Effect of phenylalanine on the fragmentation of deprotonated peptides

Abstract

The fragmentation reactions of a variety of deprotonated dipeptides and tripeptides containing phenylalanine have been studied using energy-resolved collision-induced dissociation, isotopic labeling and MS/MS/MS experiments. The benzyl ␣-group has a substantial effect on the fragmentation reactions observed. When the phenylalanine is in the C-terminal position of dipeptides or tripeptides a major fragmentation reaction is elimination of neutral cinnamic acid to from a deprotonated amino acid amide (c 1 ion) for dipeptides and a deprotonated dipeptide amide (c 2 ion) for tripeptides. As a result of many studies, the main features of the fragmentation of protonated peptides have been elucidated, at least at the phenomenological level [5,6]. On the other hand much less is known concerning the fragmentation modes of deprotonated peptides. The majority of studies [7][8][9][10][11][12][13][14][15][16][17][18] have involved high-energy collision-induced dissociation (CID) and have been largely restricted to the [M Ϫ H] Ϫ ions of dipeptides with only a few tripeptides having been studied.A recent paper from this laboratory [19] has reported the low-energy CID of the [M Ϫ H] Ϫ ions of a variety of dipeptides to pentapeptides containing H or alkyl ␣-groups. The fragmentation reactions observed are illustrated schematically in Scheme 1 using nomenclature adapted from that used [6,7] for fragmentation of protonated peptides. A comparison of the low-energy CID results with the high-energy CID results reported by Eckersley et al. [12] showed that more extensive and sequence-specific fragmentation was observed in the low-energy CID experiments. This observation is in line with earlier work in this laboratory [20 -23] which showed that low-energy collisional activation of negative ions imparted, on average, greater energy to the anion than did high-energy collisional activationThe early studies [7][8][9][10][11][12][13][14][15][16][17][18] of small deprotonated peptides suggested that the fragmentation modes of the [M Ϫ H]Ϫ ions depended significantly on the identity of the ␣-groups of the constituent amino acids. The present work reports a study of the low-energy CID of deprotonated peptides containing phenylalanine in order to evaluate the role of the benzyl ␣-group on the fragmentation of the deprotonated peptides. The fragmentation reactions of a number of deprotonated dipeptides and two tripeptides containing phenylalanine have been examined by high-energy CID by Waugh et al. [15]. A comparison will be made of the high-energy and low-energy CID results. ExperimentalCollision-induced dissociation (CID) studies were performed using an electrospray/quadrupole mass spectrometer (VG Platform, Micromass, Manchester, UK) with CID in the interface region between the atmospheric pressure source and the quadrupole mass analyzer. It is well known [24,25] that CID can be achieved in this interface region, so-called cone voltage CID, and it has been clearly established [26 -28] that the average energy imparted to the decomposing i...

Formation of c1 fragment ions in collision‐induced dissociation of glutamine‐containing peptide ions: a tip for de novo sequencing

“…There are two other CID conditions that have previously shown formation of c ions from peptides. One of these involves negative ion mode CID of specific peptides; c 1 and c 2 fragment ions were observed when peptide ions ([MH] − ) containing Phe at the second or third position were fragmented in negative mode 22. The other condition, high‐energy CID, demonstrated sequence‐dependent generation of c ions by cleavage on the amino side of Thr, Try, Lys, Ser, and Gln of protonated peptides 23–25.…”

Fragmentation of deprotonated cyclic dipeptides by electrospray ionization mass spectrometry

“…The yield of cyclic dipeptide was 20-60%. The structures were characterized by 1 H NMR, 13 C NMR, ESI-MS, high resolution mass spectrometer (HRMS) and IR methods. The symmetrical cyclic dipeptides investigated in this study are cyclo(Ala-Ala)(1), cyclo(Leu-Leu)(2), cyclo(Ile-Ile)(3), cyclo(ValVal)(4), cyclo(Phe-Phe)(5), cyclo(Trp-Trp)(6), cyclo(Tyr-Tyr)(7) and cyclo(Met-Met) (8).…”

“…[13] Although there are many reports about the fragmentation pathways of deprotonated peptides and protonated cyclic dipeptides, to the best of our knowledge, much less is known so far concerning the investigation of structure-fragmentation relationships of deprotonated cyclic dipeptides. J. H. Bowie's group has studied the mass spectra of some deprotonated cyclic dipeptides in the negative chemical ionization (CI) mode.…”

Fragmentation reactions of deprotonated peptides containing proline. The proline effect

“…In our initial study 18 of deprotonated peptides containing only H or alkyl side chains, we observed that there was more extensive sequence-specific fragmentation under low-energy CID conditions than under high-energy CID conditions. 21 We have extended these studies to deprotonated peptides containing phenylalanine 22 and to deprotonated peptides containing glutamic acid; 23 in both cases fragmentation reactions specific to the side chain functionality were observed. In the present work, we explore…”