Software

Mass Spectrometry data analysis is conducted using a combination of licensed and open source software.

For small molecule and metabolomics data, the following software packages are routinely employed:
Compound Discoverer (Thermo Scientific)
Sieve (Thermo Scientific)
ToxID (Thermo Scientific)
Xcalibur (Thermo Scientific)
XCMS (Scripps Center for Metabolomics)
Maven (Princeton University, Rabinowitz Lab)

For proteomics data, the following software packages are routinely employed:
Proteome Discoverer (Thermo Scientific)
The GPM (Global Proteome Machine Organization)

Several useful databases for identification of molecules include:
Human Metabolome Database
Yeast Metabolome Database
E.coli Metabolome Database
Metlin
Chemspider