Dietary
deficiency of selenium is a global health hazard. Supplementation
of organic selenopeptides via food crops is a relatively safe approach.
Selenopeptides with heterogeneous selenium-encoded isotopes or a poorly
fragmented peptide backbone remain unidentified in site-specific selenoproteomic
analysis. Herein, we developed the Se-Pair Search, a UniProtKB-FASTA-independent peptide-matching
strategy, exploiting the fragmentation patterns of shared peptide
backbones in selenopeptides to optimize spectral interpretation, along
with developing new selenosite assignment schemes (steps 1–3)
to standardize selenium-localization data reporting for the selenoproteome
community and thereby facilitating the discovery of unexpected selenopeptides.
Using selenium-biofortified rice under cooking, fermentation, and
high-temperature and high-pressure processing conditions as a pyrolysis-thermolysis
dietary model, we probed the single-molecule-level kinetic evolution
of the novel selenopeptide “KKSe(M)R” with qual-quantitative
information on graph-theory-oriented localization calculations, abundance
patterns, activation energy, and rate constants at a selenoproteome-wide
scale. We ground-truth-annotated thirteen pyrolysis-thermolysis products
and inferred four pyrolysis-thermolysis pathways to characterize the
formation reactivity of the main intermediate variables of KKSe(M)R
and constructed an advanced probe-type ultrasound technique prior
to pyrolysis-thermolysis conditions for minimizing loss of KKSe(M)R
during processing. Importantly, we reveal the unappreciated pyro-excitation
diversion of KKSe(M)R at pyrolysis-thermolysis time and temperature
matrices. These findings provide pioneering theoretical guidance for
controlling dietary selenium supplementation within the safety thresholds.