Sequence-specific fragmentation of deprotonated peptides containing H or alkyl side chains

The [M - H]- ions of a variety of di- to pentapeptides containing H or alkyl side chains have been prepared by electrospray ionization and low-energy collision-induced dissociation (CID) of the deprotonated species carried out in the interface region between the atmospheric pressure source and the quadrupole mass analyzer. Using the nomenclature applied to the fragmentation of protonated peptides, deprotonated dipeptides fragment to give a2 ions (CO2 loss) and y1 ions, where the y1 ion has two fewer hydrogens than the y"1 ions formed from protonated peptides. Deprotonated tri- and tetrapeptides fragment to give primarily y1, c1, and "b2 ions, where the "b2 ion has two fewer hydrogens than the b2 ion observed for protonated peptides. More minor yields of y2, c2, and a2 ions also are observed. The a ion formed by loss of CO2 from the [M - H]- ion shows loss of the N-terminal residue for tripeptides and sequential loss of two amino acid residues from the N-terminus for tetrapeptides. The formation of c(n) ions and the sequential loss of N-terminus residues from the [M - H - CO2]- ion serves to sequence the peptide from the N-terminus, whereas the formation of y(n) ions serves to sequence the peptide from the C-terminus. It is concluded that low-energy CID of deprotonated peptides provides as much (or more) sequence information as does CID of protonated peptides, at least for those peptides containing H or alkyl side chains. Mechanistic aspects of the fragmentation reactions observed are discussed.     

Multi-stage tandem mass spectrometry of metal cationized leucine enkephalin and leucine enkephalin amide

We have examined the multi-stage collision induced dissociation (CID) of metal cationized leucine enkephalin, leucine enkephalin amide, and the N-acetylated versions of the peptides using ion trap mass spectrometry. In accord with earlier studies, the most prominent species observed during the multi-stage CID of alkali metal cationized leucine enkephalin are the [b(n) + 17 + Cat]+ ions. At higher CID stages (i.e. >MS(4)), however, dissociation of the [b2 + 17 + Cat]+ ion, a cationized dipeptide, results in the production of [a(n) -1 + Cat]+ species. The multi-stage CID of Ag+ cationized leucine enkephalin can be initiated with either the [b(n) -1 + Ag]+ or [b(n) + 17 + Ag]+ ions produced at the MS/MS stage. For the former, sequential CID stages cause, in general, the loss of CO, and then the loss of the imine of the C-terminal amino acid, to reveal the amino acid sequence. Similar to the alkali cationized species, CID of [b2 -1 + Ag]+ produces prominent [a(n) -1 + Ag]+ ions. The multi-stage CID of argentinated peptides is reminiscent of fragmentation observed for protonated peptides, in that a series of (b(n)) and (a(n)) type ions are generated in sequential CID stages. The Ag+ cation is similar to the alkali metals, however, in that the [b(n) + 17 + Ag]+ product is produced at the MS/MS and MS3 stages, and that sequential CID stages cause the elimination of amino acid residues primarily from the C-terminus. We found that N-acetylation of the peptide significantly influenced the fragmentation pathways observed, in particular by promoting the formation of more easily interpreted (in the context of unambiguous sequence determination) dissociation spectra from the [b2 + 17 + Li]+, [b2 + 17 + Na]+ and [b2 -1 + Ag]+ precursor ions. Our results suggest, therefore, that N-acetylation may improve the efficacy of multi-stage CID experiments for C-terminal peptide sequencing in the gas phase. For leucine enkephalin amide, only the multi-stage CID of the argentinated peptide allowed the complete amino acid sequence to be determined from the C-terminal side.     

