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ASMS Presentations - Basics, Fundamentals, Drug discovery, Quality control, Forensics and Imaging

BioGRID - Curated biological database of protein-protein interactions, genetic interactions, chemical interactions and PTMs

Blast - NCBI Basic Local Alignment Search Tool

ChemCalc - Molecular mass calculator 

Commonly observed ions in ESI spectra - from University of Alberta

Cytoscape - Software for visualizing complex protein networks

Delta Mass - Database of protein PTMs

Entrez - NCBI database search and retrieval system

ExPASy - Bioinformatics resource portal

GeneONTOLOGY AmiGO - Set of tools for GO database search. Search for annotations, ontology, genes and gene products

GeneONTOLOGY PANTHER - Tool for protein classifications in high-throughput analysis. Proteins are classified according to their family, molecular function, biological process and pathway

Integrative Omics Software (by PNL) - Tools and software

IonSource - Tools and tutorials

Mascot - Online database search for protein IDs

MS Tools for Mass Spec Users (by SIS) - Tools including mass spectrum generator and periodic table 

PRIDE - Resource that stores mass spectrometry-based protein expression data, including spectra, peptide and protein identifications, derived from user submissions. 

Proteomics Tools (from the Institute for Systems Biology) - Tools including MS/MS fragment ion calculator and protein digestor

PubChem - Database of small molecules

Reactome - Proteins and pathways analysis tool

Scaffold - Download free viewer to read Scaffold files 

SharedProteomics - An online proteomics community 

STRING - Database of known and predicted protein-protein interactions

IUPAC interactive periodic table - Elements and isotopes

Unimod - Public domain database of protein modifications for MS

Uniprot - Resource for protein sequences, annotations and databases

Venny - An interactive tool for comparing lists with Venn's diagrams

WebGestalt - Tool for functional enrichment analysis