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. 2010 Dec 15;82(24):10068-74.
doi: 10.1021/ac1020358. Epub 2010 Nov 9.

Activated-ion electron transfer dissociation improves the ability of electron transfer dissociation to identify peptides in a complex mixture

Aaron R Ledvina  1 , Nicole A Beauchene, Graeme C McAlister, John E P Syka, Jae C Schwartz, Jens Griep-Raming, Michael S Westphall, Joshua J Coon
Affiliations

Activated-ion electron transfer dissociation improves the ability of electron transfer dissociation to identify peptides in a complex mixture

Aaron R Ledvina et al. Anal Chem. .

Abstract

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.

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Figures

Figure 1
Figure 1
Modified QLT allowing for IR activation concomitant to ETD ion-ion reactions.
Figure 2
Figure 2
Peptide Spectral Matches as a function of precursor peptide m/z for AI-ETD at 12, 36, and 60 W AI-ETD laser power.
Figure 3
Figure 3
The probability of observing cn- (A) and zn- (B) as a function of n for ETD and AI-ETD at various laser powers. At low n values, low laser powers result in the greatest chance of observation, but with increasing n, higher laser powers lead to the highest probability of observation.
Figure 4
Figure 4
Spectra (single scan) resulting from either ETD (A) or AI-ETD (B) following dissociation of the doubly protonated peptide cation ISSLLEEQFQQGK. AI-ETD results almost exclusively in the formation of c- and z·- type ions which match their theoretically predicted m/z values.
Figure 5
Figure 5
Spectra (single scan) resulting from either ETD (A) or AI-ETD (B) of the doubly protonated phosphopeptide cation LRISSADsEK.
See this image and copyright information in PMC

References

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