Characterization of Nα-Fmoc-protected dipeptide isomers by electrospray ionization tandem mass spectrometry (ESI-MS(n)): effect of protecting group on fragmentation of dipeptides

A series of positional isomeric pairs of Fmoc-protected dipeptides, Fmoc-Gly-Xxx-OY/Fmoc-Xxx-Gly-OY (Xxx=Ala, Val, Leu, Phe) and Fmoc-Ala-Xxx-OY/Fmoc-Xxx-Ala-OY (Xxx=Leu, Phe) (Fmoc=[(9-fluorenylmethyl)oxy]carbonyl) and Y=CH(3)/H), have been characterized and differentiated by both positive and negative ion electrospray ionization ion-trap tandem mass spectrometry (ESI-IT-MS(n)). In contrast to the behavior of reported unprotected dipeptide isomers which mainly produce y(1)(+) and/or a(1)(+) ions, the protonated Fmoc-Xxx-Gly-OY, Fmoc-Ala-Xxx-OY and Fmoc-Xxx-Ala-OY yield significant b(1)(+) ions. These ions are formed, presumably with stable protonated aziridinone structures. However, the peptides with Gly- at the N-terminus do not form b(1)(+) ions. The [M+H](+) ions of all the peptides undergo a McLafferty-type rearrangement followed by loss of CO(2) to form [M+H-Fmoc+H](+). The MS(3) collision-induced dissociation (CID) of these ions helps distinguish the pairs of isomeric dipeptides studied in this work. Further, negative ion MS(3) CID has also been found to be useful for differentiating these isomeric peptide acids. The MS(3) of [M-H-Fmoc+H](-) of isomeric peptide acids produce c(1)(-), z(1)(-) and y(1)(-) ions. Thus the present study of Fmoc-protected peptides provides additional information on mass spectral characterization of the dipeptides and distinguishes the positional isomers.     

Investigation of several unique tandem mass spectrometric fragmentation patterns of NFDEIDR, an orcokinin analog, and its N-terminal dimethylated form

Orcokinins are a family of myotropic neuropeptides widely present in various decapod crustaceans and insect species. The majority of the orcokinins identified to date share a conserved sequence of NFDEIDR at their N-termini. Electrospray ionization quadrupole time-of-flight tandem mass spectrometric (ESI-QTOF-MS/MS) analysis of doubly charged orcokinin precursor ions reveals the presence of a y(n - 1) + 10 peak, which is more intense than that for the y(n - 1) ion. To elucidate the identity of this novel fragment ion and understand the mechanism underlying this fragmentation, we employed a combined approach involving the use of isotopic N-terminal dimethylation, methyl esterification, and isotope-encoded NFDEIDR. Comparison of the fragmentation patterns of these chemically modified orcokinin analogs allowed the determination of the structure of the y(n - 1) + 10 ion as y(n - 1) + CO--H2O. The yx + CO--H2O ions, along with the yx + CO and yx + CO--NH3 ions, are also present in the MS/MS spectra of NFDEIDR and several other peptides. Additionally, we report two other unusual fragmentation ions in the MS/MS spectra of N-terminal dimethyl NFDEIDR (2+), which yields the novel fragment ions of the y(n - 1) + 38 ion and the [M+2H-59]2+ ion. These two ion series involve the neutral loss of the asparagine side chain. The same sets of ions are also present in other peptides with dimethyl-modified asparagines at the N-terminus. The competition between the side-chain loss and loss of dimethylamine is described. The loss of the side chain of N-terminal dimethyl Asp1 is reported as well. We also report for the first time the neutral loss of ammonia from the N-terminal amino group of Asn1 and the loss of CO2 from the side chain of aspartic acid.     

Novel rearranged ions observed for

C-terminal rearrangement ions [b(n-1) + H2O] (where n refers to the total number of residues of peptides) are frequently observed for peptides which contain basic amino acid(s), especially arginine, at or near their N termini in low- and high-energy collision-induced dissociation or post-source decay (PSD) spectra. Here we report a novel rearrangement, associated with PSD for serine- or threonine-containing peptides that are susceptible to C-terminal rearrangement. Based on PSD analyses of serine- or threonine-containing bradykinin and its analogs, which have been ethyl-esterified or 18O labeled at their C termini, the [b(k) + H2O] (where k denotes the position adjacent to the left of the Ser/Thr residue) ion is generally thought to be formed by the transfer of the hydroxyl moiety of a serine or threonine residue to the carbonyl group of the residue to its left accompanied by the loss of the remaining C-terminal portion of the peptide. When the Ser/Thr is at or near the C terminus, the present [b(k) + H2O] ion could be formed via two pathways, i.e., the Ser/Thr-related rearrangement and the conventional C-terminal rearrangement, which has been clearly verified by 18O labeling at the C terminus. In addition, the ions which are formally designated as [y(m)b(l) + H2O], where y(m)b(l) denotes a b-type internal ion, are also briefly described.     

