Identifying the presence of a disulfide linkage in peptides by the selective elimination of hydrogen disulfide from collisionally activated alkali and alkaline earth metal complexes

We report a new method for identifying disulfide linkages in peptides using mass spectrometry. This is accomplished by collisional activation of singly charged cationic alkali and alkaline earth metal complexes, which results in the highly selective elimination of hydrogen disulfide (H2S2). Complexes of peptides possessing disulfide bonds with sodium and alkaline earth metal are generated using electrospray ionization (ESI). Isolation followed by collision induced dissociation (CID) of singly charged peptide complexes results in selective elimination of H2S2 to leave newly formed dehydroalanine residues in the peptide. Further activation of the product yields sequence information in the region previously short circuited by the disulfide bond. For example, singly charged magnesium and calcium ion bound complexes of [Lys8]-vasopressin exhibit selective elimination of H2S2 via low-energy CID. Further isolation of the product followed by CID yields major b- and z-type fragments revealing the peptide sequence in the region between the newly formed dehydroalanine residues. Numerous model peptides provide mechanistic details for the selective elimination of H2S2. The process is initiated starting with a metal stabilized enolate anion at Cys, followed by cleavage of the S-C bond. An examination of the peptic digest of insulin provides an example of the application of the selective elimination of H2S2 for the identification of peptides with disulfide linkages. The energetics and mechanisms of H2S2 elimination from model compounds are investigated using density functional theory (DFT) calculations.     

Stereospecific control of peptide gas‐phase ion chemistry with cis and trans cyclo ornithine residues

We report non‐chiral amino acid residues cis‐ and trans‐1,4‐diaminocyclohexane‐1‐carboxylic acid (cyclo‐ornithine, cO) that exhibit unprecedented stereospecific control of backbone dissociations of singly charged peptide cations and hydrogen‐rich cation radicals produced by electron‐transfer dissociation. Upon collision‐induced dissociation (CID) in the slow heating regime, peptide cations containing trans‐cO residues undergo facile backbone cleavages of amide bonds C‐terminal to trans‐cO. By contrast, peptides with cis‐cO residues undergo dissociations at several amide bonds along the peptide ion backbone. Diastereoisomeric cO‐containing peptides thus provide remarkably distinct tandem mass spectra. The stereospecific effect in CID of the trans‐cO residue is explained by syn‐facially directed proton transfer from the 4‐ammonium group at cO to the C‐terminal amide followed by neighboring group participation in the cleavage of the CO―NH bond, analogous to the aspartic acid and ornithine effects. Backbone dissociations of diastereoisomeric cO‐containing peptide ions generate distinct [b_n]⁺‐type fragment ions that were characterized by CID‐MS³ spectra. Stereospecific control is also reported for electron‐transfer dissociation of cis‐ and trans‐cO containing doubly charged peptide ions. The stereospecific effect upon electron transfer is related to the different conformations of doubly charged peptide ions that affect the electron attachment sites and ensuing N―C_α bond dissociations.     

Mass spectra of doubly charged ions

The mass spectra of biological molecules, whose molecular mass exceeds 10 kDa, invariably contain multiply charged ions. For example, a survey scan of a small protein will produce singly, doubly and triply protonated molecules, the intensity of the doubly charged species often being greater than that of the singly charged entity. Although the spectra resulting from doubly charged peptides have not previously been studied, collisional activation of such doubly charged species may result in significant additional information pertaining to molecular structure. The techniques employed to study ions originating from multiply charged species were linked scanning of constant B/E and tandem mass spectrometry, namely low collision energy spectra acquired on a BEQQ hybrid instrument. The methodology was applied to model compounds whose tandem mass spectrometry characteristics are well known, e.g. gramicidin S and angiotensin I. The results for the product ions of the [M + 2H]²⁺ species of the models were obtained which highlight the methodology required for high-mass materials.     

