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)
ToxID (Thermo Scientific)
Xcalibur (Thermo Scientific)
XCMS (Scripps Center for Metabolomics)
METLIN (Scripps Center for Metabolomics)

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