Proton Mobility in b<Subscript>2</Subscript> Ion Formation and Fragmentation Reactions of Histidine-Containing Peptides

A detailed energy-resolved study of the fragmentation reactions of protonated histidine-containing peptides and their b₂ ions has been undertaken. Density functional theory calculations were utilized to predict how the fragmentation reactions occur so that we might discern why the mass spectra demonstrated particular energy dependencies. We compare our results to the current literature and to synthetic b₂ ion standards. We show that the position of the His residue does affect the identity of the subsequent b₂ ion (diketopiperazine versus oxazolone versus lactam) and that energy-resolved CID can distinguish these isomeric products based on their fragmentation energetics. The histidine side chain facilitates every major transformation except trans-cis isomerization of the first amide bond, a necessary prerequisite to diketopiperazine b₂ ion formation. Despite this lack of catalyzation, trans-cis isomerization is predicted to be facile. Concomitantly, the subsequent amide bond cleavage reaction is rate-limiting.

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Deamidation Reactions of Asparagine- and Glutamine-Containing Dipeptides Investigated by Ion Spectroscopy

Deamidation is a major fragmentation channel upon activation by collision induced dissociation (CID) for protonated peptides containing glutamine (Gln) and asparagine (Asn) residues. Here, we investigate these NH₃-loss reactions for four Asn- and Gln-containing protonated peptides in terms of the resulting product ion structures using infrared ion spectroscopy with the free electron laser FELIX. The influence of the side chain length (Asn versus Gln) and of the amino acid sequence on the deamidation reaction has been examined. Molecular structures for the product ions are determined by comparison of experimental IR spectra with spectra predicted by density functional theory (DFT). The reaction mechanisms identified for the four dipeptides AlaAsn, AsnAla, AlaGln, and GlnAla are not the same. For all four dipeptides, primary deamidation takes place from the amide side chain (and not from the N-terminus) and, in most cases, resembles the mechanisms previously identified for the protonated amino acids asparagine and glutamine. Secondary fragmentation reactions of the deamidation products have also been characterized and provide further insight in – and confirmation of – the identified mechanisms. Overall, this study provides a comprehensive molecular structure map of the deamidation chemistry of this series of dipeptides.

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Participation of C-H Protons in the Dissociation of a Proton Deficient Dipeptide

The dissociation of anionic dipeptides Phe*Gly and GlyPhe*, where Phe* refers to sulfonated phenyl alanine, has been investigated by using ion trap mass spectrometry. The dipeptides undergo collision-induced dissociation (CID) to give the same products, indicating that they rearrange to a common structure before dissociation. The rearrangement does not occur with the dipeptide methyl esters. The structures of the b₂ ions were investigated to determine the effect that having a remote, anionic site has on product formation. Comparison with the CID spectra for authentic structures shows that the b₂ ion obtained from GlyPhe* has predominantly a diketopiperazine structure. The CID spectra for the Phe*Gly b₂ ion and the authentic oxazolone are similar, but differences in intensity suggest a two-component mixture. Isotopic labeling studies are consistent with the formation of two products, with one resulting from loss of a non-mobile proton on the Gly α-carbon. The results are attributed to the formation of an oxazole and oxazolone enol product. Electronic structure calculations predict that the enol structure of the Phe*Gly b₂ ion is lower in energy than the keto version due to intramolecular hydrogen bonding with the sulfonate group.

