Systematic
analysis and interpretation of the large number of tandem
mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck
in discovery-driven research. MS/MS mass spectral libraries are small
compared to all known small molecule structures and are often not
freely available. MS2Analyzer was therefore developed to enable user-defined
searches of thousands of spectra for mass spectral features such as
neutral losses, <i>m</i>/<i>z</i> differences,
and product and precursor ions from MS/MS spectra in MSP/MGF files.
The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/. As the reference query set, 147 literature-reported neutral losses
and their corresponding substructures were collected. This set was
tested for accuracy of linking neutral loss analysis to substructure
annotations using 19 329 accurate mass tandem mass spectra
of structurally known compounds from the NIST11 MS/MS library. Validation
studies showed that 92.1 ± 6.4% of 13 typical neutral losses
such as acetylations, cysteine conjugates, or glycosylations are correct
annotating the associated substructures, while the absence of mass
spectra features does not necessarily imply the absence of such substructures.
Use of this tool has been successfully demonstrated for complex lipids
in microalgae
