Electrospray ionisation-mass spectrometry of hydroxamate siderophores

Electrospray ionisation-mass spectrometry (ESI-MS) was applied to the detection of the iron complexes of the hydroxamate type siderophores ferrioxamine (FO), ferrichrome (FC) and iron(III) rhodotoluate (FR). Mass spectra of the three siderophores produced by ESI-MS were dominated by the protonated (M + 1)+ parent ions, except for FR at pH 4.3, which was present as the positively charged 1:1 complex. On collision with He ions, fragmentation proceeded largely via cleavage of C-N bonds. Flow injection analysis of the siderophores with detection by ESI-MS produced detection limits of 1.9 fmol for FO, 31.1 fmol for FC and 524 fmol for FR.     

Collision-induced dissociation tandem mass spectrometry of desferrioxamine siderophore complexes from electrospray ionization of UO2(2+), Fe3+ and Ca2+ solutions

Desferrioxamine (DEF) is a trihydroxamate siderophore typical of those produced by bacteria and fungi for the purpose of scavenging Fe(3+) from environments where the element is in short supply. Since this class of molecules has excellent chelating properties, reaction with metal contaminants such as actinide species can also occur. The complexes that are formed can be mobile in the environment. Because the natural environment is extremely diverse, strategies are needed for the identification of metal complexes in aqueous matrices having a high degree of chemical heterogeneity, and electrospray ionization mass spectrometry (ESI-MS) has been highly effective for the characterization of siderophore-metal complexes. In this study, ESI-MS of solutions containing DEF and either UO(2)(2+), Fe(3+) or Ca(2+) resulted in generation of abundant singly charged ions corresponding to [UO(2)(DEF - H)](+), [Fe(DEF - 2H)](+) and [Ca(DEF - H)](+). In addition, less abundant doubly charged ions were produced. Mass spectrometry/mass spectrometry (MS/MS) studies of collision-induced dissociation (CID) reactions of protonated DEF and metal-DEF complexes were contrasted and rationalized in terms of ligand structure. In all cases, the most abundant fragmentation reactions involved cleavage of the hydroxamate moieties, consistent with the idea that they are most actively involved with metal complexation. Singly charged complexes tended to be dominated by cleavage of a single hydroxamate, while competitive fragmentation between two hydroxamate moieties increased when the doubly charged complexes were considered. Rupture of amide bonds was also observed, but these were in general less significant than the hydroxamate fragmentations. Several lower abundance fragmentations were unique to the metal examined: abundant loss of H(2)O occurred only for the singly charged UO(2)(2+) complex. Further, NH(3) was eliminated only from the singly charged Fe(3+) complex; this and fragmentation of C-C and C-N bonds derived from neither the hydroxamate nor the amide groups suggested that Fe(3+) insertion reactions were competing with ligand complexation. In no experiments were coordinating solvent molecules observed, attached either to the intact complexes or to the fragment ions, which indicated that both intact DEF and its fragments were occupying all of the coordination sites around the metal centers. This conclusion was based on previous experiments that showed that undercoordinated UO(2)(2+) and Fe(3+) readily added H(2)O and methanol in the ESI quadrupole ion trap mass spectrometer that was used in this study.     

Bacterial iron transport: coordination properties of azotobactin, the highly fluorescent siderophore of Azotobacter vinelandii

