PubChem - Chemical properties for 1000s of compounds

MassBank of North America - Mass spectrum database

MassBank Europe - Mass spectrum database

Expasy Protein Property Calculator - Useful for calculating chemical formulas

Peptide Synthetics Monoisotopic Mass Calculator - Calculates the monoisotopic mass for peptides

SIS Web Exact Mass Calculator - Calculate the monoisotopic mass of any chemical formula

Human Metabolome Database

Small Molecule Pathway Database

Wiki Pathways (Biological pathways database)

KEGG Pathway Database

Reactome

PhenoMeNal

ProteomeTools project

The Global Proteome Machine

UniProt - Protein information for many species

NCBI RefSeq (comprehensive, annotated sequence database that includes proteins )

EMBL-EBI collection of protein resources