Activated-Ion Electron Transfer Dissociation Improves the Ability of Electron Transfer Dissociation to Identify Peptides in a Complex Mixture

摘要

Using a modified electron transfer dissociation (ETD)-nenabled quadrupole linear ion trap (QLT) mass spectrometer,nwe demonstrate the utility of IR activation concomitantnwith ETD ion-ion reactions (activated-ion ETD,nAI-ETD). Analyzing 12 strong cation exchanged (SCX)nfractions of a LysC digest of human cell protein extractnusing ETD, collision-activated dissociation (CAD), and AIETD,nwe find that AI-ETD generates 13 405 peptidenspectral matches (PSMs) at a 1% false-discovery rate (1%nFDR), surpassing both ETD (7 968) and CAD (10 904).nWe also analyze 12 SCX fractions of a tryptic digest ofnhuman cell protein extract and find that ETD producesn6 234 PSMs, AI-ETD 9 130 PSMs, and CAD 15 209nPSMs. Compared to ETD with supplemental collisionalnactivation (ETcaD), AI-ETD generates ∼80% more PSMsnfor the whole cell lysate digested with trypsin and ∼50%nmore PSMs for the whole cell lysate digested with LysC.