Negative Ion Fragmentation of Cysteic Acid Containing Peptides: Cysteic Acid as a Fixed Negative Charge

We present here a study of the collision induced dissociation (CID) of deprotonated cysteic acid containing peptides produced by MALDI. The effect of cysteic acid (C_ox) position is interrogated by considering the positional isomers, C_oxLVINVLSQG, LVINVLSQGC_ox, and LVINVC_oxLSQG. Although considerable variation between the CID spectra is observed, the mechanistic picture that emerges involves charge retention at the deprotonated cysteic acid side chain. Fragmentation occurs in the proximity of the cysteic acid group by charge directed mechanisms as well as remote from this group to form ions, which may be rationalized by charge remote mechanisms. Additionally, the formation of the SO₃^–• ion is observed in all cases. Fragmentation of C_oxLVINVLSQC_ox provides both N- and C-terminal, y and b ions, respectively indicating that the negative charge may be retained at either of the cysteic acids; however, there is some evidence that charge retention at the C-terminal cysteic acid may be preferred. Fragmentation of tryptic type peptides containing a C-terminal arginine or lysine residue is considered through comparison of three peptides C_oxLVINKLSQG, C_oxLVINVLSQK, and C_oxLVINVLSQR. Lastly, we rationalize the formation of b _n–1 + H₂O and a _n–1 ions through a mechanism involving rearrangement of the C-terminal residue to form a mixed anhydride intermediate.     

Influence of cysteine to cysteic acid oxidation on the collision-activated decomposition of protonated peptides: Evidence for intraionic interactions

Oxidation of cysteine residues to cysteic acids in C-terminal arginine-eontaining peptides (such as those derived by tryptic digestion of proteins) strongly promotes the formation of multiple members of the Y? series of fragment ions following low energy collision-activated decomposition (CAD) of the protonated peptides, Removal of the arginine residue abolishes the effect, which is also attenuated by conversion of the arginine to dimethylpyrim-idylornithine. The data indicate the importance of an intraionic interaction between the cysteic acid and arginine side-chains. Low energy CAD of peptides which include cysteic acid and histidine residues, also provides evidence for intraionic interactions. It is proposed that these findings are consistent with the general hypothesis that an increased heterogeneity (with respect to location of charge) of the protonated peptide precursor ion population is beneficial to the generation of a high yield of product ions via several charge-directed, low energy fragmentation pathways. Furthermore, these data emphasize the significance of gas-phase conformations of protonated peptides in determining fragmentation pathways.     

Observation of phosphorylation site-specific dissociation of singly protonated phosphopeptides

In ultraviolet photodissociation of phosphopeptide ions with a basic residue (arginine, lysine, or histidine) at the N-terminus, intense a_n − 97 peaks were observed. These ions were formed by cleavage at phosphorylated residues only. For multiply phosphorylated peptides, this site-specific cleavage occurred at every phosphorylated residue. H/D exchange studies showed that a_n − 97 was formed by H₃PO₄ loss from a_n+1 radical cations. The site-specificity of phosphate loss observed here is in contrast to the nonspecific phosphate loss from b_n and y_n reported previously. Characteristics of the reaction and its potential utility for phosphopeptide analysis are discussed.     

Effect of the his residue on the cyclization of b ions

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

Studies of peptide a- and b-type fragment ions using stable isotope labeling and integrated ion mobility/tandem mass spectrometry

The structures of peptide a- and b-type fragment ions were studied using synthetic peptides including a set of isomeric peptides, differing in the sequence location of an alanine residue labeled with ¹⁵N and uniformly with ¹³C. The pattern of isotope labeling of second-generation fragment ions derived via a _n and b _n ions (where n=4 or 5) suggested that these intermediates existed in part as macrocyclic structures, where alternative sites of ring opening gave rise to different linear forms whose simple cleavage might give rise to the observed final products. Similar conclusions were derived from combined ion mobility/tandem MS analyses where different fragmentation patterns were observed for isomeric a- or b-type ions that display different ion mobilities. These analyses were facilitated by a new approach to the processing of ion mobility/tandem MS data, from which distinct and separate product ion spectra are derived from ions that are incompletely separated by ion mobility. Finally, an example is provided of evidence for a macrocyclic structure for b _n ions where n=8 or 9.     