Modelling of the gas-phase phosphate group loss and rearrangement in phosphorylated peptides

The gas-phase dissociation of phosphorylated peptides was modelled using a combination of quantum mechanics and the Rice-Ramsperger-Kassel-Marcus theory. Potential energy surfaces and unimolecular reaction rates for several low-energy fragmentation and rearrangement pathways were estimated, and a general mechanism was proposed. The neutral loss of the phosphoric acid was mainly an outcome of the intramolecular nucleophilic substitution mechanism. The mechanism involves a nucleophilic attack of the phosphorylated amino acid N-terminal carbonyl oxygen on β-carbon, yielding a cyclic five-membered oxazoline product ion. Regardless of the proton mobility, the pathway was charge directed either by a mobile proton or by a positively charged side chain of some basic residue. Although the mechanistic aspects of the phosphate loss are not influenced by the proton mobility environment, it does affect ion abundances. Results suggest that under the mobile proton environment, the interplay between phosphoric acid neutral loss product ion and backbone cleavage fragments should occur. On the other hand, when proton mobility is limited, neutral loss product ion may predominate. The fragmentation dynamics of phosphoserine versus phosphothreonine containing peptides suggests that H(3)PO(4) neutral loss from phosphothreonine containing peptides is less abundant than that from their phosphoserine containing analogs. During the low-energy CID of phosphorylated peptides in the millisecond time range, typical for ion trap instruments, a phosphate group rearrangement may happen, resulting in an interchange between the phosphorylated and the hydroxylated residues. Unimolecular dissociation rate constants imply the low abundance of such scrambled product ions.     

Observation of an unusually facile fragmentation pathway of gas-phase peptide ions: a study on the gas-phase fragmentation mechanism and energetics of tryptic peptides modified with 4-sulfophenyl isothiocyanate (SPITC) and 4-chlorosulfophenyl isocyanate (SPC) and their 18-crown-6 complexes

Various peptide modifications have been explored recently to facilitate the acquisition of sequence information. N-terminal sulfonation is an interesting modification because it allows unambiguous de novo sequencing of peptides, especially in conjunction with MALDI-PSD-TOF analysis; such modified peptide ions undergo fragmentation at energies lower than those required conventionally for unmodified peptide ions. In this study, we systematically investigated the fragmentation mechanisms of N-terminal sulfonated peptide ions prepared using two different N-terminal sulfonation reagents: 4-sulfophenyl isothiocyanate (SPITC) and 4-chlorosulfophenyl isocyanate (SPC). Collision-induced dissociation (CID) of the SPC-modified peptide ions produced a set of y-series ions that were more evenly distributed relative to those observed for the SPITC-modified peptides; y(n-1) ion peaks were consistently and significantly larger than the signals of the other y-ions. We experimentally investigated the differences between the dissociation energies of the SPITC- and SPC-modified peptide ions by comparing the MS/MS spectra of the complexes formed between the crown ether 18-crown-6 (CE) and the modified peptides. Upon CID, the complexes formed between 18-crown-6 ether and the protonated amino groups of C-terminal lysine residues underwent either peptide backbone fragmentation or complex dissociation. Although the crown ether complexes of the unmodified ([M + CE + 2H]2+) and SPC-modified ([M* + CE + 2H]2+) peptides underwent predominantly noncovalent complex dissociation upon CID, the low-energy dissociations of the crown ether complexes of the SPITC-modified peptides ([M' + CE + 2H]2+) unexpectedly resulted in peptide backbone fragmentations, along with a degree of complex dissociation. We performed quantum mechanical calculations to address the energetics of fragmentations observed for the modified peptides.     

