Primary and secondary locations of charge sites in angiotensin II (M + 2H)2+ ions formed by electrospray ionization

Evaluation of Hydrogen-Deuterium Exchange during Transient Vapor Binding of MeOD with Model Peptide Systems Angiotensin II and Bradykinin

The advancement of hybrid mass spectrometric tools as an indirect probe of molecular structure and dynamics relies heavily upon a clear understanding between gas-phase ion reactivity and ion structural characteristics. This work provides new insights into gas-phase ion-neutral reactions of the model peptides (i.e., angiotensin II and bradykinin) on a per-residue basis by integrating hydrogen/deuterium exchange, ion mobility, tandem mass spectrometry, selective vapor binding, and molecular dynamics simulations. By comparing fragmentation patterns with simulated probabilities of vapor uptake, a clear link between gas-phase hydrogen/deuterium exchange and the probabilities of localized vapor association is established. The observed molecular dynamics trends related to the sites and duration of vapor binding track closely with experimental observation. Additionally, the influence of additional charges and structural characteristics on exchange kinetics and ion-neutral cluster formation is examined. These data provide a foundation for the analysis of solvation dynamics of larger, native-like conformations of proteins in the gas phase.

Thiol-ene micropillar array electrospray ionization platform for zeptomole level bioanalysis

A micropillar array electrospray ionization (μPESI) platform fabricated from thiol-enes with 56 individual polyethylene glycol coated μPESI chips for bioanalytical mass spectrometry is introduced. Bioanalysis capability is shown by measurement of a protein, a protein digest and a cell lysate sample. The thiol-ene polyethylene glycol (PEG) coated μPESI chip allows the use of a wide range of aqueous-organic solvent compositions and provides a detection limit at 60 zeptomole level (6 × 10^-20 mol) for a peptide standard.

Use of doubly charged precursors to validate dissociation mechanisms of singly charged poly(dimethylsiloxane) oligomers

Collision-induced dissociation of doubly charged poly(dimethylsiloxane) (PDMS) molecules was investigated to provide experimental evidence for fragmentation reactions proposed to occur upon activation of singly charged oligomers. This study focuses on two PDMS species holding trimethylsilyl or methoxy end-groups and cationized with ammonium. In both cases, introduction of the additional charge did not induce significant differences in dissociation behavior, and the use of doubly charged precursors enabled the occurrence of charge-separation reactions, allowing molecules always eliminated as neutrals upon activation of singly charged oligomers to be detected as cationized species. In the case of trimethylsilyl-terminated oligomers, random location of the adducted charge combined with rapid consecutive reactions proposed to occur from singly charged precursors could be validated based on MS/MS data of doubly charged oligomers. In the case of methoxy-terminated PDMS, favored interaction of the adducted ammonium with both end-groups, proposed to rationalize the dissociation behavior of singly charged molecules, was also supported by MS/MS data obtained for molecules adducted with two ammonium cations.

Modification of the secondary structure of angiotensin II by substitution of hydrogen with Cs cations: an experimental and theoretical study

MALDI mass spectrometry in combination with post-source decay (PSD) analysis is a fast and easy to apply method for peptide sequencing. In this study, the PSD technique was used to investigate the influence of the adaption of one, two, and three caesium cations to angiotensin II in the gas phase. The PSD spectra of caesium-aggregated angiotensin II show far less fragmentation in comparison to the protonated one. In the case of singly (doubly) Cs(+) substituted angiotensin II, the PSD mass spectrum shows only fragments with one (two) Cs cation(s). These results are interpreted in terms of additional interactions of the caesium cation(s) with the peptide. In order to investigate this suggestion, the molecular structures were calculated with semi-empirical molecular dynamic (MD) simulations and further optimized at the quantum chemical level (BP86, SVP) of theory. On the one hand, secondary structures of Cs(+) substituted angiotensin II are more compact than the structure of protonated angiotensin II, indicating electrostatic interactions of the Cs cations and the heterocyclic structures. Moreover, oxyphilic interactions of the cations with the oxygen atoms of the peptide backbone also contribute as further van-der-Waals interactions of the Cs(+) substituted angiotensin II. These interactions are able to explain its higher stability due to reduced dissociation in comparison to the protonated angiotensin II. On the other hand, most MD simulations of doubly and triply Cs(+) substituted angiotensin II show a formation of a [2 Cs] cluster, surrounded by the peptide molecule. The formation of this cluster would explain the lack of singly Cs(+) substituted fragments in the PSD mass spectrum of doubly Cs(+) substituted angiotensin II.