Mechanisms and energetics of free radical initiated disulfide bond cleavage in model peptides and insulin by mass spectrometry

We investigate the mechanism of disulfide bond cleavage in gaseous peptide and protein ions initiated by a covalently-attached regiospecific acetyl radical using mass spectrometry (MS). Highly selective S–S bond cleavages with some minor C–S bond cleavages are observed by a single step of collisional activation. We show that even multiple disulfide bonds in intact bovine insulin are fragmented in the MS2 stage, releasing the A- and B-chains with a high yield, which has been challenging to achieve by other ion activation methods. Yet, regardless of the previous reaction mechanism studies, it has remained unclear why (1) disulfide bond cleavage is preferred to peptide backbone fragmentation, and why (2) the S–S bond that requires the higher activation energy conjectured in previously suggested mechanisms is more prone to be cleaved than the C–S bond by hydrogen-deficient radicals. To probe the mechanism of these processes, model peptides possessing deuterated β-carbon(s) at the disulfide bond are employed. It is suggested that the favored pathway of S–S bond cleavage is triggered by direct acetyl radical attack at sulfur with concomitant cleavage of the S–S bond (S_H2). The activation energy for this process is substantially lower by ∼9–10 kcal mol^–1 than those of peptide backbone cleavage processes determined by density functional quantum chemical calculations. Minor reaction pathways are initiated by hydrogen abstraction from the α-carbon or the β-carbon of a disulfide, followed by β-cleavages yielding C–S or S–S bond scissions. The current mechanistic findings should be generally applicable to other radical-driven disulfide bond cleavages with different radical species such as the benzyl and methyl pyridyl radicals.     

Direct differentiation of A‐ring single attachment versus A‐ and D‐ring double attachment of phycoerythrobilin chromophores to phycobiliproteins using MALDI mass spectrometry

Bilin chromophore attachment to phycobiliproteins is an enzyme‐catalyzed post‐translational modification process. Bilin‐lyases attach a bilin chromophore to their cognate protein through a thioether bond between the chromophore and a cysteine moiety. Bilin chromophores are attached to their phycobiliproteins through the 3¹ carbon of the bilin. Double attachment may also occur, and in this case, carbons 3¹ and 18¹ of the bilin are both forming covalent linkages to cysteine moieties. There is a mass spectrometric limitation when examining tryptic peptides containing two (or more) cysteines if one seeks to ascertain whether chromopeptides are singly or doubly attached. The problem is that singly and doubly attached chromopeptides appear at the same m/z value; thus, up until the present, only NMR analysis has been successful at determining whether the chromophore is singly or doubly attached. We report in this work a new, fast and accurate method for discriminating singly from doubly attached chromophores using MALDI‐TOF mass spectrometry. This method was developed from mass spectral analysis of chromopeptides that had undergone in vitro or in vivo attachment of bilin chromophores to phycobiliproteins. Distinction is based on a characteristic neutral loss that appears in the MALDI‐TOF mass spectrum only when the bilin is singly attached. Copyright © 2013 John Wiley & Sons, Ltd.     

Doubly charged sodium clusters: plasmon response and photoproduction

The optical response of doubly charged sodium clusters Na _n+2 ⁺⁺ was measured for n = 20, 40, and 58 valence electrons, for which the jellium model predicts spherical clusters. A new experimental scheme was developed which allows to separate doubly charged clusters of even mass from the singly charged with half the mass. The optical spectra are dominated by a plasmon-like resonance which is blue shifted and narrower than that of the singly charged clusters. The smallest doubly charged cluster observed was Na ₉ ⁺⁺ . The photo ionization cross section for singly charged clusters was found to be typically 2.6·10^-19cm² per Na atom for photon energies of around 6 eV, which is a factor of 400 smaller than the maximum in the plasmon absorption in the region of hω=2.6 eV.     

Proton transfer reactions for improved peptide characterisation

The combination of deprotonation (via ion/molecule and ion/ion reactions) and low-energy collision-induced dissociation (CID) has been explored for the enhanced characterisation of tryptic peptides via access to different precursor charge states. This approach allows instant access to fragmentation properties of singly and doubly protonated precursors (arising from the availability of mobile protons) in a single experiment. Considering both charge states extended our base of structurally informative data (in comparison with considering just a single charge state) due to generation of additional sequence ions and by obtaining supplementary structural information derived from selective cleavages. Roughly 37% of combined data sets (CID spectra of doubly and singly charged precursor) showed a greater database identification confidence than each set alone. Moreover, comparison between a number of sequence ions of the singly charged precursor and the doubly charged precursor provided a mean of distinguishing the two classes of tryptic peptides (arginine or lysine containing).     

