Collision-Induced Dissociation of Diazirine-Labeled Peptide Ions. Evidence for Brønsted-Acid Assisted Elimination of Nitrogen (original) (raw)
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Fast atom bombardment mass spectra of peptides. Dimer ion studies. Part VI
Biological Mass Spectrometry, 1989
The following experiments have been carried out: (i) dimer studies [ZM + 11'; (ii) decompositions of dimers: daughter ions from (YGGFL), , (YGGFL-YGGFL-2H2) and (YGGFL-2H2), as well as (YGGFM-YGGFL) and (YGGFM), dimers; (¡U) solvation site and pyridine collision-activated dissociation studies for dimer ions; (iv) mechanism of formation of [(ZM + 1) -Gly,]+ ions.
The structure and fragmentation of B n (n≥3) ions in peptide spectra
Journal of the American Society for Mass Spectrometry, 1996
The unimolecular and low energy collision-induced fragmentation reactions of the MI-I+ ions of N-acetyl-tri-alanine, N-acetyl-tri-alanine methyl ester, N-acetyl-tetra-alanine, tetra-alanine, penta-alanine, hexa-glycine, and Leu-enkephalin have been studied with a particular emphasis on the formation and fragmentation of B, (n = 3,4,5) ions. In addition, the metastable ion fragmentation reactions of protonated tetra-glycine, penta-glycine, and Leu-enkephalin amide have been studied. B, ions are prominent stable species in all spectra. The B, ions fragment, in part, by elimination of CO to form A ,, ions; this reaction occurs on the metastable ion time scale with a substantial release of kinetic energy U1,2 = 0.3-0.5 eV) that indicates that a stable configuration of the B,, ion fragments by way of a reacting configuration that is higher in energy than the fragmentation products, An + CO. Ab initio calculations strongly suggest that the stable configuration of the B, and B, ions is a protonated oxazolone formed by interaction of the developing charge with the next-nearest carbonyl group as HX is lost from the protonated species H-(Yyy),,-X * H+. The higher B,, ions also fragment, in part, to form the next-lower B ion, presumably in its stable protonated oxazolone form. This reaction is rationalized in terms of the three-dimensional structure of the B,, ions and it is proposed that the neutral eliminated is an cY-lactam. (J Am Sot Muss Spectrom 2996, 7, 233-242) Address reprint requests to
Electron transfer to gas-phase peptide ions with diazirine-containing amino acid residue photoleucine (L*) triggers diazirine ring reduction followed by cascades of residue-specific radical reactions. Upon electron transfer, substantial fractions of (GL*GGR +2H)+● cation-radicals undergo elimination of [NH4O] radicals and N2H2 molecules from the side chain. The side-chain dissociations are particularly prominent on collisional activation of long-lived (GL*GGR+2H)+● cation-radicals formed by electron transfer dissociation of noncovalent peptide-18-crown-6-ether ion complexes. The ion dissociation products were characterized bymultistage tandemmass spectrometry (MS n ) and ion mobility measurements. The elimination of [NH4O] was elucidated with the help of 2H, 15N, and 18O-labeled peptide ions and found to specifically involve the amide oxygen of the N-terminal residue. The structures, energies, and electronic states of the peptide radical species were elucidated by a combination of near-UV photodissociation experiments and electron structure calculations combining ab initio and density functional theory methods. Electron transfer reaching the ground electronic states of charge reduced (GL*GGR +2H)+● cation-radicals was found to reduce the diazirine ring. In contrast, backbone N−Cα bond dissociations that represent a 60%–75% majority of all dissociations because of electron transfer are predicted to occur from excited electronic states. Keywords: Electron transfer dissociation, Diazirine peptides, Excited states, Conformational analysis
Rapid Communications in Mass Spectrometry, 2007
A tandem time-of-flight mass spectrometer was built for photodissociation (PD) of singly protonated peptides and small proteins generated by matrix-assisted laser desorption/ionization. PD was performed in a second source after deceleration of precursor ions. The delayed extraction/postacceleration scheme was used for the product ions. For the PD at 193 nm of small singly protonated peptides, the present instrument showed much better sensitivity and resolution for product ions than the previous one (Moon JH, Yoon SH, Kim MS, Bull. Korean Chem. Soc. 2005; 26: 763) even though the overall spectral patterns obtained with the two instruments were similar. The present instrument was inferior in precursor ion selection and background noise level. PD was achieved for precursor ions as large as the singly protonated ubiquitin (m/z 8560.63), indicating that the photoexcitation is capable of supplying a sufficient amount of internal energy to dissociate large singly protonated proteins. As the precursor ion m/z increased, however, product ion signals deteriorated rather rapidly. As in the PD of small peptide ions with m/z around 1000, the types of the product ions generated from singly protonated peptides with m/z in the range 2000-4000 were mostly determined by the positions of arginine residues. Namely, a n and d n ions dominated when an arginine residue(s) was near the N-terminus while v n , w n , x n and y n dominated when the same residue(s) was near the C-terminus. In addition, d n , v n and w n ions were generated according to the correlation rules previously observed in the collisionally activated dissociation. Isoleucine and leucine isomers could be easily distinguished based on the w n and d n ions.