Azotobacter vinelandii, a nitrogen-fixing soil bacterium, secretes in iron deficiency azotobactin delta, a highly fluorescent pyoverdin-like chromopeptidic hexadentate siderophore. The chromophore, derived from 2,3-diamino-6,7 dihydroxyquinoline, is bound to a peptide chain of 10 amino acids: (L)-Asp-(D)-Ser-(L)-Hse-Gly-(D)-beta-threo-HOAsp-(L)-Ser-(D)-Cit-(L)-Hse-(L)-Hse lactone-(D)-N(delta)-Acetyl, N(delta)-HOOrn. Azotobactin delta has three different iron(III) binding sites which are one hydroxamate group at the C-terminal end of the peptidic chain (N(delta)-Acetyl, N(delta)-HOOrn), one alpha-hydroxycarboxylic function in the middle of the chain (beta-threo-hydroxyaspartic acid), and one catechol group on the chromophore. The coordination properties of its iron(III) and iron(II) complexes were measured by spectrophotometry, potentiometry, and voltammetry after the determination of the acid-base functions of the uncomplexed free siderophore. Strongly negatively charged ferric species were observed at neutral p[H]'s corresponding to a predominant absolute configuration Lambda of the ferric complex in solution as deduced from CD measurements. The presence of an alpha-hydroxycarboxylic chelating group does not decrease the stability of the iron(III) complex when compared to the main trishydroxamate siderophores or to pyoverdins. The value of the redox potential of ferric azotobactin is highly consistent with a reductive step by physiological reductants for the iron release. Formation and dissociation kinetics of the azotobactin delta ferric complex point out that both ends of this long siderophore chain get coordinated to Fe(III) before the middle. The most striking result provided by fluorescence measurements is the lasting quenching of the fluorophore in the course of the protonation of the ferric azotobactin delta complex. Despite the release of the hydroxyacid and of the catechol, the fluorescence remains indeed quenched, when iron(III) is bound only to the hydroxamic acid, suggesting a folded conformation at this stage, around the metal ion, in contrast to the unfolded species observed for other siderophores such as ferrioxamine or pyoverdin PaA.     

Iron transport-mediated drug delivery using mixed-ligand siderophore-β-lactam conjugates

background: Assimilation of iron is essential for microbial growth. Most microbes synthesize and excrete low molecular weight iron chelators called siderophores to sequester and deliver iron by active transport processes. Specific outer membrane proteins recognize, bind and initiate transport of species-selective ferric siderophore complexes. Organisms most often have specific receptors for multiple types of siderophores, presumably to ensure adequate acquisition of the iron that is essential for their growth. Conjugation of drugs to synthetic hydroxamate or catechol siderophore components can facilitate active iron-transport-mediated drug delivery. While resistance to the siderophore—drug conjugates frequently occurs by selection of mutants deficient in the corresponding siderophore-selective outer membrane receptor, the mutants are less able to survive under iron-deficient conditions and in vivo. We anticipated that synthesis of mixed ligand siderophore—drug conjugates would allow active drug delivery by multiple iron receptor recognition and transport processes, further reducing the likelihood that resistant mutants would be viable.Results: Mixed ligand siderophore-drug conjugates were synthesized by combining hydroxamate and catechol components in a single compound that could chelate iron, and that also contained a covalent linkage to carbacephalosporins, as representative drugs. The new conjugates appear to be assimilated by multiple active iron-transport processes both in wild type microbes and in selected mutants that are deficient in some outer membrane iron-transport receptors.Conclusions: The concept of active iron-transport-mediated drug delivery can now be extended to drug conjugates that can enter the cell through multiple outer membrane receptors. Mutants that are resistant to such conjugates should be severely impaired in iron uptake, and therefore particularly prone to iron starvation.     

Matrix-assisted laser desorption/ionization time-of-flight and nano-electrospray ionization ion trap mass spectrometric characterization of 1-cyano-2-substituted-benz[f]isoindole derivatives of peptides for fluorescence detection

