Fragmentation Reactions of a2 Ions Derived From Deprotonated DipeptidesA Synergy Between Experiment and Theory

Activated ion negative electron transfer dissociation of multiply charged peptide anions

We report the implementation and evaluation of activated ion negative electron transfer dissociation (AI-NETD) in order to enhance the analytical capabilities of NETD for the elucidation of doubly deprotonated peptide anions. The analytical figures-of-merit and fragmentation characteristics are compared for NETD alone and with supplemental collisional activation of the charge reduced precursors or infrared photoactivation of the entire ion population during the NETD reaction period. The addition of supplemental collisional activation of charge reduced precursor ions or infrared photoactivation of the entire ion population concomitant with the NETD reaction period significantly improves sequencing capabilities for peptide anions as evidenced by the greater abundances of product ions and overall sequence coverage. Neither of these two AI-NETD methods significantly alters the net fragmentation efficiencies relative to NETD; however, the sequence ion conversion percentages with respect to formation of diagnostic product ions are notably higher. Supplemental infrared photoactivation outperforms collisional activation for most of the peptide fragmentation metrics evaluated.

Spectroscopic evidence for an oxazolone structure in anionic b-type peptide fragments

Infrared spectra of anionic b-type fragments generated by collision induced dissociation (CID) from deprotonated peptides are reported. Spectra of the b(2) fragments of deprotonated AlaAlaAla and AlaTyrAla have been recorded over the 800-1800 cm(-1) spectral range by multiple-photon dissociation (MPD) spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Structural characterization of the b-type fragments is accomplished by comparison with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. Although diketopiperazine structures represent the energetically lowest isomers, the IR spectra suggest an oxazolone structure for the b(2) fragments of both peptides. Deprotonation is shown to occur on the oxazolone α-carbon, which leads to a conjugated structure in which the negative charge is practically delocalized over the entire oxazolone ring, providing enhanced gas-phase stability.

Determination of apparent decomposition threshold energies of lithium adducts of acylglycerols using tandem mass spectrometry and a novel derived effective reaction path length approach

Apparent decomposition threshold energies for the fragmentation pathways of lithiated acylglycerols were experimentally determined by collisional activation in a quadrupole-hexapole-quadrupole (QhQ) mass spectrometer. A previously developed 'derived effective reaction path length' approach for predicting bond dissociation energies (BDEs) of simple dissociations of electrostatic complexes such as alkali metal adducts (Li+), or halide adducts (Cl(-)) of acylglycerols, was extended to predict covalent bond apparent decomposition threshold energies of lithium adducts of a mono-acylglycerol, a 1,2-diacylglycerol, and a 1,3-diacylglycerol. The ability of the model to treat relatively large ionic systems (e.g. more than 100 atoms) represents a huge advantage of this approach. The model's calculated apparent decomposition threshold energies (Ea) are used in conjunction with the method of energy-resolved mass spectrometry, employing breakdown graphs, to give a more complete quantitative description of the fragmentation processes. Calculated Ea values allowed ranking of the 1,2-diacylglycerol as more reactive than the 1,3-diacylglycerol; the mono-acylglycerol was ranked the least reactive. The method was applied to the low molecular weight product ions generally associated with the hydrocarbon series CnH2n+1+, where two separate pathways are deduced as contributing to the production of the abundant m/z 81 fragment ion. The favored ranking of the neutral losses of fatty acyl substituents for the 1,2-diacylglycerol was determined as: loss of lithium fatty acetate > loss of fatty acid > loss of fatty acyl chain as ketene. For the 1,3-diacylglycerol, the descending order of ease of neutral loss was: loss of fatty acyl ketene > loss of lithium fatty acetate > loss of fatty acid. The results of this study demonstrate that the newly developed method is general in nature, and it can be used for the measurement of covalent bond decomposition threshold energies, as well as for the previously documented electrostatic (noncovalent) bond energies.

Towards liquid chromatography time-scale peptide sequencing and characterization of post-translational modifications in the negative-ion mode using electron detachment dissociation tandem mass spectrometry

Electron detachment dissociation (EDD) of peptide poly-anions is gentle towards post-translational modifications (PTMs) and produces predictable and interpretable fragment ion types (a., x ions). However, EDD is considered an inefficient fragmentation technique and has not yet been implemented in large-scale peptide characterization strategies. We successfully increased the EDD fragmentation efficiency (up to 9%), and demonstrate for the first time the utility of EDD-MS/MS in liquid chromatography time-scale experiments. Peptides and phosphopeptides were analyzed in both positive- and negative-ion mode using electron capture/transfer dissociation (ECD/ETD) and EDD in comparison. Using approximately 1 pmol of a BSA tryptic digest, LC-EDD-MS/MS sequenced 14 peptides (27% aa sequence coverage) and LC-ECD-MS/MS sequenced 19 peptides (39% aa sequence coverage). Seven peptides (18% aa sequence coverage) were sequenced by both EDD and ECD. The relative small overlap of identified BSA peptides demonstrates the complementarity of the two dissociation modes. Phosphopeptide mixtures from three trypsin-digested phosphoproteins were subjected to LC-EDD-MS/MS resulting in the identification of five phospho-peptides. Of those, one was not found in a previous study using a similar sample and LC-ETD-MS/MS in the positive-ion mode. In this study, the ECD fragmentation efficiency (15.7% av.) was superior to the EDD fragmentation efficiency (3.6% av.). However, given the increase in amino acid sequence coverage and extended PTM characterization the new regime of EDD in combination with other ion-electron fragmentation techniques in the positive-ion mode is a step towards a more comprehensive strategy of analysis in proteome research.