Disulfide bond cleavage in TEMPO-free radical initiated peptide sequencing mass spectrometry

The gas‐phase free radical initiated peptide sequencing (FRIPS) fragmentation behavior of o‐TEMPO‐Bz‐conjugated peptides with an intra‐ and intermolecular disulfide bond was investigated using MSⁿ tandem mass spectrometry experiments. Investigated peptides included four peptides with an intramolecular cyclic disulfide bond, Bactenecin (RLC RIVVIRVC R), TGF‐α (C HSGYVGVRC ), MCH (DFDMLRC MLGRVFRPC WQY) and Adrenomedullin (16–31) (C RFGTC TVQKLAHQIY), and two peptides with an intermolecular disulfide bond. Collisional activation of the benzyl radical conjugated peptide cation, which was generated through the release of a TEMPO radical from o‐TEMPO‐Bz‐conjugated peptides upon initial collisional activation, produced a large number of peptide backbone fragments in which the S? S or C? S bond was readily cleaved. The observed peptide backbone fragments included a‐, c‐, x‐ or z‐types, which indicates that the radical‐driven peptide fragmentation mechanism plays an important role in TEMPO‐FRIPS mass spectrometry. FRIPS application of the linearly linked disulfide peptides further showed that the S? S or C? S bond was selectively and preferentially cleaved, followed by peptide backbone dissociations. In the FRIPS mass spectra, the loss of ?SH or ?SSH was also abundantly found. On the basis of these findings, FRIPS fragmentation pathways for peptides with a disulfide bond are proposed. For the cleavage of the S? S bond, the abstraction of a hydrogen atom at C_β by the benzyl radical is proposed to be the initial radical abstraction/transfer reaction. On the other hand, H‐abstraction at C_α is suggested to lead to C? S bond cleavage, which yields [ion ± S] fragments or the loss of ?SH or ?SSH. Copyright © 2011 John Wiley & Sons, Ltd.     

A study of the electron capture induced decompositions and charge separation reactions of the doubly charged isomeric ions of the methylpyridines and aniline

The doubly charged isomeric ions [C₆H₇N]²⁺ formed from 2-, 3- and 4-methylpyridine and aniline were investigated via their unimolecular charge separation reactions and by electron capture induced decompositions (ECID). The ECID spectra were compared with the collision induced decomposition (CID) spectra of the singly charged ions in an attempt to investigate the structure of the doubly charged ions. The four isomers could be unambiguously identified by their unimolecular charge separations. These differences were greater than in the mass spectra, ECID spectra or CID spectra of singly charged ions.     

Study of diketone/metal ion complexes by electrospray ionization mass spectrometry: Influence of Keto-Enol tautomerism and chelation

The formation and collisionally activated dissociation (CAD) behavior of a series of complexes containing cyclic or linear diketone ligands and alkali, alkaline earth, or transition metal ions are investigated. Electrospray ionization (ESI) is utilized for introduction of the metal ion complexes into a quadrupole ion trap mass spectrometer. The proximity of the carbonyl groups is crucial for formation and detection of ion complexes by ESI. For example, no metal ion complexes are observed for 1,4-cyclohexanedione, but they are readily detected for the isomers, 1,2-and 1,3-cyclohexanedione. Although the diketones form stable doubly charged complexes, the formation of singly charged alkaline earth complexes of the type (nL + M²⁺ ? H⁺)⁺ where L = 1,3-cyclohexanedione or 2,4-pentanedione is the first evidence of charge reduction. CAD investigations provide further evidence of charge reduction processes occurring in the gas-phase complexes. The CAD studies indicate that an intramolecular proton transfer between two diketone ligands attached to a doubly charged metal ion, followed by elimination of the resulting protonated ligand, produces the charge reduced complex. For transition metal complexation, the preference for formation of doubly charged versus singly charged complexes correlates with the keto-enol distribution of the diketones in solution.     