A series of hexa- to decapeptides (molecular mass range 800-1200) were labeled with naphthalene-2,3-dicarboxaldehyde, which preferentially reacts with the primary amino groups of a peptide. A highly stable peptide conjugate is formed, which allows selective analysis by fluorescence at excitation and emission wavelengths of 420 and 490 nm, respectively. After removal of unreacted compounds, the peptide conjugates were characterized by matrix-assisted laser desorption/ionization (MALDI) time-of-flight and nano-electrospray ionization (ESI) ion trap mass spectrometry. They readily form both [M + H]+ ions by MALDI and both [M + H]+ and [M + 2H]2+ ions by ESI. Furthermore, the fragmentation behavior of the N-terminally tagged peptides, exhibiting an uncharged N-terminus, was investigated applying post-source decay fragmentation with a curved field reflector and collision-induced dissociation with a quadrupole ion trap. Fragmentation is dominated in both cases by series of a-, b- and y-type ions and [M + H - HCN]+ ions. Peptide bonds adjacent to the fluorescence label were less susceptible to cleavage than the bonds of the non-derivatized peptide ions. In general, the resulting fragment ion patterns were less complex than those of the underivatized peptides.     

Biotin-enhanced fragmentation for direct deoxyribonucleic acid sequencing using matrix-assisted laser desorption/ionization mass spectrometry

Fragmentation of synthetic oligonucleotides under the influence of biotin was investigated using 3-hydroxypicolinic acid (3-HPA) as a matrix-assisted laser desorption/ionization (MALDI) matrix. Addition of biotin into the sample enhanced fragmentation of the oligonucleotide between bases. However, when the biotin was tagged to the 5'-terminus of the oligonucleotide, enhancements were observed not only in desorption/ionization efficiency but also in the fragmentation of molecular ions. The protonation/deprotonation process occurs on the tagged biotin is a possible reason for the enhancement in desorption/ionization. Site-specific backbone cleavage fragmentation patterns were observed. The sequences of oligonucleotides can be obtained from their fragment ions. The direct sequencing of a 5'-biotin-tagged 25-mer is demonstrated.     

Study of metal complexes of a tripodal hydroxypyridinone ligand by electrospray tandem mass spectrometry

The tripodal ligand N,N,N-tris[(1,hydroxy-2-pyridinon-6-yl)amide]propylamine was synthesized. It is composed of an anchor (nitrogen atom), a functional group (hydroxamate), and also a spacer of variable length defined by the number of methylene groups linking the anchor and the functional group. The characterization of this ligand in the presence of several divalent metal cations (Fe(II), Mn(II), Co(II) and Cu(II)), performed by electrospray ionization mass spectrometry (ESI-MS and ESI-MS/MS), allowed elucidation of oxidation states and also of different fragmentation patterns. The importance of the spacer length was studied in the case of the iron binary complex by comparing this ligand with another with a shorter spacer. In this way the stabilizing conditions, in which hydrogen bonds are implicated, were clarified.     

Electrospray tandem mass spectrometry analysis of S- and N-nitrosopeptides: Facile loss of NO and radical-induced fragmentation

The covalent addition of nitric oxide (NO) to protein thiols, a posttranslational modification termed S-nitrosation, is a ubiquitous event that modulates diverse cellular processes. The in vivo addition of NO to protein amines (N-nitrosation) has also been described and may similarly modify protein structure and function. While mass spectrometry has been employed for identification of nitrosoproteins, little is known about how S- and N-nitrosopeptides fragment. Such knowledge is important for its potential to inform on sites of protein nitrosation. Here we used electrospray tandem mass spectrometry to elucidate collision-induced dissociation (CID) features of S- and N-nitrosopeptide ions. We show that S- and N-nitrosopeptide ions readily lose NO, giving rise to species that contain thiyl and aminyl radicals, respectively. Fragmentation (MS3) of these radical peptide ions revealed an atypical pattern, characterized by the cleavage of select alphaCC and NalphaC bonds, rather than the more usual cleavage of amide bonds that result in b- and y-ions. These unanticipated fragmentation patterns are reconciled by radical-mediated abstraction of hydrogen from beta-carbon followed by beta-fragmentation. For thiyl radical peptides, we also observed dominant loss of SH and CH2SH from the Cys side-chain. Our findings provide new insights into the gas-phase chemistry of NO-modified peptide ions and suggest an unusual fragmentation pattern that may aid in future MS-based attempts to define the nitrosoproteome.     

