Links and Tools
Main content start
INTEREST GROUPS FOR THE STANFORD METABOLOMICS AND PROTEOMICS COMMUNITY
STANFORD ORGANIZATIONS & LINKS
- Listing of Stanford Core Resource Labs
- Stanford Mass Spectrometry Library Guide
- BioX
- Stanford Cancer Institute
- Chemistry Department NMR Facility
- Earth Sciences EM-1:Environmental Measurements
- Glassblowing Shop - O.Z. Glass, custom scientific glass work
- Stanford Magnetic Resonance Laboratory (SMRL)
- Stanford Libraries
- Stanford e-journals
- Campus eateries
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:
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
TUTORIALS & INFORMATION
- Tutorials at IonSource
- What is Mass Spectrometry?
- How electrospray works
- How ion trap mass spectrometers work
- Dr. Jack Henion's Practical LC/MS e-Learning program
- Introduction to MS-based proteomics and metabolomics from Proteome Software
- Mass spec subject guide at Stanford's Swain Library
- Mass Spectrometry Contaminant Database
- Learn about the theory and practice of the most utilized chromatographic techniques CHROMacademy
- mzXML: Converting mass spec data to a common file format from various manufacturers' proprietary format
- Overview flowchart - Data conversion tools & free mzXML viewers are accessible through links on the chart
- Tutorial on using ReAdW to convert Xcalibur files to mzXML - from IonSource.com
LINKS TO COMPANIES PROVIDING STANDARDS - STABLE ISOTOPE LABELED AND UNLABELED:
- Cambridge Isotope Labs
- Medical Isotopes
- Sigma-Aldrich
- Avanti Polar Lipids
- Steraloids
- JPT Peptide Technologies
- Anaspec
- TLC PharmaChem
- Cerilliant
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
- TOF-MS cartoon - VIAS.org
- Ion trap MS cartoon - VIAS.org
- Beware of dihydrogen monoxide! - DHMO.org
- PhD comic strip (Piled Higher and Deeper) - a Stanford original!
- The Mass Spec & the Spider - a true story