Activated-ion electron transfer dissociation improves the ability of electron transfer dissociation to identify peptides in a complex mixture.
Using a modified electron transfer dissociation (ETD)-enabled quadrupole linear ion trap (QLT) mass spectrometer, we demonstrate the utility of IR activation concomitant with ETD ion-ion reactions (activated-ion ETD, AI-ETD). Analyzing 12 strong cation exchanged (SCX) fractions of a LysC digest of human cell protein extract using ETD, collision-activated dissociation (CAD), and AI-ETD, we find that AI-ETD generates 13 405 peptide spectral matches (PSMs) at a 1% false-discovery rate (1% FDR), surpassing both ETD (7 968) and CAD (10 904). We also analyze 12 SCX fractions of a tryptic digest of human cell protein extract and find that ETD produces 6 234 PSMs, AI-ETD 9 130 PSMs, and CAD 15 209 PSMs. Compared to ETD with supplemental collisional activation (ETcaD), AI-ETD generates ∼80% more PSMs for the whole cell lysate digested with trypsin and ∼50% more PSMs for the whole cell lysate digested with LysC.
Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States.
Aaron R
AR
Ledvina
Nicole A
NA
Beauchene
Graeme C
GC
McAlister
John E P
JE
Syka
Jae C
JC
Schwartz
Jens
J
Griep-Raming
Michael S
MS
Westphall
Joshua J
JJ
Coon
D002457:Cell Extracts / Q000737:chemistry*; D006801:Humans; D007259:Infrared Rays; D013058:Mass Spectrometry / Q000295:instrumentation / Q000379:methods*; D008666:Metalloendopeptidases / Q000378:metabolism; D010446:Peptide Fragments / Q000032:analysis / Q000302:isolation & purification*; D011506:Proteins / Q000032:analysis / Q000378:metabolism; D014357:Trypsin / Q000378:metabolism
D002457:Cell Extracts; D010446:Peptide Fragments; D011506:Proteins; D014357:Trypsin; D008666:Metalloendopeptidases; C039830:peptidyl-Lys metalloendopeptidase