A study of b<Subscript>1</Subscript>+H<Subscript>2</Subscript>O and b<Subscript>1</Subscript>-ions in the product ion spectra of dipeptides containing N-terminal basic amino acid residues

The product ion spectra of approximately 200 dipeptides were acquired under low-energy conditions using a triple quadrupole mass spectrometer. The spectra of dipeptides containing an N-terminal arginine (R), histidine (H), or lysine (K) were observed to yield a b(1) + H(2)O ion corresponding to the protonated basic amino acid. This was equivalent to the y(1)-ion in the corresponding C-terminal isomer. The formation of a b(1) + H(2)O ion was not a significant fragmentation channel in any dipeptides analyzed including those containing a C-terminal basic amino acid unless they also contained an N-terminal basic amino acid. Occurring simultaneously and under equal energy conditions an apparent b(1)-ion was formed, which has its corresponding C-terminal equivalent in the y(1)-H(2)O ion. Energy resolved mass spectrometry (ERMS), deuterium labeling, and accurate mass experiments as well as data reported were used to show the relationships between the b(1)+H(2)O and b(1)-ions in the dipeptides containing an N-terminal basic amino acid and the y(1) and y(1)-H(2)O ions in the corresponding C-terminal isomers.     

Electrospray ionization tandem mass spectrometric study on the effect of N-terminal beta- and gamma-carbo amino acids on fragmentation of GABA-hybrid peptides

The fragmentations of protonated and deprotonated ions of a new class of N-blocked hybrid Boc-carbopeptides containing repeats of gamma-Caa/gammaAbu- and beta-Caa/gammaAbu- (Caa==C-linked carbo gamma(4)-/beta(3)- amino acids derived from D-xylose, gammaAbu = gamma-aminobutyric acid) have been studied using electrospray ionization (ESI) ion-trap tandem mass spectrometry (MS/MS). MS/MS of a pair of these protonated diastereomers produces distinct fragmentation of the Boc group. The formation of [M + H-56](+) corresponding to loss of isobutylene is more pronounced for Boc-NH-(R)-gamma-Caa-gammaAbu-OH (2) whereas it is of low abundance for Boc-NH-(S)-gamma-Caa-gammaAbu--OH (1). Similarly, MS(2) of [M--H](-) of 2 produces an abundant [M--H--C(CH(3))(3)OH--CO(2)](-) ion, which is absent for its diastereomeric isomer 1. From this, it can be suggested that MS/MS of N-blocked Boc-protected carbopeptides may be helpful in distinguishing the stereochemistry of the N-terminus Caa. MS(3) of [M + H-Boc + H](+) ions of peptides with a gamma-amino acid (gamma-Caa/gammaAbu) at the N-terminus produces only abundant y(n) (+) ions. On the other hand, characteristic fragmentations involving the peptide backbone (b(n) (+) and y(n) (+)) and the side chain are seen when beta-Caa is at the N-terminus of the peptides. MS(3) of the [M--H--C(CH(3))(3)OH](-) ion of peptides containing gamma-Caa/gammaAbu at the N-terminus gave y(n) (-) and [M--H--C(CH(3))(3)OH--CO(2)](-) ions, whereas the presence of beta-Caa at the N-terminus yielded predominantly [M--H--C(CH(3))(3)OH--HNCO](-). Thus, on the basis of our previous study and that presented here we propose that the fragmentation of these hybrid carbopeptides is highly influenced by the type of carbo amino acid present at the N-terminus.     

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.     