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Spontaneous Isomerization of Peptide Cation Radicals Following Electron Transfer Dissociation Revealed by UV-Vis Photodissociation Action Spectroscopy

Peptide cation radicals of the z-type were produced by electron transfer dissociation (ETD) of peptide dications and studied by UV-Vis photodissociation (UVPD) action spectroscopy. Cation radicals containing the Asp (D), Asn (N), Glu (E), and Gln (Q) residues were found to spontaneously isomerize by hydrogen atom migrations upon ETD. Canonical N-terminal [z₄ + H]^+● fragment ion-radicals of the R-C^●H-CONH- type, initially formed by N?C_α bond cleavage, were found to be minor components of the stable ion fraction. Vibronically broadened UV-Vis absorption spectra were calculated by time-dependent density functional theory for several [^●DAAR + H]⁺ isomers and used to assign structures to the action spectra. The potential energy surface of [^●DAAR + H]⁺ isomers was mapped by ab initio and density functional theory calculations that revealed multiple isomerization pathways by hydrogen atom migrations. The transition-state energies for the isomerizations were found to be lower than the dissociation thresholds, accounting for the isomerization in non-dissociating ions. The facile isomerization in [^●XAAR + H]⁺ ions (X = D, N, E, and Q) was attributed to low-energy intermediates having the radical defect in the side chain that can promote hydrogen migration along backbone C_α positions. A similar side-chain mediated mechanism is suggested for the facile intermolecular hydrogen migration between the c- and [z + H]^●-ETD fragments containing Asp, Asn, Glu, and Gln residues.

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Spectroscopic Evidence for an Oxazolone Structure in Anionic <Emphasis Type="BoldItalic">b</Emphasis>-Type Peptide Fragments

Infrared spectra of anionic b-type fragments generated by collision induced dissociation (CID) from deprotonated peptides are reported. Spectra of the b₂ 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 b₂ 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.     

Electron Capture Dissociation of Trivalent Metal Ion-Peptide Complexes

With electrospray ionization from aqueous solutions, trivalent metal ions readily adduct to small peptides resulting in formation of predominantly (peptide + M_T ? H)²⁺, where M_T = La, Tm, Lu, Sm, Ho, Yb, Pm, Tb, or Eu, for peptides with molecular weights below ~1000 Da, and predominantly (peptide + M_T)³⁺ for larger peptides. ECD of (peptide + M_T ? H)²⁺ results in extensive fragmentation from which nearly complete sequence information can be obtained, even for peptides for which only singly protonated ions are formed in the absence of the metal ions. ECD of these doubly charged complexes containing M_T results in significantly higher electron capture efficiency and sequence coverage than peptide-divalent metal ion complexes that have the same net charge. Formation of salt-bridge structures in which the metal ion coordinates to a carboxylate group are favored even for (peptide + M_T)³⁺. ECD of these latter complexes for large peptides results in electron capture by the protonation site located remotely from the metal ion and predominantly c/z fragments for all metals, except Eu³⁺, which undergoes a one electron reduction and only loss of small neutral molecules and b/y fragments are formed. These results indicate that solvation of the metal ion in these complexes is extensive, which results in the electrochemical properties of these metal ions being similar in both the peptide environment and in bulk water.      

Differentiation of Positional Isomers of Hybrid Peptides Containing Repeats of β-Nucleoside Derived Amino Acid (β-Nda-) and L-Amino Acids by Positive and Negative Ion Electrospray Ionization Tandem Mass Spectrometry (ESI-MS<Superscript><Emphasis Type="Italic">n</Emphasis></Superscript>)

A new class of positional isomeric pairs of -Boc protected oligopeptides comprised of alternating nucleoside derived β-amino acid (β-Nda-) and L-amino acid residues (alanine, valine, and phenylalanine) have been differentiated by both positive and negative ion electrospray ionization ion-trap tandem mass spectrometry (ESI-MS ⁿ ). The protonated dipeptide positional isomers with β-Nda- at the N-terminus lose CH₃OH, NH₃, and C₂H₄O₂, whereas these processes are absent for the peptides with L-amino acids at the N-terminus. Instead, the presence of L-amino acids at the N-terminus results in characteristic retro-Mannich reaction involving elimination of imine. A good correlation has been observed between the conformational structure of the peptides and the abundance of y_n⁺ and b_n⁺ ions in MS ⁿ spectra. In the case of tetrapeptide isomers that are reported to form helical structures in solution phase, no y_n⁺ and b_n⁺ ions are observed when the corresponding amide -NH- participates in the helical structures. In contrast, significant y_n⁺ and b_n⁺ ions are formed when the amide -NH- is not involved in the H-bonding. In the case of tetra- and hexapeptides, it is observed that abundant b_n⁺ ions are formed, presumably with stable oxazolone structures when the C-terminus of the b_n⁺ ions possessed L-amino acid and the β-Nda- at the C-terminus appears to prevent the cyclization process leading to the absence of corresponding b_n⁺ ions.     