Effect of Cysteic Acid Position on the Negative Ion Fragmentation of Proteolytic Derived Peptides

A study on the effect of cysteic acid position on the types of fragment ions formed by collision-induced dissociation (CID) of [M – H]⁻ ions is presented. Of particular note is the observation of d-type fragment ions for peptides that contain an N-terminal cysteic acid (fixed negative charge) and cleavable amino acid side chains possessing a β-γ carbon–carbon bond. For example, the CID mass spectrum of oxidized cys-kemptide (C_oxLRRASLG) [M – H + O₃]⁻ ions contains abundant series of d-type fragment ions, and similar results are observed for oxidized cysteine-containing ribonuclease A proteolytic peptides. The d _i fragment ions are assumed to arise by a charge-remote and/or charge-assisted fragmentation mechanism, which both occur at high collision energies and involve consecutive reactions (i.e., the formation of a _i ions followed by the elimination of the side chain to form d _i ions).     

Charge-remote fragmentations are energy-dependent processes

Fast atom bombardment-produced [M + Na]⁺ ions of tristearoylglycerol and [M ? H]^? ions of stearic or nervonic acid undergo charge-remote fragmentations (CRFs) to produce one series of product ions reflecting C _n H_2n+2 losses, whereas electrospray ionization-produced ions fragment to give two series of product ions reflecting C _n H_2n+2 and C _n H_2n+1 losses. These results and those from previous studies show that the mechanisms and energetics of CRFs are complex and unsettled. We demonstrate that several pathways are simultaneously involved in CRFs, and the preference for certain pathways (by C _n H_2n+1 and C _n H_2n+2 losses) is determined by the internal energy of the compound itself and the ionization and activation energies that are applied to it.     

A mechanism for the loss of 60 u from peptides containing an arginine residue at the C-terminus

The loss of 60 u from protonated peptide ions containing an arginine residue at the C-terminus has been investigated by means of low energy tandem mass spectrometry. The lowest energy conformation of singly charged bradykinin is thought to involve a salt-bridge structure, which may lead to the formation of two isomeric forms. It is thought that one isomer retains the ionizing proton at the C-terminal end of the peptide, leading to the formation of the [b _n?1 + H + OH]⁺ fragment ion, and the other isomer retains the charge at the N-terminus, leading to the formation of the [M + H ? 60]⁺ fragment ion. It was found that the formation of the [M + H ? 60]⁺ ion occurs only from singly charged precursor ions. In addition, the loss of 60 u occurs from peptides in which the charge is localized at the N-terminus. These results indicate that the mechanism of formation of the [M + H ? 60]⁺ ion may be driven by a charge-remote process.     

Electron attachment to SO2 clusters

Electron attachment to SO₂ clusters formed by nozzle expansion was investigated (n up to 8) in a molecular-beam electron-ionization mass-spectrometer system. Electron ionization of SO₂ clusters was also studied (n up to 18) showing no pronounced structure in the mass spectra and no strong dependence on electron energy, the dominant positive ion being the (SO₂) _n ⁺ series. Also present but less abundant are the fragment ion series (SO₂) _n SO⁺, (SO₂) _n S⁺ and (SO₂) _n O⁺ with decreasing intensities in that order. The dominant negative ion is (SO₂) _n ^? . The homologous series (SO₂) _n O^? and (SO₂) _n SO^? are less abundant, the series (SO₂) _n S^? has not been observed at all (except SO₂·S^? produced in the background gas via secondary processes). The negative ion mass spectra show a strong dependence on electron energy due to a rich resonance like structure of the attachment cross sections involved. These attachment cross sections have been determined (up to 40 eV) and they show significant differences for the different homologous series. The most striking feature is that for instance (SO₂) _n SO^? ions do not show any signal at the first main resonance of SO^? from SO₂. Likewise (SO₂) _n O^? ions only show a strongly diminished signal at the first main resonance of O^? from SO₂. This is in contrast to results in O₂, CO₂ and N₂O. Conversely, (SO₂) _n ^? ions show — besides peaks at the position of the first and second O^? resonance — additional resonances below and above these peaks. In addition, (SO₂) ₅ ^? and larger ones show a zero energy peak consisting of stoichiometric SO₂ cluster ions similar to observations in O₂, CO₂ and H₂O. The attachment cross section of S^? from SO₂ has been found to show an additional previously undetected peak at ～1 eV. Moreover, the present study revealed the existence of a S _n ^? (n up to 8) series being produced with nearly zero energy electrons via volume and surface processes in and around the ion source.     

