Inferring the nominal molecular mass of an analyte from its electron ionization mass spectrum

The performance of three algorithms for predicting nominal molecular mass from an analyte’s electron ionization mass spectrum are presented. The Peak Interpretation Method (PIM) attempts to quantify the likelihood that a molecular ion peak is contained in the mass spectrum, whereas the Simple Search Hitlist Method (SS-HM) and iterative Hybrid Search Hitlist Method (iHS-HM) leverage results from mass spectral library searching. These predictions can be employed in combination (recommended) or independently. The methods were tested on two sets of query mass spectra searched against libraries that did not contain reference mass spectra of the same compounds: 19,074 spectra of various organic molecules searched against NIST17 mass spectral library, and 162 spectra of small molecule drugs searched against SWGDRUG version 3.3. Individually, each molecular mass prediction method had computed precisions (the fraction of positive predictions that were correct) of 91 %, 89 % and 74 %, respectively. The methods become more valuable when predictions are taken together as an ensemble. When all three predictions were identical, which occurred in 33% of the test cases, the predicted molecular mass was almost always correct (> 99 %).