Application of tandem analyser to SIMS studies of hydrocarbon polymers

The fragmentation of ions sputtered from the surface of low-density poly(ethylene) (LDPE) has been investigated by studying their collisionally activated dissociation (CAD) when incident upon a variety of target gases in the collision cell of a triple quadrupole SIMS instrument. It was found that heavier targets resulted in more extensive CAD than was observed with lighter targets but that sulphur hexafluoride is inefficient target because of the amount opf energy that is transferred to its vibrational modes of motion (rather than being available to induce fragmentation in the parent ion.) The behaviour observed for an oxygen target was quite different to that observed for other targets (at higher pressures). In general oxygen induced markedly greater fragmentation for the small parent ions but xenon was the preferred target for the larger parent ions. Fragmentation patterns could readily be assembled for all of the parent ions observed in the SIMS spectrum of LDPE using the CAD data. There are good indications that the data obtained may assist in indentification of ion structures and in elucidation of general rules governing the fragmentation of organic materials during SIMS. For example, LDPE fragment ions were found to obey quite strictly the Even Electron Rule, a well-known rule in mass spectrometry.     

On the collision-activated fragmentation of proferrioxamines: Evidence for a succinimide-mediated mechanism

The fragmentation mechanism of acyclic proferrioxamines has been studied by tandem mass spectrometry in a triple stage quadrupole mass analyzer by using activation in the collision cell as well as in the high pressure region prior to the first mass analyzer. The data suggest that proferrioxamines fragment preferentially at the hydroxamate bonds via cyclic rearrangement to succinimide derivatives. This pattern was observed most clearly for the peracetyl derivatives, in which the influence of terminal functional groups was masked. Free amino or carboxylic acid functions may modify this basic fragmentation pattern. Using hydrogen-deuterium exchange, we also were able to show that the hydrogen atoms that are “recruited” in the formation of ammonium ions are “acidic” ones from elsewhere in the molecule or the matrix. At the same time, this rules out that they originate from “activated” methylene groups, as previously proposed     

Siderophoregenic Bradyrhizobia boost yield of soybean

After screening for siderophore (microbial iron chelator) production, of seven available cultures of soybean (Glycine max L.) root nodule bradyrhizobia, one strain, Bradyrhizobium japonicum NCIM 2746, was selected to confirm its phytopathogenic suppression and soybean growth promotion. Based on chromatographic and spectrophotometric studies, two different siderophores, a hydroxamate type (MW 734) and another catecholate type (MW 1000), were observed. Randomized block design (RBD) analysis of sickpot studies (soil inoculated with phytopathogens) with an MACS 124 variety of soybean, bacterized with siderophoregenic B. japonicum, showed a marked increase in the percentage of germination, nodulation, chlorophyll, oil, protein content, and number of pods. Field trial study confirmed these pot results, which were evident from enhancement in shoot length, number of branches, chlorophyll content, number of nodules, root length, and number of pods. These results suggest the possibility of exploiting B. japonicum NCIM 2746 as a potential bioinoculant.     

Separation of siderophores by capillary electrophoresis

Capillary electrophoresis (CE) was applied as a fast method of siderophore separation. Siderophores are iron binding and regulating cell products, which facilitate iron transport into cells. A fast and efficient method of siderophore analysis is important for better understanding of the iron pathways in a sea environment or marine organisms. The best results of CE analysis were obtained using free zone CE in 25 mM phosphate buffer at basic pH using a constant voltage of 20 kV. Under these conditions it was possible to detect the presence of siderophores in seawater.     