Journal of the American Society for Mass Spectrometry, 2007
Collisional activation of [M + H] + parent ions from peptides of n amino acid residues may yield a rearrangement that involves loss of the C-terminal amino acid residue to produce (b n−1 +H 2 O) daughters. We have studied this reaction by a retrospective examination of the m/z spectra of two collections of data. The first set comprised 398 peptides from coat protein digests of a number of plant viruses by various enzymes, where conditions in the tryptic digests were chosen so as to produce many missed cleavages. In this case a large effect was observed-323 (b n−1 +H 2 O) daughter ions (~81%), including 185 (~ 46%) "strong" decays with ratios (b n−1 +H 2 O)/(b n−1 )>1. The second set comprised 1200 peptides, all from tryptic digests, which were carried out under more stringent conditions, resulting in relatively few missed cleavages. Even here, 190 (b n−1 +H 2 O) ions (~ 16 %) were observed, including 87 (> 7%) "strong" decays, so the effect is still appreciable. The results suggest that the tendency for (b n−1 +H 2 O) ion formation is promoted by the protonated side chain of a non-C-terminal basic amino acid residue, in the order arginine ≫ lysine ≥ histidine, and that its (non-C-terminal) position is not critical. The results can be interpreted by a mechanism in which hydrogen bonding between the protonated side chain and the (n-1) carbonyl oxygen facilitates loss of the C-terminal amino acid residue to give a product ion having a carboxyl group at the new Cterminus.
Journal of the American Society for Mass Spectrometry, 2008
The fragmentation reactions of isomeric dipeptides containing ␣and -alanine residues (␣Ala-␣Ala, ␣Ala-Ala, Ala-␣Ala, and Ala-Ala) were studied using a combination of low-energy and energy resolved collision induced dissociation (CID). Each dipeptide gave a series of different fragment ions, allowing for differentiation. For example, peptides containing an N-terminal -Ala residue yield a diagnostic imine loss, while lactam ions at m/z 72 are unique to peptides containing -Ala residues. In addition, MS 3 experiments were performed. Structure-specific fragmentation reactions were observed for y 1 ions, which help identify the C-terminal residue. The MS 3 spectra of the b 2 ions are different suggesting they are unique for each peptide. Density functional theory (DFT) calculations predict that b 2 ions formed via a neighboring group attack by the amide are thermodynamically favored over those formed via neighboring group attack by the N-terminal amine. Finally, to gain further insight into the unique fragmentation chemistry of the peptides containing an N-terminal -alanine residue, the fragmentation reactions of protonated -Ala-NHMe were examined using a combination of experiment and DFT calculations. The relative transition-state energies involved in the four competing losses (NH 3 , H 2 O, CH 3 NH 2 , and CH 2 ϭNH) closely follow the relative abundances of these as determined via CID experiments.
Dissociation of the peptide bond in protonated peptides
Journal of Mass Spectrometry, 2000
The dissociation of the amide (peptide) bond in protonated peptides, [M Y H] Y , is discussed in terms of the structures and energetics of the resulting N -terminal b n and C -terminal y n sequence ions. The combined data provide strong evidence that dissociation proceeds with no reverse barriers through interconverting proton-bound complexes between the segments emerging upon cleavage of the protonated peptide bond. These complexes contain the C -terminal part as a smaller linear peptide (amino acid if one residue) and the N -terminal part either as an oxazolone or a cyclic peptide (cyclic amide if one residue). Owing to the higher thermodynamic stability but substantially lower gas-phase basicity of cyclic peptides vs isomeric oxazolones, the N -terminus is cleaved as a protonated oxazolone when ionic (b n series) but as a cyclic peptide when neutral (accompanying the C -terminal y n series). It is demonstrated that free energy correlations can be used to derive thermochemical data about sequence ions. In this context, the dependence of the logarithm of the abundance ratio log[y 1 /b 2 ], from protonated GGX (G, glycine; X, varying amino acid) on the gas-phase basicity of X is used to obtain a first experimental estimate of the gas-phase basicity of the simplest b-type oxazolone, viz. 2-aminomethyl-5-oxazolone (b 2 ion with two glycyl residues).
Rapid Communications in Mass Spectrometry, 2009
Tandem mass spectrometric data from peptides are routinely used in an unsupervised manner to infer product ion sequence and hence the identity of their parent protein. However, significant variability in relative signal intensity of product ions within peptide tandem mass spectra is commonly observed. Furthermore, instrument-specific patterns of fragmentation are observed, even where a common mechanism of ion heating is responsible for generation of the product ions. This information is currently not fully exploited within database searching strategies; this motivated the present study to examine a large dataset of tandem mass spectra derived from multiple instrumental platforms. Here, we report marked global differences in the product ion spectra of protonated tryptic peptides generated from two of the most common proteomic platforms, namely tandem quadrupoletime-of-flight and quadrupole ion trap instruments. Specifically, quadrupole-time-of-flight tandem mass spectra show a significant under-representation of N-terminal b-type fragments in comparison to quadrupole ion trap product ion spectra. Energy-resolved mass spectrometry experiments conducted upon test tryptic peptides clarify this disparity; b-type ions are significantly less stable than their y-type N-terminal counterparts, which contain strongly basic residues. Secondary fragmentation processes which occur within the tandem quadrupole-time-of-flight device account for the observed differences, whereas this secondary product ion generation does not occur to a significant extent from resonant excitation performed within the quadrupole ion trap. We suggest that incorporation of this stability information in database searching strategies has the potential to significantly improve the veracity of peptide ion identifications as made by conventional database searching strategies.