Influences of Proline and Cysteine Residues on Fragment Yield in Matrix-Assisted Laser Desorption/Ionization In-Source Decay Mass Spectrometry

Matrix-assisted laser desorption/ionization in-source decay produces highly informative fragments for the sequencing of peptides/proteins. Among amino acids, cysteine and proline residues were found to specifically influence the fragment yield. As they are both frequently found in small peptide structures for which de novo sequencing is mandatory, the understanding of their specific behaviors would allow useful fragmentation rules to be established. In the case of cysteine, a c?/w fragment pair originating from Xxx–Cys is formed by side-chain loss from the cysteine residue. The presence of a proline residue contributes to an increased yield of ISD fragments originating from N–C_α bond cleavage at Xxx₁–Xxx₂Pro, which is attributable to the cyclic structure of the proline residue. Our results suggest that the aminoketyl radical formed by MALDI-ISD generally induces the homolytic N–C_α bond cleavage located on the C–terminal side of the radical site. In contrast, N–C_α bond cleavage at Xxx–Pro produces no fragments and the N–C_α bond at the Xxx₁–Xxx₂Pro bond is alternatively cleaved via a heterolytic cleavage pathway.      

Effect of the his residue on the cyclization of b ions

The MSⁿ spectra of the [M + H]⁺ and b ₅ peaks derived from the peptides HAAAAA, AHAAAA, AAHAAA, AAAHAA, and AAAAHA have been measured, as have the spectra of the b ₄ ions derived from the first four peptides. The MS² spectra of the [M + H]⁺ ions show a substantial series of b_n ions with enhanced cleavage at the amide bond C-terminal to His and substantial cleavage at the amide bond N-terminal to His (when there are at least two residues N-terminal to the His residue). There is compelling experimental and theoretical evidence for formation of nondirect sequence ions via cyclization/reopening chemistry in the CID spectra of the b tons when the His residue is near the C-terminus. The experimental evidence is less clear for ions when the His residue is near the N-terminus, although this may be due to the use of multiple alanine residues in the peptide making identifying scrambled peaks more difficult. The product ion mass spectra of the b ₄ and b ₅ ions from these isomeric peptides with cyclically permuted amino acid sequences are similar, but also show clear differences. This indicates less active cyclization/reopening followed by fragmentation of common structures for b _n ions containing His than for sequences of solely aliphatic residues. Despite more energetically favorable cyclization barriers for the b ₅ structures, the b ₄ ions experimental data show more clear evidence of cyclization and sequence scrambling before fragmentation. For both b ₄ and b ₅ the energetically most favored structure is a macrocyclic isomer protonated at the His side chain.     

Fragmentation Reactions of Methionine-Containing Protonated Octapeptides and Fragment Ions Therefrom: An Energy-Resolved Study

The fragmentation reactions of the MH⁺ ions as well as the b₇, a₇, and a₇* ions derived therefrom have been studied in detail for the octapeptides MAAAAAAA, AAMAAAAA, AAAAMAAA, and AAAAAAMA. Ionization was by electrospray using a QqToF mass spectrometer, which allowed a study of the evolution of the fragmentation channels as a function of the collision energy. Not surprisingly, the product ion mass spectra for the b₇ ions are independent of the original precursor sequence, indicating macrocyclization and reopening to the same mixture of protonated oxazolones prior to fragmentation. The results show that this sequence scrambling results in a distinct preference to place the Met residue in the C-terminal position of the protonated oxazolones. The a₇ and a₇* ions also produce product ion mass spectra independent of the original peptide sequence. The results for the a₇ ions indicate that fragmentation occurs primarily from an amide structure analogous to that observed for a₄ ions (Bythell et al. in J Am Chem Soc 132:14766–14779, 2010). Clearly, the rearrangement reaction they have proposed applies equally well to a_n ions as large as a₇. The major fragmentation modes of the MH⁺ ions at low collision energies produce b₇, b_6, and b₅ ions. As the collision energy is increased further fragmentation of these primary products produces, in part, non-direct sequence ions, which become prominent at lower m/z values, particularly for the peptides with the Met residue near the N-terminus.

