Database of elucidated mass spectra

A database of elucidated spectra is indispensable for both quality assessment of ranking functions and for calculation of MS classifiers. Here, we use spectra and structures from the NIST MS library [224]. This 1998 version of NIST contains 107,888 spectra of 107,812 structures. Spectra and structures are two separate files, linked by numerical identifiers. 

The data were subjected to very rigorous consistency checks to ensure only the inclusion of coherent spectrum-structure pairs, before further use The spectrum file needed to contain the molecular formulas and names of compounds as well as peak 

We then examined the spectra for the presence of molecular ions. 73,845 out of the 86,052 spectra have a peak at the respective nominal mass. The moleculeu ion is missing in 12,207 spectra (14.186%), which is quite a bit lower than other estimates indicating this peak is absent in approximately 30% [180] emd even 42% (for only 1426 spectra, see [135]) of El-MS spectra. 

we investigated the difference between the mass of the base peak of the peak cluster (defined as a sequences of peaks with masses differing by at most 2) at highest mass and the nominal molecular mass nif. The differences eue distributed as follows  

The negative entries above result when the first emd second isotope peaks are more intense than the lowest isotopomer peak. The remedning 6855 spectrum-structure pairs are distributed over another 360 mass differences. Knowledge of this mass 

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