Fig. 6. Analysis of the coverage and distribution of ion identities in public LC-MS² spectral libraries (refer to Supplementary Table 3 for library origins).

Two-thirds of the MassBank of North America LC-MS²-positive ion mode library entries were entered as [M + H]⁺ while only four other ion types reached more than 1000 entries, namely, [M + Na]⁺, [M + NH₄]⁺, [M + K]⁺, and [M − H₂O + H]⁺. Other in-source fragments, multiply charged species, and multimers are only covered for a few compounds. A significant number of entries were either annotated as negatively charged adducts (e.g., [M − H]⁻) or were missing an annotation. As the ion identity naming was not harmonized, different versions pointing to the same ion identity were added to a total count. A similar ion annotation coverage was found in the GNPS spectral libraries. In contrast, libraries that were generated with the recently described MSMS-Chooser²⁹ workflow on GNPS or the IIMN-based library extraction workflow, described here, show an overall broader coverage of different adducts, multimers, and in-source fragments. The depicted statistical visualization compares a subset of significant or representative ion identities. The IIMN-based numbers summarize the libraries from both the 24 experimental datasets and the two NIH natural product standards datasets with a total of 2659 library entries. Source data are provided as a Source Data file.