Tribromogermyl monochelates — derivatives of N,N-disubstituted 2-hydroxycarboxylic amides

Reactions of GeBr₄ with N,N-dimethyl-2-trimethylsiloxypropionamide (2a), (S)-2-trime-thylsiloxypropionpyrrolidide ((S)-2b), and N,N-dimethyl-O-(trimethylsilyl)mandelamide (2c) afforded pentacoordinated neutral (O,O)-monochelates, viz., N,N-dimethyl-2-tribromoger-myloxypropionamide (3a), (S)-2-tribromogermyloxypropionpyrrolidide ((S)-3b), and N,N-dimethyl-O-(tribromogermyl)mandelamide (3c), respectively. X-ray diffraction study was performed for tribromides 3a, (S)-3b, and 3c, as well as for the N,N-dimethylmandelamide (1c) described earlier. According to the X-ray diffraction data, the Ge atom in tribromides 3a, (S)-3b, and 3c is pentacoordinated and has trigonal bipyramidal configuration with two halogen atoms and oxygen atom of the ether group in the equatorial positions and the halogen atom and the amide oxygen atom in the axial fragment, the bonds in which are somewhat longer as compared to the analogous bonds in tetracoordinated Ge compounds.     

Fragmentation of doubly-protonated Pro-His-Xaa tripeptides: Formation of b 2 2+ ions

When ionized by electrospray from acidic solutions, the tripeptides Pro-His-Xaa (Xaa=Gly, Ala, Leu) form abundant doubly-protonated ions, [M+2H]²⁺. Collision-induced dissociation (CID) of these doubly-protonated species results, in part, in formation of b ₂ ²⁺ ions, which fragment further by loss of CO to form a ₂ ²⁺ ions; the latter fragment by loss of CO to form the Pro and His iminium [immonium is commonly used in peptide MS work] ions. Although larger doubly-charged b ions are known, this represents the first detailed study of b ₂ ²⁺ ions in CID of small doubly protonated peptides. The most abundant CID products of the studied doubly-protonated peptides arise mainly in charge separation involving two primary fragmentation channels, formation of the b ₂ /y ₁ pair and formation of the a ₁ /y ₂ pair. Combined molecular dynamics and density functional theory calculations are used to gain insight into the structures and fragmentation pathways of doubly-protonated Pro-His-Gly including the energetics of potential protonation sites, backbone cleavages, post-cleavage charge-separation reactions and the isomeric structures of b ₂ ²⁺ ions. Three possible structures are considered for the b ₂ ²⁺ ions: the oxazolone, diketopiperazine, and fused ring isomers. The last is formed by cleavage of the His-Gly amide bond on a pathway that is initiated by nucleophilic attack of one of the His side-chain imidazole nitrogens. Our calculations indicate the b ₂ ²⁺ ion population is dominated by the oxazolone and/or fused ring isomers.     

Gas-Phase Structure of Amyloid-β (12 – 28) Peptide Investigated by Infrared Spectroscopy, Electron Capture Dissociation and Ion Mobility Mass Spectrometry

The gas-phase structures of doubly and triply protonated Amyloid-β_12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N – C_α bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 3₁₀- and α-helix motifs.      

