The Identity Algorithm:\nHow the Most Popular Electron\nIonization Mass Spectral Library Search Engine Actually Works

The\nIdentity algorithm\nimplemented in the MS Search (NIST)\nsoftware\nis widely used for library searches of gas chromatography/mass spectrometry\ndata against electron ionization mass spectral databases. It has been\navailable to researchers since 1993, with the release of MS Search\n1.5a. Despite its extensive use, the operational details of the algorithm\nhave remained ambiguous. Attempts to replicate the algorithm have\nbeen unsuccessful because, as found in this research, the description\nin the manual is neither fully complete nor accurate. The main novelty\nof this work is the development of a unique approach for deconstructing\nthe Identity algorithm. It is purely based on analyzing library search\nresults obtained from several groups of synthetic mass spectra, each\ntailored to isolate and examine specific components of the algorithm.\nThis approach facilitated a comprehensive understanding of the Identity\nalgorithm and led to the development of a custom implementation that\nfully replicates the results obtained from the original MS Search\nsoftware. The custom implementation of the Identity algorithm is now\navailable in the mssearchr R package, enhancing\naccessibility for researchers.