Collisional energy dependence of peptide ion fragmentation

The energy dependence of fragmentation in a collision cell was measured for 2400 protonated peptide ions derived from the digestion of 24 proteins. The collision voltage at which the sum of the fragment ion abundances was equal to the remaining parent ion (V _1/2) was the principal measure of fragmentation effectiveness. Each class of peptides was characterized by a linear relation between V _1/2 and m/z whose slope depended on the peptide class and, with little adjustment, intersected the origin. Peptide ions where the number of protons is no greater than the number of arginine residues show the greatest slope, V _1/2/(m/z)=0.0472 (all slopes in units of V Da⁻¹ e). For peptides where the number of protons is greater than the number of arginines, but not greater than the total number of basic residues, the slope decreases to 0.0414 for singly charged ions, 0.0382 for doubly charged, 0.0346 for triply charged, and 0.0308 for more highly charged ions. With one mobile proton, the slope is about 0.029 for singly and doubly charged ions and slightly lower for more highly charged ions. With two or more mobile protons the slope is 0.0207. By removing m/z dependence, the deviation of V _1/2 from a line provides a relative measure of the ease of fragmentation of an ion in each class. This information can guide the selection of optimal conditions for tandem mass spectrometry studies in collision cells for selected peptide ions as well as aid in comparing the reactivity of ions differing in m/z and charge state.     

Electron Capture Dissociation of Hydrogen-Deficient Peptide Radical Cations

Hydrogen-deficient peptide radical cations exhibit fascinating gas phase chemistry, which is governed by radical driven dissociation and, in many cases, by a combination of radical and charge driven fragmentation. Here we examine electron capture dissociation (ECD) of doubly, [M + H]^2+?, and triply, [M + 2H]^3+?, charged hydrogen-deficient species, aiming to investigate the effect of a hydrogen-deficient radical site on the ECD outcome and characterize the dissociation pathways of hydrogen-deficient species in ECD. ECD of [M + H]^2+? and [M + 2H]^3+? precursor ions resulted in efficient electron capture by the hydrogen-deficient species. However, the intensities of c- and z-type product ions were reduced, compared with those observed for the even electron species, indicating suppression of N?CC_?? backbone bond cleavages. We postulate that radical recombination occurs after the initial electron capture event leading to a stable even electron intermediate, which does not trigger N?CC_?? bond dissociations. Although the intensities of c- and z-type product ions were reduced, the number of backbone bond cleavages remained largely unaffected between the ECD spectra of the even electron and hydrogen-deficient species. We hypothesize that a small ion population exist as a biradical, which can trigger N?CC_?? bond cleavages. Alternatively, radical recombination and N?CC_?? bond cleavages can be in competition, with radical recombination being the dominant pathway and N?CC_?? cleavages occurring to a lesser degree. Formation of b- and y-type ions observed for two of the hydrogen-deficient peptides examined is also discussed.     

Mass spectrometric study on 2-amino-as-triazino[6,5-c]quinoline and some of its derivatives

Electron impact induced fragmentations of 2-amino-as-triazino[6,5-c]quinoline and its 2-methylamino, 2-dimethylamino and 2-benzylamino analogues have been investigated. The main primary decomposition route of both the singly and the doubly charged molecular ions is the N₂ loss. For the singly charged ions the critical energy of this reaction is 110±10 kJ mol^?1 and the kinetic energy release is 61±4 kJ mol^?1. For the doubly charged ions these values are 90±10 kJ mol^?1 and 5±2 kJ mol^?1, respectively, indicating a significantly different reaction profile. The further fragmentation of [M? N₂]⁺˙ ions consists of radical eliminations from the 2-amino group with cleavages of the α- and β-bonds. Here a significant substituent effect is eliminations found suggesting an intramolecular cyclization reaction with a substituent migration. D and ¹⁵N labelling experiments have shown a minor extent of randomization of the labelled atoms and the occurrence of other hidden skeletal rearrangements during the fragmentation.     

Investigation of cationic organic dyes used as molecular probes by liquid secondary ion mass spectrometry

The positive-ion mass spectra of twelve organic dyes used as molecular probes were measured using liquid secondary ion mass spectrometry (LSIMS). Nine of the twelve dyes were singly charged cations and the other three were doubly charged cations. The mass spectra of each of the dyes in m-nitrobenzyl alcohol contain abundant signals for the intact cation, C⁺ (singly charged cation dyes), or for singly-charged forms of the doubly charged cation formed by proton loss, [C²⁺? H⁺]⁺, or halogen counter ion attachment, [C²⁺ + X^?]⁺. Fragmentation is usually minimal under the conditions used. However, the cations of five of the singly charged compounds appear to undergo charge-remote fragmentation. Collision-induced dissociation experiments on a hybrid mass spectrometer of EBqQ geometry at collision energies up to 300 eV failed to access this fragmentation pathway. In contrast to the LSIMS of many other doubly charged organic compounds, two of the dicationic dyes produced a doubly charged ion of reasonable abundance (2–20%) in the mass spectrum. When glycerol was used as a matrix solvent, the addition of the matrix modifier trifluoroacetic acid increased the abundance of C²⁺.     