On the zwitterionic nature of gas-phase peptides and protein ions

Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation.

Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1

Biomolecular surface mapping methods offer an important alternative method for characterizing protein-protein and protein-ligand interactions in cases in which it is not possible to determine high-resolution three-dimensional (3D) structures of complexes. Hydroxyl radical footprinting offers a significant advance in footprint resolution compared with traditional chemical derivatization. Here we present results of footprinting performed with hydroxyl radicals generated on the nanosecond time scale by laser-induced photodissociation of hydrogen peroxide. We applied this emerging method to a carbohydrate-binding protein, galectin-1. Since galectin-1 occurs as a homodimer, footprinting was employed to characterize the interface of the monomeric subunits. Efficient analysis of the mass spectrometry data for the oxidized protein was achieved with the recently developed ByOnic (Palo Alto, CA) software that was altered to handle the large number of modifications arising from side-chain oxidation. Quantification of the level of oxidation has been achieved by employing spectral intensities for all of the observed oxidation states on a per-residue basis. The level of accuracy achievable from spectral intensities was determined by examination of mixtures of synthetic peptides related to those present after oxidation and tryptic digestion of galectin-1. A direct relationship between side-chain solvent accessibility and level of oxidation emerged, which enabled the prediction of the level of oxidation given the 3D structure of the protein. The precision of this relationship was enhanced through the use of average solvent accessibilities computed from 10 ns molecular dynamics simulations of the protein.

Use of 157-nm photodissociation to probe structures of y- and b-type ions produced in collision-induced dissociation of peptide ions

y- and b-type fragment ions produced in the collisional dissociation of arginine-terminated peptide ions are photodissociated with 157-nm light in a linear trap. y-type ions are shown to have the same structure as that of intact peptides of the same sequence with the ionizing proton located at the most basic residue(s). For generic b-type ions, the ionizing proton is shown to be sequestered at the N-terminal arginine, which is consistent with the proposed oxazolone structure.

A mechanistic investigation of the enhanced cleavage at histidine in the gas-phase dissociation of protonated peptides

Enhanced gas-phase cleavage of peptides adjacent to histidine was investigated. The peptides examined were angiotensins III (RVYIHPF) and IV (VYIHPF) as well as synthetic peptide analogues with altered key residues ((R)VYI-X-Z-F; X = F or H and Z = A, P, or Sar) or a fixed charge M3P(+)CH(2)C(O)-VYIHPF. While all singly protonated peptide ions containing both histidine and arginine fragment nonselectively, the doubly protonated peptide ions with arginine and histidine, and the singly protonated peptides containing histidine but not arginine, cleave in a selective manner. In particular, dominant complementary b+/y+ product ions resulting from cleavage between the HP amide bond are observed. For the fixed-charge derivative, selective cleavage occurs only if a proton is added to produce a doubly charged precursor. The results are consistent with involvement of a protonated histidine in the selective cleavage. The ratio of b+/y+ is determined by the identity of the residue C-terminal to histidine and by the ability of protonated histidine to transfer a proton to the C-terminal leaving fragment. This was probed further by systematically changing the residue C-terminal to histidine and by alkylating histidine. The results indicate that while b+/y+ complementary ion pairs dominate in doubly protonated RVYIHPF, b5(2+) and b6(2+) product ions dominate the spectra of doubly protonated RVYIHAF. Also, dominant b5(2+) product ions are observed when the histidine side chain is alkylated (H) in doubly protonated RVYIHPF. Based on all of the results, a selective fragmentation mechanism for enhanced cleavage at histidine involving an atypical b ion structure is proposed.

Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra

Fragmentation at the Xxx-Pro bond was analyzed for a group of peptide mass spectra that were acquired in a Finnigan ion trap mass spectrometer and were generated from proteins digested by enzymes and identified by the Sequest algorithm. Cleavage with formation of a + b + y ions occurred more readily at the Xxx-Pro bond than at other locations in these peptides, and the importance of this cleavage varied by the identity of Xxx. The most abundant Xxx-Pro relative bond cleavage ratios were observed when Xxx was Val, His, Asp, Ile, and Leu, whereas the least abundant cleavage ratios occurred when Xxx was Gly or Pro. Rationalization for these cleavage ratios at Xxx-Pro may include contribution of the Asp or His side chain to enhanced cleavage or the conformation of Pro, Gly, and the aliphatic residues Val, Ile, and Leu at the Xxx location in the Xxx-Pro bond. Although unusual fragmentation behavior has been noted for Pro-containing peptides, this analysis suggests that fragmentation at the Xxx-Pro bond is predictable and that this information may be used to improve the identification of proteins if it is incorporated into peptide sequencing algorithms.

Kinetic energy release distributions in mass spectrometry

Kinetic energy releases (KERs) in unimolecular fragmentations of singly and multiply charged ions provide information concerning ion structures, reaction energetics and dynamics. This topic is reviewed covering both early and more recent developments. The subtopics discussed are as follows: (1) introduction and historical background; (2) ion dissociation and kinetic energy release: kinematics; potential energy surfaces; (3) the kinetic energy release distribution (KERD); (4) metastable peak observations: measurements on magnetic sector and time-of-flight instruments; energy selected results by photoelectron photoion coincidence (PEPICO); (5) extracting KERDs from metastable peak shapes; (6) ion structure determination and reaction mechanisms: singly and multiply charged ions; biomolecules and fullerenes; (7) theoretical approaches: phase space theory (PST), orbiting transition state (OTS)/PST, finite heat bath theory (FHBT) and the maximum entropy method; (8) exit channel interactions; (9) general trends: time and energy dependences; (10) thermochemistry: organometallic reactions, proton-bound clusters, fullerenes; and (11) the efficiency of phase space sampling.

Mass analysis at the advent of the 21st century

There have been many new and exciting developments in mass spectrometer systems in recent years. Many of these developments are being driven by challenges presented by molecular biology. The activity is fueled by resources being devoted to drug development, for example, and other medically and biologically related activities. Progress in these applications will be accelerated by improved sensitivity, specificity, and speed. In mass spectrometry, this translates to greater mass resolving power, mass accuracy, mass-to-charge range, efficiency, and speed. It is safe to say that the demands resulting from current analytical needs are likely to be met to varying degrees but probably not by a single analyzer technology or hybrid instrument. On-line and/or off-line separations and manipulations combined with mass spectrometry will also play increasingly important roles. For any analyzer, or combination of analyzers, to become widely used it must have an important application for which its figures of merit are best suited, relative to competing approaches. The relative cost of competing technologies is also an important factor. The mass filter has seen so much use in the past 30 years because its characteristics best fit a wide range of applications. As an example, biological applications, which are currently driving many instrument development activities in mass spectrometry, demand more information, of higher quality, from less material, faster, and at lower cost. Which technologies will dominate biological applications in the coming years is open to speculation. However, in considering the relative merits of today's dominant mass analyzers, areas of opportunity for improvement are apparent. Furthermore, new and more demanding measurement needs are constantly being recognized that will continue to exercise the creativity of the mass spectrometry community.

Collision-induced dissociation of ring-opened cyclic depsipeptides with a guanidino group by electrospray ionization/ion trap mass spectrometry

The characteristics shown in the electrospray ionization/ion trap mass spectra of ring-opened LI-F antibiotics (cyclic depsihexapeptides with a 15-guanidino-3-hydroxypentadecanoic group as a side-chain) were examined. Collision-induced dissociation (CID) MS of protonated molecules of the depsipeptides produced many fragment ions. Most of these fragment ions contained information for determining the amino acid sequences of antifungal antibiotics. The fragment ions were classified into six groups (b(n'), B(n'), B'(n'), beta(n'), y(n) and Y(n)). According to MS(3) spectra, the B(n'), B'(n) and beta(n) ions can be considered to be derived with a cleavage at each CO--NH in the peptide bonds of [MH--NH(3)](+),[MH--NH(3)--OH](+) and [MH--NH(3)--2H(2)O](+), respectively, in ion trap MS. Losses of NH(3) and H(2)O from the amino acid residues of the depsipeptides in ion trap MS are likely to be smaller than those from the side-chain. The measurements with electrospray ionization (ESI)/ion trap MS of depsipeptides with a side chain containing polar groups may provide useful information for structural determination.