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Communication

Electron Transfer Dissociation of iTRAQ Labeled Peptide Ions

Hongling Han^†, Darryl J. Pappin^‡, Philip L. Ross^‡ and Scott A. McLuckey*^†

Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404

J. Proteome Res., 2008, 7 (9), pp 3643–3648

DOI: 10.1021/pr8001113

Publication Date (Web): July 23, 2008

†

Purdue University.

‡

Applied Biosystems.

* To whom correspondence should be addressed. Phone: (765) 494-5270. Fax: (765) 494-0239. E-mail: mcluckey@purdue.edu.

Abstract

Triply and doubly charged iTRAQ (isobaric tagging for relative and absolute quantitation) labeled peptide cations from a tryptic peptide mixture of bovine carbonic anhydrase II were subjected to electron transfer ion/ion reactions to investigate the effect of charge bearing modifications associated with iTRAQ on the fragmentation pattern. It was noted that electron transfer dissociation (ETD) of triply charged or activated ETD (ETD and supplemental collisional activation of intact electron transfer species) of doubly charged iTRAQ tagged peptide ions yielded extensive sequence information, in analogy with ETD of unmodified peptide ions. That is, addition of the fixed charge iTRAQ tag showed relatively little deleterious effect on the ETD performance of the modified peptides. ETD of the triply charged iTRAQ labeled peptide ions followed by collision-induced dissociation (CID) of the product ion at m/z 162 yielded the reporter ion at m/z 116, which is the reporter ion used for quantitation via CID of the same precursor ions. The reporter ion formed via the two-step activation process is expected to provide quantitative information similar to that directly produced from CID. A 103 Da neutral loss species observed in the ETD spectra of all the triply and doubly charged iTRAQ labeled peptide ions is unique to the 116 Da iTRAQ reagent, which implies that this process also has potential for quantitation of peptides/proteins. Therefore, ETD with or without supplemental collisional activation, depending on the precursor ion charge state, has the potential to directly identify and quantify the peptides/proteins simultaneously using existing iTRAQ reagents.

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