Phosphorylated serine and threonine residues promote site‐specific fragmentation of singly charged,arginine‐containing peptide ions

In order to investigate gas‐phase fragmentation reactions of phosphorylated peptide ions, matrix‐assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) tandem mass (MS/MS) spectra were recorded from synthetic phosphopeptides and from phosphopeptides isolated from natural sources. MALDI‐TOF/TOF (TOF: time‐of‐flight) spectra of synthetic arginine‐containing phosphopeptides revealed a significant increase of y ions resulting from bond cleavages on the C‐terminal side of phosphothreonine or phosphoserine. The same effect was found in ESI‐MS/MS spectra recorded from the singly charged but not from the doubly charged ions of these phosphopeptides. ESI‐MS/MS spectra of doubly charged phosphopeptides containing two arginine residues support the following general fragmentation rule: Increased amide bond cleavage on the C‐terminal side of phosphorylated serines or threonines mainly occurs in peptide ions which do not contain mobile protons. In MALDI‐TOF/TOF spectra of phosphopeptides displaying N‐terminal fragment ions, abundant b–H₃PO₄ ions resulting from the enhanced dissociation of the pSer/pThr–X bond were detected (X denotes amino acids). Cleavages at phosphoamino acids were found to be particularly predominant in spectra of phosphopeptides containing pSer/pThr–Pro bonds. A quantitative evaluation of a larger set of MALDI‐TOF/TOF spectra recorded from phosphopeptides indicated that phosphoserine residues in arginine‐containing peptides increase the signal intensities of the respective y ions by almost a factor of 3. A less pronounced cleavage‐enhancing effect was observed in some lysine‐containing phosphopeptides without arginine. The proposed peptide fragmentation pathways involve a nucleophilic attack by phosphate oxygen on the carbon center of the peptide backbone amide, which eventually leads to cleavage of the amide bond. Copyright © 2009 John Wiley & Sons, Ltd.     

Ion trap collisional activation of disulfide linkage intact and reduced multiply protonated polypeptides.

The presence of disulfide linkages in multiply charged polypeptide ions tends to inhibit the formation of structurally informative product ions under conventional quadrupole ion trap collisional activation conditions. In particular, fragmentation that requires two cleavages (i.e., cleavage of a disulfide linkage and a peptide linkage) is strongly suppressed. Reduction of the disulfide linkage(s) by use of dithiothreitol yields parent ions upon electrospray without this complication. Far richer structural information is revealed by ion trap collisional activation of the disulfide-reduced species than from the native species. These observations are illustrated with doubly protonated native and reduced somatosin, the [M + 5H](5+) ion of native bovine insulin and the [M + 4H](4+) and [M + 3H](3+) ions of the B-chain of bovine insulin produced by reduction of the disulfide linkages in insulin, and the [M + 11H](11+) ion of native chicken lysozyme and the [M + 11H](11+) and [M + 14H](14+) ions of reduced lysozyme. In each case, the product ions produced by ion trap collisional activation were subjected to ion/ion proton transfer reactions to facilitate interpretation of the product ion spectra. These studies clearly suggest that the identification of polypeptides with one or more disulfide linkages via application of ion trap collisional activation to the multiply charged parent ions formed directly by electrospray could be problematic. Means for cleaving the disulfide linkage, such as reduction by dithiothreitol prior to electrospray, are therefore desirable in these cases.     