Gas-phase conformation-specific photofragmentation of proline-containing peptide ions

Singly-protonated proline-containing peptides with N-terminal arginine are photodissociated with vacuum ultraviolet (VUV) light in an ESI linear ion trap/orthogonal-TOF (LIT/o-TOF). When proline is the n^th residue from the N-terminus, unusual b _n + 2 and a _n + 2 ions are observed. Their formation is explained by homolytic cleavage of the C_α− C bond in conjunction with a rearrangement of electrons and an amide hydrogen. The latter is facilitated by a proline-stabilized gas-phase peptide conformation.     

A Systematic Study of Acidic Peptides for b-Type Sequence Scrambling

A systematic study was carried out to examine the effects of acidic amino acid residues and the position of the acidic group on the cyclization of b ions. The study utilized the model C-terminal amidated peptides XAAAAAA, AXAAAAA, AAXAAAA, AAAXAAA, AAAAXAA, AAAAAXA, AAAAAAX, XXAAAAAA, AAXXAAAA, AAAAXXAA, and AAAAAAXX, where X is a glutamic acid (E) or aspartic acid (D) residue. The CID mass spectra of b _n (where n = 7 and 8) ions derived from XAAAAAA, AAAXAAA, AAAAAAX and XXAAAAAA, AAXXAAAA, AAAAXXAA, and AAAAAAXX exhibited very similar fragmentation patterns for both the glutamic and the aspartic acid peptide series. The CID mass spectra of MH⁺ derived from model peptides presented substantial direct and non-direct sequence b ions. The results indicate that b ions produced from acidic peptides can also undergo head-to-tail cyclization, which is the reason for the formation of the non-direct sequence b ions. The b ion spectra derived from the peptides became more complex as the number of acidic residues in the peptides increased. Side chains of glutamic and aspartic acid did not inhibit the cyclization of the b ions. Substantial water elimination was observed in all CID spectra of b ₇ and b ₈ ions. Finally, the preferential cleavage of glutamic or aspartic acid residues from macrocyclic structures of b ions was also investigated under various collision energy conditions.     

Mass spectrometric methods for distinguishing structural isomers of glutathione conjugates of estrone and estradiol

Collisionally activated decompositions (CAD) of [M+H]⁺ ions from two sets (estrone and estradiol) of three isomeric glutathione (GSH) conjugates were studied by using five tandem mass spectrometric methods: (1) low energy (LE) CAD in an ion trap, (2) LE CAD in a triple quadrupole, (3) electrospray ionization (ESI)-source CAD in a tandem four sector, (4) high energy (HE) CAD of both ESI-produced and fast-atom bombardment (FAB)-produced ions in a tandem four-sector mass spectrometer, and (5) metastable-ion decompositions of FAB-produced ions. Four types of fragment ions are produced. The first type, formed from cleavage of the peptide backbone, gives rise to modified b₂, modified y₂, y₂, and b₁ ions. These fragments are observed with all the methods and show that the catechol estrogen attachment is at the cysteine moiety of the GSH. Internal fragment ions are the second type, and they also support that the modification is at cysteine. The third type involves fragmentation of the C–S bond to give an ion containing the steroid bonded to the sulfur. The fourth type of fragment ion is similar to the third but involves oxidation of the steroid ring and reduction of the GSH moiety; it is the most isomer specific of the four. The isomer-specific ions are of relatively low abundance in the product-ion spectra taken on the triple quadrupole and ion trap, but their abundances can be improved by increasing the collision energy. ESI source-CAD and the HE-CAD spectra of the isomers are the most distinctive because abundant product ions of all four types are seen in a single spectrum.     

