Figure 2
From: PTMselect: optimization of protein modifications discovery by mass spectrometry
(a) Number of missed cleavages per peptide detected in LC-MS analysis of Citron-kinase digested with trypsin, Lys-C, V8-DE, V8-E and chymotrypsin. (b–e): Phosphosites of Citron-kinase detected by LC-MS after digestion with trypsin, V8-DE, Lys-C, chymotrypsin and V8-E compared with PMTselect simulations. Proteases producing a lot of missed cleavages (V8 and chymotrypsin) were simulated with one (V8) or two (chymotrypsin) missed cleavages (MC). Phosphosites exactly matching PTMselect simulation are in blue. Phosphosites predicted by PTMselect, but not observed (false positives) are in yellow. Phosphosites experimentally observed but not predicted by PTMselect (false negatives) are in red. (b) Effect of peptides sizes min and max [7–35], [8–30], [7–40] on the % of concordance between experimental and simulated phosphosites*. (c) Effect of peptides sizes min and max [7–35], [8–30], [7–40] on the number of phosphosites detected by LC-MS simulated by PTMselect*. (d) Effect of parallel digestion on the number of phosphosites detected by LC-MS simulated by PTMselect*. (e) Effect of parallel digestion on the % of concordance between experimental and simulated phosphosites*. *: same color code as in a).