C alpha-C backbone fragmentation dominates in electron detachment dissociation of gas-phase polypeptide polyanions

Fragmentation of peptide polyanions by electron detachment dissociation (EDD) has been induced by electron irradiation of deprotonated polypeptides [M-nH](n-) with >10 eV electrons. EDD has been found to lead preferentially to a* and x fragment ions (C(alpha)-C backbone cleavage) arising from the dissociation of oxidized radical anions [M-nH]((n-1)-*. We demonstrate that C(alpha)-C cleavages, which are otherwise rarely observed in tandem mass spectrometry, can account for most of the backbone fragmentation, with even-electron x fragments dominating over radical a* ions. Ab initio calculations at the B3 LYP level of theory with the 6-311+G(2 p,2 d)//6-31+G(d,p) basis set suggested a unidirectional mechanism for EDD (cleavage always N-terminal to the radical site), with a*, x formation being favored over a, x* fragmentation by 74.2 kJ mol(-1). Thus, backbone C(alpha)-C bonds N-terminal to proline residues should be immune to EDD, in agreement with the observations. EDD may find application in mass spectrometry for such tasks as peptide sequencing and localization of labile post-translational modifications, for example, those introduced by sulfation and phosphorylation. EDD can now be performed not only in Fourier transform mass spectrometry, but also in far more widely used quadrupole (Paul) ion traps.

Fragmentation reactions of deprotonated peptides containing proline. The proline effect

The collision-induced dissociation (CID) fragmentation reactions of a variety of deprotonated peptides containing proline have been studied in detail using MS(2) and MS(3) experiments, deuterium labelling and accurate mass measurements when necessary. The [M--H--CO(2)](-) (a(2)) ion derived from H-Pro-Xxx-OH dipeptides shows an unusual fragmentation involving loss of C(2)H(4); this fragmentation reaction is not observed for larger peptides. The primary fragmentation reactions of deprotonated tripeptides with an N-terminal proline are formation of a(3) and y(1) ions. When proline is in the central position of tripeptides, a(3), y(2) and y(1) ions are the primary fragmentation products of [M--H](-), while when the proline is in the C-terminal position, a(3)and y(1) ions are the major primary products. In the latter case, the a(3) ion fragments primarily to the ''b(2) ion; further evidence is presented that the ''b(2) ions have a deprotonated oxazolone structure. Larger deprotonated peptides having at least two amino acid residues N-terminal to proline show a distinct preference for cleavage of the amide bond N-terminal to proline to form, mainly, the appropriate y ion. This proline effect is compared and contrasted with the similar proline effect observed in the fragmentation of protonated peptides containing proline.

Characterization of the Conformational Probability of N-Acetyl-Phenylalanyl-NH2 by RHF, DFT, and MP2 Computation and AIM Analyses, Confirmed by Jet-Cooled Infrared Data

Computational and experimental determinations were carried out in parallel on the conformational probability of N-Acetyl-Phenylalanine-NH2 (NAPA). Ab initio computations were completed at the BLYP/6-311G(df,p), B3LYP/6-31G(d), B3LYP/6-31G(d,p), and B3LYP/6-31+G(d) levels of theory, labeled L/61fp, B/6, B/6p, and B/6+, respectively. Three experimentally identified conformers were compared with theoretical data, confirming their identities as the betaLanti, gammaLgauche+, and gammaLgauche- (BACKBONESIDECHAIN) conformers. Evidence comes from matching experimental and theoretical data for all three constituent N-H stretches of NAPA, with a Delta(Experimental-Theoretical) = approximately 1-3 cm(-1), approximately 0-5 cm(-1), and approximately 1-6 cm(-1), at the L/61fp and B/6+ levels, respectively. Corrected-ZPE relative energies were computed to be 0.14, 0.00, 0.26 and 0.00, 0.67, 0.57 (kcal*mol(-1)) for the betaLanti, gammaLgauche+, and gamma(Lgauche- conformers, respectively, at the L/61fp and B/6+ levels, respectively. The MP2/6-31+G(d) level of theory was subsequently found to give similar relative energies. Characterization of the intramolecular interactions responsible for red and blue shifting of the N-H stretches showed the existence of the following intramolecular interactions: C=O[i]- - -HN[i], (Ar[i])-Cgamma- - -HN[i+1], (Ar[i])-Cdelta-H- - -O=C[i-1] for betaLanti; C=O[i-1]- - -HN[i+1], (Ar[i])-Cgamma- - -HN[i+1], (Ar[i])-C-H- - -O=C[i] for gammaLgauche+; and C=O[i-1]- - -HN[i+1] for gammaLgauche-. Each of these interactions were further investigated and subsequently characterized by orbital population and Atoms-In-Molecules (AIM) analyses, with the identity of overlap and bond critical points (BCP) serving as 'scoring criteria', respectively. Experimental and theoretical carbonyl stretches were also compared and showed good agreement, adding further strength to the synergy between experiment and theory.

Fragmentation of deprotonated N-benzoylpeptides: formation of deprotonated oxazolones

The fragmentation reactions of deprotonated N-benzoyl peptides, specifically hippurylglycine, hippurylglyclyclycine, and hippurylphenylalanine (hippuryl = N-benzoylGly) have been studied using MS2 and MS3 experiments as well as deuterium labeling. A major fragment ion is observed at m/z 160 ([C9H6NO2]-) which, upon collisional activation, mainly eliminates CO2 indicating that the two oxygen atoms have become bonded to the same carbon. This observation is rationalized in terms of formation of deprotonated 2-phenyl-5-oxazolone. Various pathways to the deprotonated oxazolone have been elucidated through MS3 experiments. Fragmentation of deprotonated N-acetylalanylalanine gives a relatively weak signal at m/z 112 which, upon collisional activation, fragments, in part, by loss of CO2 leading to the conclusion that the m/z 112 ion is deprotonated 2,4-dimethyl-5-oxazolone.