Cluster ions ejected from an Li-Mg alloy liquid metal ion source: Observation of MG 2 2+ and MG 3 2+

Ions ejected from a liquid metal ion source of an Li-Mg (10 atom %) alloy have been investigated by using a magnetic mass analyzer. In addition to singly charged homonuclear Li _n ⁺ (n ≤ 9) and Mg _n ⁺ (n ≤ 4) and heteronuclear Mg_mLi _n ⁺ (m, n ≤ 2) clusters, doubly charged diatomic and triatomic Mg clusters are observed. Discussion is focused on the observability and the formation mechanism of the doubly charged small Mg clusters. A postionization process is suggested for the formation of the doubly charged clusters.     

Comparison of collision‐ versus electron‐induced dissociation of sodium chloride cluster cations

The collision‐induced dissociation (CID) and electron‐induced dissociation (EID) spectra of the [(NaCl)_m(Na)_n]ⁿ⁺ clusters of sodium chloride have been examined in a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer. For singly charged cluster ions (n = 1), mass spectra for CID and EID of the precursor exhibit clear differences, which become more pronounced for the larger cluster ions. Whereas CID yields fewer product ions, EID produces all possible [(NaCl)_xNa]⁺ product ions. In the case of doubly charged cluster ions, EID again leads to a larger variety of product ions. In addition, doubly charged product ions have been observed due to loss of neutral NaCl unit(s). For example, EID of [(NaCl)₁₁(Na)₂]²⁺ leads to formation of [(NaCl)₁₀(Na)₂]²⁺, which appears to be the smallest doubly charged cluster of sodium chloride observed experimentally to date. The most abundant product ions in EID spectra are predominantly magic number cluster ions. Finally, [(NaCl)_m(Na)₂]^{+ .} radical cations, formed via capture of low‐energy electrons, fragment via the loss of [(NaCl)_n(Na)] ^. radical neutrals. Copyright © 2008 John Wiley & Sons, Ltd.     

Fragmentation of Singly,Doubly, and Triply Charged Hydrogen Deficient Peptide Radical Cations in Infrared Multiphoton Dissociation and Electron Induced Dissociation

Gas phase fragmentation of hydrogen deficient peptide radical cations continues to be an active area of research. While collision induced dissociation (CID) of singly charged species is widely examined, dissociation channels of singly and multiply charged radical cations in infrared multiphoton dissociation (IRMPD) and electron induced dissociation (EID) have not been, so far, investigated. Here, we report on the gas phase dissociation of singly, doubly and triply charged hydrogen deficient peptide radicals, [M + nH]^(n+1)+· (n = 0, 1, 2), in MS³ IRMPD and EID and compare the observed fragmentation pathways to those obtained in MS³ CID. Backbone fragmentation in MS³ IRMPD and EID was highly dependent on the charge state of the radical precursor ions, whereas amino acid side chain cleavages were largely independent of the charge state selected for fragmentation. Cleavages at aromatic amino acids, either through side chain loss or backbone fragmentation, were significantly enhanced over other dissociation channels. For singly charged species, the MS³ IRMPD and EID spectra were mainly governed by radical-driven dissociation. Fragmentation of doubly and triply charged radical cations proceeded through both radical- and charge-driven processes, resulting in the formation of a wide range of backbone product ions including, a-, b-, c-, y-, x-, and z-type. While similarities existed between MS³ CID, IRMPD, and EID of the same species, several backbone product ions and side chain losses were unique for each activation method. Furthermore, dominant dissociation pathways in each spectrum were dependent on ion activation method, amino acid composition, and charge state selected for fragmentation.     

Electron transfer dissociation with supplemental activation to differentiate aspartic and isoaspartic residues in doubly charged peptide cations

Electron-transfer dissociation (ETD) with supplemental activation of the doubly charged deamidated tryptic digested peptide ions allows differentiation of isoaspartic acid and aspartic acid residues using the c + 57 or z ^• − 57 peaks. The diagnostic peak clearly localizes and characterizes the isoaspartic acid residue. Supplemental activation in ETD of the doubly charged peptide ions involves resonant excitation of the charge reduced precursor radical cations and leads to further dissociation, including extra backbone cleavages and secondary fragmentation. Supplemental activation is essential to obtain a high quality ETD spectrum (especially for doubly charged peptide ions) with sequence information. Unfortunately, the low-resolution of the ion trap mass spectrometer makes detection of the diagnostic peak, [M-60], for the aspartic acid residue difficult due to interference with side-chain loss from arginine and glutamic acid residues.