Investigation of bn-44 Peptide Fragments Using High Resolution Mass Spectrometry and Isotope Labeling

An N-terminal deuterohemin-containing hexapeptide (DhHP-6) was designed as a short peptide cytochrome c (Cyt c) mimetic to study the effect of N-terminal charge on peptide fragmentation pathways. This peptide gave different dissociation patterns than normal tryptic peptides. Upon collision-induced dissociation (CID) with an ion trap mass spectrometer, the singly charged peptide ion containing no added proton generated abundant and characteristic b_n-44 ions instead of b_n-28 (a_n) ions. Studies by high resolution mass spectrometry (HRMS) and isotope labeling indicate that elimination of 44 Da fragments from b ions occurs via two different pathways: (1) loss of CH₃CHO (44.0262) from a Thr side chain; (2) loss of CO₂ (43.9898) from the oxazolone structure in the C-terminus. A series of analogues were designed and analyzed. The experimental results combined with Density Functional Theory (DFT) calculations on the proton affinity of the deuteroporphyrin demonstrate that the production of these novel b_n-44 ions is related to the N-terminal charge via a charge-remote rather than radical-directed fragmentation pathway. Graphical Abstract

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Charge-separation reactions of doubly-protonated peptides: Effect of peptide chain length

The collision induced dissociation of doubly-protonated (Ala)_xHis (x=5, 6, 7, 8, 10) peptides have been studied. The major fragmentation reactions observed are symmetrical amide bond cleavages to give the complementary b_m and y_N-m ions, where N is the total number of residues in the peptide. Minor asymmetric cleavage to give doubly-protonated y ions also is observed, involving cleavage near the N-terminus. The shorter peptides (x=5, 6, 7) show major cleavage of the second amide bond to yield b₂ and y_N-2 ions, while (Ala)₁₀His shows major symmetrical cleavage at the fourth and fifth amide bonds. (Ala)₈His appears to be a transitional peptide in showing substantial symmetrical cleavage at the second, fourth, and fifth amide bonds. The results are in general agreement with the bifurcating nature of charge separation noted by Zubarev (J. Am. Soc. Mass Spectrom. 2008, 19, 1755–1763) from a statistical analysis of a large body of doubly-protonated tryptic peptide CID mass spectra. It is shown that the b₂ ion derived from doubly-protonated (Ala)₅His has a protonated oxazolone structure.     

Synthesis and structure of lithium and rubidium compounds with 2-(diphenylacetyl)-1,3-indanedione

Complexes RbL (I) and [Li₂(C₂H₅OH)L₂] (II) (L = C₂₃H₁₅O₃) have been synthesized and their crystal structures have been studied. Both compounds have monoclinic crystals with space group P2₁/c and Z = 4; I: a = 11.632(2) Å, b = 15.154(3) Å, c = 11.457(2) Å, β = 104.34(3)°; II: a = 12.982(3)Å, b = 12.083(2) Å, c = 25.317(5) Å β = 100.11(3)°. In the structure of I, dimeric groups [Rb₂O₆] with a shared edge are linked by the ligands to give infinite layers perpendicular to the x axis and cavities that form oblong channels. In the structure of II, Li₂O₇ dimers are formed by vertex sharing. The coordination of one of the lithium atoms (Li(1)) is completed to tetrahedral by the oxygen atom of the ethanol molecule. The structure of II, like that of I, is layered.     

Proton affinities of the N- and C-terminal segments arising upon the dissociation of the amide bond in protonated peptides

