N‑Acylated Dipeptide Tags Enable Precise Measurement of Ion Temperature in Peptide Fragmentation

• Published in: The journal of physical chemistry. B 2012-12, Vol.116 (48), p.13982-13990
• Main Authors: Seo, Jongcheol, Suh, Min-Soo, Yoon, Hye-Joo, Shin, Seung Koo
• Format: Article
• Language: English
• Subjects: Acylation; Amino Acid Sequence; Chains; Dipeptides - chemistry; Fragmentation; Ion temperature; Ions - chemistry; Mathematical analysis; Models, Molecular; Molecular Sequence Data; Peptide Fragments - chemistry; Peptides; Rate constants; Spectrometry, Mass, Electrospray Ionization; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Tags; Temperature; Thermodynamics
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp308697v

Peptide fragmentations into b- and y-type ions are useful for the identification of proteins. The b ion, having the structure of a N-protonated oxazolone, dissociates to the a-type ion with loss of CO. This CO-loss process affords the possibility of characterizing the temperature of the b ion. Herein, we used N-acylated dipeptide tags, isobaric tags originally developed for protein quantification, as internal standards for the measurement of the ion temperature in peptide fragmentation. Amine-reactive dipeptide tags were attached to the N-termini of sample peptides. Collision-induced dissociation (CID) of the tagged peptides yielded a b-type quantitation signal (bS) from the tag, which subsequently dissociated into the aS ion with CO-loss. As the length of alkyl side chain on the dipeptide tag was extended from C1 to C8, the yield of aS ion gradually increased for the 4-alkyl-substituted oxazolone ion but decreased for the 2-alkyl-substituted one. To gain insights into the unimolecular dissociation kinetics, we obtained the potential energy surface from ab initio calculations. Theoretical study suggested that the 4-alkyl substitution on N-protonated oxazolone decreased the enthalpy of activation by stabilizing the productlike transition state, whereas the 2-alkyl substitution increased it by stabilizing the reactant. Resulting potential energy surfaces were used to calculate the microcanonical and canonical rate constants as well as the aS-ion yield. Arrhenius plots of canonical rate constants provided activation energies and pre-exponential factors for the CO-loss processes in the 600–800 K range. Comparison of experimental aS-ion yields with theoretical values led to precise determination of the temperature of bS ion. Thus, the bS-ion temperature of tagged peptide can be measured simply by combining kinetic parameters provided here and aS-ion yields obtained experimentally. Although the b-type fragment patterns varied with the chain length and position of alkyl substituent on the N-protonated oxazolone, the y-type fragment patterns were almost identical under these conditions. Furthermore, bS-ion temperatures were nearly the same with only a few degrees K difference. Our results demonstrate a novel use of N-acylated dipeptide tags as internal temperature standards, which enables the reproducible acquisition of peptide fragment spectra.