The Identity Algorithm: How the Most Popular Electron Ionization Mass Spectral Library Search Engine Actually Works.

The Identity algorithm implemented in the MS Search (NIST) software is widely used for library searches of gas chromatography/mass spectrometry data against electron ionization mass spectral databases. It has been available to researchers since 1993, with the release of MS Search 1.5a. Despite its extensive use, the operational details of the algorithm have remained ambiguous. Attempts to replicate the algorithm have been unsuccessful because, as found in this research, the description in the manual is neither fully complete nor accurate. The main novelty of this work is the development of a unique approach for deconstructing the Identity algorithm. It is purely based on analyzing library search results obtained from several groups of synthetic mass spectra, each tailored to isolate and examine specific components of the algorithm. This approach facilitated a comprehensive understanding of the Identity algorithm and led to the development of a custom implementation that fully replicates the results obtained from the original MS Search software. The custom implementation of the Identity algorithm is now available in the mssearchr R package, enhancing accessibility for researchers.