Iron(III) coordination properties of a pyoverdin siderophore produced by Pseudomonas putida ATCC 33015

The iron complexation of a fluorescent green pyoverdin siderophore produced by the environmental bacterium Pseudomonas putida was characterized by solution thermodynamic methods. Pyoverdin binds iron through three bidentate chelate groups, a catecholate, a hydroxamate, and an alpha-hydroxycarboxylic acid. The deprotonation constants of the free pyoverdin and Fe(III)-pyoverdin complex were determined through a series of potentiometric and spectrophotometric experiments. The ferric complex of pyoverdin forms at very low pH (pH < 2), but full iron coordination does not occur until neutral pH. The calculated pM value of 25.13 is slightly lower than that for pyoverdin PaA (pM = 27), which coordinates iron by a catecholate and two hydroxamate groups. The redox potential of Fe-pyoverdin was found to be very pH sensitive. At high pH (approximately pH 9-11) where pyoverdin coordinates Fe in a hexadentate mode the redox potential is -0.480 V (NHE); however, at neutral pH where full Fe coordination is incomplete, the redox potential is more positive (E(1/2) = -0.395 V). The positive shift in the redox potential and the partial dissociation of the Fe-pyoverdin complex with pH decrease provides a path toward in vivo iron release.     

Simultaneous fragmentation of multiple ions using IMS drift time dependent collision energies

Ion mobility spectrometry coupled with mass spectrometry (IMS-MS) was utilized to evaluate an ion collision energy ramping technique that simultaneously fragments a variety of species. To evaluate this technique, the fragmentation patterns of a mixture of ions ranging in mass, charge state, and drift time were analyzed to determine their optimal fragmentation conditions. The precursor ions were pulsed into the IMS-MS instrument and separated in the IMS drift cell based on mobility differences. Two differentially pumped short quadrupoles were used to focus the ions exiting the drift cell, and fragmentation was induced by collision induced dissociation (CID) between the conductance limiting orifice behind the second short quadrupole and before the first octopole in the mass spectrometer. To explore the fragmentation spectrum of each precursor ion, the bias voltages for the short quadrupoles and conductance limiting orifices were increased from 0 to 50 V above nonfragmentation voltage settings. An approximately linear correlation was observed between the optimal fragmentation voltage for each ion and its specific drift time, so a linear voltage gradient was employed to supply less collision energy to high mobility ions (e.g., small conformations or higher charge state ions) and more to low mobility ions. Fragmentation efficiencies were found to be similar for different ions when the fragmentation voltage was linearly ramped with drift time, but varied drastically when only a single voltage was used.     

Sequencing of oligosaccharides derivatized with benzylamine using electrospray ionization-quadrupole time of flight-tandem mass spectrometry

Oligosaccharides were derivatized by reductive amination using benzylamine and analyzed by nanoelectrospray ionization-quadrupole time of flight-tandem mass spectrometry (nanoESI-QTOF-MS/MS) in the positive ion mode. The major signals were obtained under these conditions from the [M+H]+ ions for all benzylamine-derivatized oligosaccharides. To obtain structural information from these derivatized oligosaccharides, MS/MS was applied. Protonated molecular ions underwent extensive fragmentation, even under low-energy collision-induced dissociation. MS/MS spectra of [M+H]+ ions are characterized by simple fragmentation patterns which result from cleavage of the glycosidic bonds and thus allow a straightforward interpretation. Fragmentation of the [M+H]+ ions gave predominantly B- and Y-type glycosidic fragments. A systematic study of various oligosaccharides showed that information on sugar sequence and branching could easily be obtained. Predictable and reproducible fragmentation patterns could be obtained in all cases. This derivatization procedure and mass spectrometric methodology were applied successfully to neutral and acidic glycans released from 10 microg of glycoproteins separated by gel electrophoresis. Moreover, the derivatives retain their sensitivity to exoglycosidases. Thus a series of sequential on-target exoglycosidase treatments combined with matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) was found to be useful for the determination of structural features of the glycans released from proteins separated by gel electrophoresis such as the monosaccharide sequence, branching pattern, and anomeric configurations of the corresponding glycosidic linkages. Our strategy can be used successfully to assign the major glycans released from proteins separated by gel electrophoresis.     