Influence of a 4-aminomethylbenzoic acid residue on competitive fragmentation pathways during collision-induced dissociation of metal-cationized peptides

Formation of [bn+17+cat]+ is a prominent collision-induced dissociation (CID) pathway for Li+- and Na+-cationized peptides. Dissociation of protonated and Ag+-cationized peptides instead favors formation of the rival bn+/[bn-1+cat]+ species. In this study the influence of a 4-aminomethylbenzoic acid (4AMBz) residue on the relative intensities of [b(3)-1+cat]+ and [b(3)+17+cat]+ fragment ions was investigated using several model tetrapeptides including those with the general formula A(4AMBz)AX and A(4AMBz)GX (where X=G, A, V). For Li+- and Na+-cationized versions of the peptides there was a significant increase in the intensity of [b(3)-1+cat]+ for the peptides that contain the 4AMBz residue, and in some cases the complete elimination of the [b(3)+17+cat]+ pathway. The influence of the 4AMBz residue may be attributed to the fact that [b(3)-1+cat]+ would be a highly conjugated species containing an aromatic ring substituent. Comparison of CID profiles generated from Na+-cationized AAGV and A(4AMBz)GV suggests an apparent decrease in the critical energy for generation of [b(3)-1+Na]+ relative to that of [b(3)+17+Na]+ when the aromatic amino acid occupies a position such that it leads to the formation of the highly conjugated oxazolinone, thus leading to an increase in formation rate for the former compared to the latter.     

Non-covalent interactions of alkali metal cations with singly charged tryptic peptides

The complexes formed by alkali metal cations (Cat(+) = Li(+), Na(+), K(+), Rb(+)) and singly charged tryptic peptides were investigated by combining results from the low-energy collision-induced dissociation (CID) and ion mobility experiments with molecular dynamics and density functional theory calculations. The structure and reactivity of [M + H + Cat](2+) tryptic peptides is greatly influenced by charge repulsion as well as the ability of the peptide to solvate charge points. Charge separation between fragment ions occurs upon dissociation, i.e. b ions tend to be alkali metal cationised while y ions are protonated, suggesting the location of the cation towards the peptide N-terminus. The low-energy dissociation channels were found to be strongly dependant on the cation size. Complexes containing smaller cations (Li(+) or Na(+)) dissociate predominantly by sequence-specific cleavages, whereas the main process for complexes containing larger cations (Rb(+)) is cation expulsion and formation of [M + H](+). The obtained structural data might suggest a relationship between the peptide primary structure and the nature of the cation coordination shell. Peptides with a significant number of side chain carbonyl oxygens provide good charge solvation without the need for involving peptide bond carbonyl groups and thus forming a tight globular structure. However, due to the lack of the conformational flexibility which would allow effective solvation of both charges (the cation and the proton) peptides with seven or less amino acids are unable to form sufficiently abundant [M + H + Cat](2+) ion. Finally, the fact that [M + H + Cat](2+) peptides dissociate similarly as [M + H](+) (via sequence-specific cleavages, however, with the additional formation of alkali metal cationised b ions) offers a way for generating the low-energy CID spectra of 'singly charged' tryptic peptides.     

Positive and negative ion electrospray tandem mass spectrometry (ESI MS/MS) of Boc-protected peptides containing repeats of L-Ala-gamma4Caa/gamma4Caa-L-Ala: differentiation of some positional isomeric peptides

High-resolution electrospray ionization (ESI) quadrupole time-of-flight and ion trap tandem mass spectrometry has been used to distinguish the positional isomers of a new class of N-blocked hybrid peptides containing repeats of the amino acids, L-Ala-gamma(4)Caa ((l))/gamma(4)Caa((l))-L-Ala [Caa((l)) = Carbo (lyxose) amino acid, derived from D-mannose]. Both MS/MS and MS(3) of protonated isomeric peptides produce characteristic fragmentation involving the peptide backbone, Boc-group, and the side-chain. It is interesting to observe that the abundant y(n)(+) ions are formed when the corresponding amide -NH does not participate in the helical structures in solution phase and relatively low abundance y(n)(+) ions resulted when the amide -NH involves in the H-bonding. Thus, it was possible to identify the amide -NH hydrogens that participate in the helical structures through H-bonding in solution phase. Further, negative ion ESI MS/MS has also been found to be useful for differentiating these isomeric peptide acids.     

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.     