Dissociation of the amide bonds in a protonated peptide leads to N-terminal sequence fragments with cyclic structures and C-terminal sequence fragments with linear structures. The ionic fragments containing the N-terminus (b _n ) have been shown to be protonated oxazolones, whereas those containing the C-terminus (y _n ) are protonated linear peptides. The coproduced neutral fragments are cyclic peptides from the N-terminus and linear peptides from the C-terminus. A likely determinant of these structural choices is the proton affinity (PA) of the described peptide segments. This study determines the PA values of such segments (Pep), i.e., cyclic and linear dipeptides and a relevant oxazolone, based on the dissociations of proton-bound dimers [Pep + B _i ]H⁺ in which B _i is a reference base of known PA value (Cooks kinetic method). The dissociations are assessed at different internal energies to thereby obtain both proton affinities as well as entropies of protonation. For species with comparable amino acid composition, the proton affinity (and gas phase basicity) follows the order cyclic peptide ≪ oxazolone ≈ linear peptide. This ranking is consistent with dissociation of the protonated peptide via interconverting proton-bound complexes involving N-terminal oxazolone (O) or cyclopeptide (C) segments and C-terminal linear peptide segments (L), viz. O ⋯ H⁺ ⋯ L ⇄ C ⋯ H⁺ ⋯ L. N-terminal sequence ions (b _n ) are formed with oxazolone structures which can efficiently compete for the proton with the linear segments. On the other hand, N-terminal neutral fragments detach as cyclic peptides, with H⁺ now being retained by the more basic linear segment from the C-terminus to yield y _n .     

Peptide Dimethylation: Fragmentation Control via Distancing the Dimethylamino Group

Direct reductive methylation of peptides is a common method for quantitative proteomics. It is an active derivatization technique; with participation of the dimethylamino group, the derivatized peptides preferentially release intense a₁ ions. The advantageous generation of a₁ ions for quantitative proteomic profiling, however, is not desirable for targeted proteomic quantitation using multiple reaction monitoring mass spectrometry; this mass spectrometric method prefers the derivatizing group to stay with the intact peptide ions and multiple fragments as passive mass tags. This work investigated collisional fragmentation of peptides whose amine groups were derivatized with five linear ω-dimethylamino acids, from 2-(dimethylamino)-acetic acid to 6-(dimethylamino)-hexanoic acid. Tandem mass spectra of the derivatized tryptic peptides revealed different preferential breakdown pathways. Together with energy resolved mass spectrometry, it was found that shutting down the active participation of the terminal dimethylamino group in fragmentation of derivatized peptides is possible. However, it took a separation of five methylene groups between the terminal dimethylamino group and the amide formed upon peptide derivatization. For the first time, the gas-phase fragmentation of peptides derivatized with linear ω-dimethylamino acids of systematically increasing alkyl chain lengths is reported. Figure

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The knoevenagel reaction of malononitrile with some cyclic β-keto-esters—II: Mechanism of formation of heterocyclic reaction products

The formation of alkoxypyridinols 3a and 3b from the Knoevenagel reaction products 2a and 2b was shown to proceed by a mechanism in which the ester CO group initiates ring closure by intramolecular nucleophilic attack on the cyano group, possibly assisted by an acidic catalyst. Opening of the oxygen ring after nucleophilic attack by a basic catalyst on the former ester carbonyl C atom results in the formation of an amide, which in turn affords the alkoxypyridinols by a conventional cyclization mechanism.     

Mass spectrometric and quantum mechanical analysis of gas-phase formation, structure, and decomposition of various b2 ions and their specifically deuterated analogs

B ions represent an important type of fragment ions derived from protonated peptides by cleavage of an amide bond with N-terminal charge retention. Such species have also been discussed as key intermediates during cyclic peptide fragmentation. Detailed structural information on such ion types can facilitate the interpretation of multiple step fragmentations such as the formation of inner chain fragments from linear peptides or the fragmentation of cyclic peptides. The structure of different b₂ ion isomers was investigated with collision-induced dissociations (CID) in combination with hydrogen/deuterium (H/D) exchange of the acidic protons. Special care was taken to investigate fragment ions derived from pure gas-phase processes. Structures deduced from the results of the CID analysis were compared with structures predicted on the basis of quantum chemical density functional theory (DFT) calculations to be most stable. The results pointed to different types of structures for b₂ ion isomers of complementary amino acid sequences. Either the protonated oxazolone structure or the N-terminally protonated immonium ion structure were proposed on the basis of the CID results and the DFT calculations. In addition, the analysis of different selectively N-alkylated peptide analogs revealed mechanistic details of the processes generating b ions.