Useful web tools, links, and resources
STANFORD ORGANIZATIONS & LINKS
- Bio-X
- Comprehensive Cancer Center
- 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
- New! 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
- 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
- Peaks Online - online de novo peptide sequencing
- PepNovo - online de novo mass spectrum interpretation
- Proteomics Tools - from the Institute for Systems Biology
- Scaffold - download free viewer to read Scaffold (.sfd) files
- Tripeptides - tripeptide mass calculator at Colby College
- Delta Mass - database of protein post-translational modifications
- IUPAC - periodic table of the elements, atomic weights (2005)
- List of Elements - exact masses & isotopic abundances
- NEWT - taxonomy database browser
- PubChem - database of small molecules and their biological activities; search by compound name, formula, structure
- Unimod - public domain database of protein modifications for mass spectrometry
- MS contaminant & detergent info:
- Common background ions for electrospray - New Objective Technical Note PV-3
- Commonly observed ions in ESI and EI spectra, from the University of Alberta
- EI spectra of common solvents - University of Bristol
- Threshold values for detergents in protein and peptide mass spectrometry - letter to RCM
- Table of common ESI polymer and cluster ions
- 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
- How to de novo sequence peptides from MS/MS data
- Introduction to MS-based proteomics from Proteome Software
- Mass spec subject guide at Stanford's Swain Library
- Tutorials at Base Peak
- Tutorials at i-mass.com
- mzXML: Converting mass spec data to a common file format from various manufacturers' proprietary formats
- Overview flowchart - Data conversion tools & free mzXML viewers are accessible through links on the chart
- Converters are available for ThermoFinnigan Xcalibur (ReAdW), Waters-Micromass MassLynx (MassWolf), AB-Sciex Analyst (mzStar), and Bruker (mzBruker) data files.
- Tutorial on using ReAdW to convert Xcalibur files to mzXML - from IonSource.com
- 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
- Proteome 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
- How to convert large format posters from Powerpoint to Adobe Acrobat - Thanks to Michelle Wetzler at the UIUC Imaging Technology Group (ITG).
- Guidelines for scientific writing - M. Alley, Penn State & co-editors
- 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
SUMS
Stanford University
Seely G. Mudd Building
Room 175
333 Campus Drive
Stanford, CA
94305-5080
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Last Modified 7.15.08