Electrospray tandem mass spectrometry of alkali-cationized BocN-carbo-alpha,beta- and -beta,alpha-peptides: Differentiation of positional isomers

Dissociation pathways of a series of alkali-cationized hybrid peptides, viz., Boc-alpha,beta- and -beta,alpha-carbopeptides, synthesized from C-linked carbo-beta3-amino acids [Caa (S)] and alpha-alanine (L-Ala), have been investigated by electrospray ionization tandem mass spectrometry. The positional isomers (six pairs) of the cationized alpha,beta- and beta,alpha-peptides can be differentiated by the collision-induced dissociation (CID) spectra of their [M + Cat-Boc + H]+ ions which give characteristic series of alkali-cationized C- (x(n)+, y(n)+, z(n)+) and N-terminal (a(n)+, b(n)+, c(n)+) ions. Another noteworthy difference is cationized beta,alpha-peptides eliminate a molecule of ammonia whereas this pathway is absent for alpha,beta-peptides. This is useful for identifying the presence of a beta-amino acid at the N-terminus. The CID spectra of [M + Cat-Boc + H]+ ions of these peptide acids show abundant rearrangement [b(n) + 17 + Cat]+ (n = 1 to n-1) ions which is diagnostic for distinguishing between alpha- and beta-amino acid at the C-terminus. MS(n) experiments of [b(n) + Li-H]+ ions from these hybrid peptides showed the loss of CO and 72 u giving rise to [a(n) + Li-H]+ and cationized nitrile product ions which render support to earlier proposals that b(n)+ or [b(n) + Cat-H]+ ions have protonated or cationized oxazolinone structures, respectively.     

Automated interpretation of low-energy collision-induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry

SeqMS, a software aid for de novo sequencing by tandem mass spectrometry (MS/MS), which was initially developed for the automated interpretation of high-energy collision-induced dissociation (CID) MS/MS spectra of peptides, has been applied to the interpretation of low-energy CID and post-source decay (PSD) spectra of peptides. Based on peptide backbone fragmented ions and their related ions, which are the dominant ions observed in the latter two techniques, the types of ions and their propensities to be observed have been optimized for efficient interpretation of the spectra. In a typical example, the modified SeqMS allowed the complete sequencing of a 31-amino acid synthetic peptide, except for the isobaric amino acids (Leu or Ile, and Lys or Gln), based on only the low-energy CID-MS/MS spectrum.     

Effects of transition metal ion coordination on the collision-induced dissociation of polyalanines

Transition metal-polyalanine complexes were analyzed in a high-capacity quadrupole ion trap after electrospray ionization. Polyalanines have no polar amino acid side chains to coordinate metal ions, thus allowing the effects metal ion interaction with the peptide backbone to be explored. Positive mode mass spectra produced from peptides mixed with salts of the first row transition metals Cr(III), Fe(II), Fe(III), Co(II), Ni(II), Cu(I), and Cu(II) yield singly and doubly charged metallated ions. These precursor ions undergo collision-induced dissociation (CID) to give almost exclusively metallated N-terminal product ions whose types and relative abundances depend on the identity of the transition metal. For example, Cr(III)-cationized peptides yield CID spectra that are complex and have several neutral losses, whereas Fe(III)-cationized peptides dissociate to give intense non-metallated products. The addition of Cu(II) shows the most promise for sequencing. Spectra obtained from the CID of singly and doubly charged Cu-heptaalanine ions, [M + Cu - H](+) and [M + Cu](2+) , are complimentary and together provide cleavage at every residue and no neutral losses. (This contrasts with [M + H](+) of heptaalanine, where CID does not provide backbone ions to sequence the first three residues.) Transition metal cationization produces abundant metallated a-ions by CID, unlike protonated peptides that produce primarily b- and y-ions. The prominence of metallated a-ions is interesting because they do not always form from b-ions. Tandem mass spectrometry on metallated (Met = metal) a- and b-ions indicate that [b(n) + Met - H](2+) lose CO to form [a(n) + Met - H](2+), mimicking protonated structures. In contrast, [a(n) + Met - H](2+) eliminate an amino acid residue to form [a(n-1) + Met - H](2+), which may be useful in sequencing.     

