Links and Tools

Interest Groups for the Stanford Metabolomics and Proteomics Community

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
Mascot - online database searching for protein ID
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
Tripeptides - tripeptide mass calculator at Colby College REFERENCE DATA
Unimod - public domain database of protein modifications for mass spectrometry
List of Elements - exact masses & isotopic abundances

Tutorials at IonSource
What is Mass Spectrometry?
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