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Interpretation and annotation of fragmentation mass spectra strongly depends on our knowledge of collision-induced fragmentation mechanisms. Computational methods for interpretation of fragmentation operate in the boundaries of recognized fragmentation rules. The prevalence of non-sodiated fragment ions in sodiated ion fragmentation spectra is not yet fully recognized by the mass spectrometry community. Here, we investigated the extent of “Sodium Assisted Inductive Cleavage” (SAIC), a charge migration fragmentation occurring in the fragmentation spectra of sodiated precursors. The NIST17 fragmentation library was mined for evidence of SAIC. A substantial amount of fragment ions in sodiated precursor spectra can be linked to SAIC. Thus, this fragmentation mechanism must be considered to allow for accurate interpretation of fragmentation spectra.
LFN was supported by the U.S. National Institutes of Health (R01 GM107550), and the European Union’s Horizon 2020 program (MSCA-GF, 704786). PCD was supported by the Gordon and Betty Moore Foundation (GBMF7622), the U.S. National Institutes of Health (P41 GM103484, R03 CA211211, R01 GM107550). ELS acknowledges funding from the Luxembourg National Research Fund (FNR) for project A18/BM/12341006. SB, KD and ML acknowledge financial support by the Deutsche Forschungsgemeinschaft (BO 1910/20). CDB was supported by the U.S. National Institutes of Health (1U01CA235507-01) and acknowledges the CSU Office of the Vice President for Research.