Mixing and Matching Siderophore Clusters: Structure and Biosynthesis of Serratiochelins from Serratia sp. V4

Interrogation of the evolutionary history underlying the remarkable structures and biological activities of natural products has been complicated by not knowing the functions they have evolved to fulfill. Siderophores-soluble, low molecular weight compounds-have an easily understood and measured function: acquiring iron from the environment. Bacteria engage in a fierce competition to acquire iron, which rewards the production of siderophores that bind iron tightly and cannot be used or pirated by competitors. The structures and biosyntheses of "odd" siderophores can reveal the evolutionary strategy that led to their creation. We report a new Serratia strain that produces serratiochelin and an analog of serratiochelin. A genetic approach located the serratiochelin gene cluster, and targeted mutations in several genes implicated in serratiochelin biosynthesis were generated. Bioinformatic analyses and mutagenesis results demonstrate that genes from two well-known siderophore clusters, the Escherichia coli enterobactin cluster and the Vibrio cholera vibriobactin cluster, were shuffled to produce a new siderophore biosynthetic pathway. These results highlight how modular siderophore gene clusters can be mixed and matched during evolution to generate structural diversity in siderophores.     

Adsorption of enterobactin to metal oxides and the role of siderophores in bacterial adhesion to metals

The potential contribution of chemical bonds formed between bacterial cells and metal surfaces during biofilm initiation has received little attention. Previous work has suggested that bacterial siderophores may play a role in bacterial adhesion to metals. It has now been shown using in situ ATR-IR spectroscopy that enterobactin, a catecholate siderophore secreted by Escherichia coli, forms covalent bonds with particle films of titanium dioxide, boehmite (AlOOH), and chromium oxide-hydroxide which model the surfaces of metals of significance in medical and industrial settings. Adsorption of enterobactin to the metal oxides occurred through the 2,3-dihydroxybenzoyl moieties, with the trilactone macrocycle having little involvement. Vibrational modes of the 2,3-dihydroxybenzoyl moiety of enterobactin, adsorbed to TiO(2), were assigned by comparing the observed IR spectra with those calculated by the density functional method. Comparison of the observed adsorbate IR spectrum with the calculated spectra of catecholate-type [H(2)NCOC(6)H(3)O(2)Ti(OH)(4)](2-) and salicylate-type [H(2)NCOC(6)H(3)O(2)HTi(OH)(4)](2-) surface complexes indicated that the catecholate type is dominant. Analysis of the spectra for enterobactin in solution and that adsorbed to TiO(2) revealed that the amide of the 2,3-dihydroxybenzoylserine group reorientates during coordination to surface Ti(IV) ions. Investigation into the pH dependence of enterobactin adsorption to TiO(2) surfaces showed that all 2,3-dihydroxybenzoyl groups are involved. Infrared absorption bands attributed to adsorbed enterobactin were also strongly evident for E. coli cells attached to TiO(2) particle films. These studies give evidence of enterobactin-metal bond formation and further suggest the generality of siderophore involvement in bacterial biofilm initiation on metal surfaces.     

Fragmentation of poly(amidoamine) dendrimers in matrix-assisted laser desorption

Fragmentation of different generations of poly(amidoamine) dendrimers was explored in five common MALDI matrices: 2,5-dihydroxybenzoic acid (DHB), 4-hydroxy-3-methoxycinnamic acid (FER), α-cyano-4-hydroxycinnamic acid (ACH), 2,4,6-trihydroxyacetophenone (THAP), and 3-hydroxypicolinic acid (HPA). Of these, DHB was the softest matrix and ACH produced significant fragment intensity already at MALDI threshold, FER and THAP being in between. HPA was not a convenient matrix for dendrimers and produced a specific fragmentation pattern. Fragmentation analysis was mainly concentrated on generation G1, which contains already all essential structural elements. Dendrimers showed complicated fragmentation behavior with multiple fragmentation channels in our MALDI experiments. The relative intensities of these channels depended selectively on choice of the matrix and showed dissimilar dependence on the laser pulse energy. This was attributed to different fragmentation mechanisms, due to different protonation pathways, occurring in the same MALDI plume. The fragmentation pathways were proposed for all observed fragmentation channels. All fragmentation sites of protonated ions were found to be directly attached to the protonation sites and the fragmentation was surplus charge driven in this sense. No charge remote fragmentation channels were detected. Cationized dendrimers showed higher stability than the protonated ions.     

