundances
  • MS contaminant & detergent info:
    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

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
  • CASSS - California Separation Science Society
  • Shared Proteomics - an online proteomics commmunity

OTHER USEFUL INFO - scientific presentations & writing

  • Scientifically Speaking - Preparing & delivering scientific talks and using visual aids; brief section on posters - The Oceanography Society
  • Advice on preparing posters - C. Purrington, Swarthmore College
  • Guidelines for scientific writing - M. Alley, Penn State & co-editors

JUST FOR FUN