Computational mass spectrometry for small-molecule fragmentation

• Identifying small molecules from mass spectrometry data remains a major challenge.
• Computational analysis of fragmentation data requires novel strategies.
• Five fundamental strategies for computational analysis of fragmentation data.
• Searching spectral libraries, fragmentation spectrum prediction, fragmentation trees.
• Combinatorial fragmentation, and predicting structural features.

The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. Computational aspects of identifying small molecules range from searching a reference spectral library to the structural elucidation of an unknown. In this review, we concentrate on five important aspects of the computational analysis. We find that novel computational methods may overcome the boundaries of spectral libraries, by searching in the more comprehensive molecular structure databases, or not requiring any databases at all.