Degradation graphs reveal hidden proteolytic activity in peptidomes
Fig 6
Degradation graph analysis of porcine wound fluid peptidomes from bacterial infections.
a Peptidomic data from porcine wound fluids infected with Staphylococcus aureus (n = 38) or Pseudomonas aeruginosa (n = 33) [11] were analyzed without enzymatic digestion using LC–MS/MS. b For each sample, edge transition probabilities were optimized by gradient descent to reproduce measured peptide distributions. c The ratio between generated and observed peptide abundance showed that neglecting sequential degradation led to an average 3.5-fold underestimation of total proteolytic activity. d Visualization of total inflow along the hemoglobin subunit alpha backbone revealed differential degradation flow between infection types, with pronounced variation in the N-terminal biomarker region and an additional differential site around residues 60–80. This figure was made with BioRender.