Adsorption to metal oxides of the Pseudomonas aeruginosa siderophore pyoverdine and implications for bacterial biofilm formation on metals

The initiation of biofilm formation is poorly understood, and in particular, the contribution of chemical bond formation between bacterial cells and metal surfaces has received little attention. We have previously used in situ infrared spectroscopy to show, during the initial stages of Pseudomonas aeruginosa biofilm formation, the formation of coordinate covalent bonds between titanium dioxide particle films and pyoverdine, a mixed catecholate and hydroxamate siderophore. Here we show using infrared spectroscopy that pyoverdine can also form covalent bonds with particle films of Fe2O3, CrOOH, and AlOOH. Adsorption to the metal oxides through the catechol-like 2,3-diamino-6,7-dihydroxyquinoline part of pyoverdine was most evident in the infrared spectrum of the adsorbed pyoverdine molecule. Weaker infrared absorption bands that are consistent with the hydroxamic acids of pyoverdine binding covalently to TiO2, Fe2O3, and AlOOH surfaces were also observed. The adsorption of pyoverdine to TiO2 and Fe2O3 surfaces showed a pH dependence that is indicative of the dominance of the catechol-like ligand of pyoverdine. Infrared absorption bands were also evident for pyoverdine associated with the cells of P. aeruginosa on TiO2 and Fe2O3 surfaces and were notably absent for genetically modified cells unable to synthesize or bind pyoverdine at the cell surface. These studies confirm the generality of pyoverdine-metal bond formation and suggest a wider involvement of siderophores in bacterial biofilm initiation on metals.     

Investigation of gas phase ion structure for proline-containing b2 ion

Unusual fragmentation was observed for doubly charged VPDPR in which cleavage C-terminal to proline and N-terminal to aspartic acid yielded b(2) (+ a(2))/y(3) complementary ions. This unique fragmentation is contradictory to trends previously established by statistical analysis of peptide tandem mass (MS/MS) spectra. Substitution of alanine for aspartic acid (i.e., VPAPR) did not change the fragmentation, indicating the cleavage was not directed by aspartic acid. Fragmentation patterns for VPAPR and V(NmA)APR (NmA = N-methyl alanine) were compared to determine whether conformational constraints from proline's cyclic side-chain contribute to b(2) ion formation. While both peptide sequences fragmented to yield b(2)/y(3) ions, only VPAPR produced a(2) ions, suggesting the VP b(2) ion is structurally different from the V(NmA) b(2) ion. Instead, the V(NmA) b(2) ion was accompanied by an ion corresponding to formal loss of 71. The suspected structural differences were confirmed by isolation and fragmentation of the respective b(2) ions (i.e., MS(3) spectra). Evidence supporting a diketopiperazine structure for the VP b(2) ion is reported. Fragmentation patterns for the VP b(2) ion and a synthetic VP diketopiperazine showed great similarity. N-terminal acetylation of VPAPR prevented the formation of the VP b(2) ion, presumably by blocking nucleophilic attack by the N-terminal amine on the carbonyl oxygen of the protonation site. Acetylation of the N-terminus for V(NmA)APR did not prevent the formation of the V(NmA) b(2) ion, indicating the V(NmA) b(2) ion has a structure, presumably that of an oxazolone, which requires no attack by the N-terminus for formation. Finally, high-resolution, accurate mass measurements determined that the V(NmA) (b(2)-71) ion results from losing a portion of valine from oxazolone V(NmA) b(2) ion, rather than cross-ring cleavage of the alternate diketopiperazine.