Formation of (b<Subscript><Emphasis Type="Italic">n</Emphasis>−1</Subscript> + H<Subscript>2</Subscript>O) ions by collisional activation of maldi-formed peptide [M + H]<Superscript>+</Superscript> ions in a QqTOF mass spectrometer

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 (approximately 81%), including 185 (approximately 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 (approximately 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 > or = 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 C-terminus.     

Derivatization of protonated peptides via gas phase ion—molecule reactions with acetone

The protonated [M + H]+ ions of glycine, simple glycine containing peptides, and other simple di- and tripeptides react with acetone in the gas phase to yield [M + H + (CH3)2CO]+ adduct ion, some of which fragment via water loss to give [M + H + (CH3)2CO - H2O]+ Schiff's base adducts. Formation of the [M + H + (CH3)2CO]+ adduct ions is dependent on the difference in proton affinities between the peptide M and acetone, while formation of the [M + H + (CH3)2CO - H2O]+ Schiff's base adducts is dependent on the ability of the peptide to act as an intramolecular proton "shuttle." The structure and mechanisms for the formation of these Schiff's base adducts have been examined via the use of collision-induced dissociation tandem mass spectrometry (CID MS/MS), isotopic labeling [using (CD3)2CO] and by comparison with the reactions of Schiff's base adducts formed in solution. CID MS/MS of these adducts yield primarily N-terminally directed a- and b-type "sequence" ions. Potential structures of the b1 ion, not usually observed in the product ion spectra of protonated peptide ions, were examined using ab initio calculations. A cyclic 5 membered pyrrolinone, formed by a neighboring group participation reaction from an enamine precursor, was predicted to be the primary product.     

Mass spectral study of Boc-carbo-beta3-peptides: differentiation of two pairs of positional and diastereomeric isomers

A mass spectral study of a series of new Boc-C-linked carbo-beta(3)-peptides prepared from C-linked carbo-beta(3)-amino acids (Caa) was carried out using liquid secondary ion mass spectrometry (LSIMS), electrospray ionization (ESI) and tandem mass spectrometry. Using the nomenclature of Roepstorff and Fohlman, the positive ion high- and low energy collision-induced dissociation (CID) of [M + H - Boc + H](+) ions of the peptides produce both N- and C-terminus ions, y(n) (+) and b(n) (+) ions, with high abundance and other ions of low abundance. Further, characteristic fragment ions of carbohydrate moiety are observed. In contrast to the CID of protonated peptide acids, the CID of [M - H](-) ions of the beta(3)-peptide acids do not give b(n)(-) ions and show abundant z(n)(-) and c(n) (-) ions which are insignificant in the former. Two pairs of positionally isomeric Boc-carbo-beta(3)-dipeptides were differentiated by the CID of [M + H](+) ions in LSIMS and ESIMS. The fragment ion [M + H - C(CH(3))(3) + H](+) formed from [M + H](+) by the loss of 2-methylprop-2-ene is relatively more abundant in the dipeptide Boc-NH-beta-hGly-Caa(S)-OCH(3) (14) containing the sugar moiety at the C-terminus whereas it is insignificant in Boc-NH-Caa(S)-beta-hGly-OCH(3) (13), which has the sugar moiety at the N-terminus. Similarly, two pairs of diastereomeric dipeptides were distinguished by the high- and low-energy CID of [M + H](+) ions. The loss of 2-methylprop-2-ene is more pronounced for Boc-NH-Caa(R)-beta-hGly-OCH(3) (17) and Boc-NH-Caa(R)-Caa(S)-OCH(3) (18) isomers whereas it is insignificant for Boc-NH-Caa(S)-beta-hGly-OCH(3) (13) and Boc-NH-Caa(S)-Caa(S)-OCH(3) (2) isomers. This was attributed to a favorable configuration of the carbohydrate moiety favoring the 'H' migration involved in the loss of 2-methylprop-2-ene from the [M + H](+) ions of isomers 17 and 18 compared with the unfavorable configuration of the carbohydrate moiety in isomers 13 and 2.