Occurrence of C-Terminal Residue Exclusion in Peptide Fragmentation by ESI and MALDI Tandem Mass Spectrometry

By screening a data set of 392 synthetic peptides MS/MS spectra, we found that a known C-terminal rearrangement was unexpectedly frequently occurring from monoprotonated molecular ions in both ESI and MALDI tandem mass spectrometry upon low and high energy collision activated dissociations with QqTOF and TOF/TOF mass analyzer configuration, respectively. Any residue localized at the C-terminal carboxylic acid end, even a basic one, was lost, provided that a basic amino acid such arginine and to a lesser extent histidine and lysine was present in the sequence leading to a fragment ion, usually depicted as (b_n-1 + H₂O) ion, corresponding to a shortened non-scrambled peptide chain. Far from being an epiphenomenon, such a residue exclusion from the peptide chain C-terminal extremity gave a fragment ion that was the base peak of the MS/MS spectrum in certain cases. Within the frame of the mobile proton model, the ionizing proton being sequestered onto the basic amino acid side chain, it is known that the charge directed fragmentation mechanism involved the C-terminal carboxylic acid function forming an anhydride intermediate structure. The same mechanism was also demonstrated from cationized peptides. To confirm such assessment, we have prepared some of the peptides that displayed such C-terminal residue exclusion as a C-terminal backbone amide. As expected in this peptide amide series, the production of truncated chains was completely suppressed. Besides, multiply charged molecular ions of all peptides recorded in ESI mass spectrometry did not undergo such fragmentation validating that any mobile ionizing proton will prevent such a competitive C-terminal backbone rearrangement. Among all well-known nondirect sequence fragment ions issued from non specific loss of neutral molecules (mainly H₂O and NH₃) and multiple backbone amide ruptures (b-type internal ions), the described C-terminal residue exclusion is highly identifiable giving raise to a single fragment ion in the high mass range of the MS/MS spectra. The mass difference between this signal and the protonated molecular ion corresponds to the mass of the C-terminal residue. It allowed a straightforward identification of the amino acid positioned at this extremity. It must be emphasized that a neutral residue loss can be misattributed to the formation of a y_m-1 ion, i.e., to the loss of the N-terminal residue following the a₁-y_m–1 fragmentation channel. Extreme caution must be adopted when reading the direct sequence ion on the positive ion MS/MS spectra of singly charged peptides not to mix up the attribution of the N- and C-terminal amino acids. Although such peculiar fragmentation behavior is of obvious interest for de novo peptide sequencing, it can also be exploited in proteomics, especially for studies involving digestion protocols carried out with proteolytic enzymes other than trypsin (Lys-N, Glu-C, and Asp-N) that produce arginine-containing peptides.     

Probing the interaction of alkali and transition metal ions with bradykinin and its des-arginine derivatives via matrix-assisted laser desorption/ionization and postsource decay mass spectrometry

The complexes of the peptides (Pep) bradykinin (RPPGFSPFR), des-Arg¹-bradykinin, and des-Arg⁹-bradykinin with the metal (M) ions Na⁺, K⁺, Cs⁺, Cu⁺, Ag⁺, Co²⁺, Ni²⁺, and Zn²⁺ are generated in the gas phase by matrix-assisted laser desorption/ionization and the structures of the corresponding [Pep + M⁺]⁺ or [Pep − H⁺ + M²⁺]⁺ cations are probed by postsource decay (PSD) mass spectrometry. The PSD spectra depend significantly on the metal ion attached; moreover, the various metal ions respond differently to the presence or absence of a basic arginine residue. The Na⁺ and K⁺ adducts of all three peptides mainly produce N-terminal sequence ions upon PSD; the fragments observed point out that these metal ions are anchored by the PPGF segment and not the arginine residue(s). In contrast, the adducts of Cu⁺ and Ag⁺ show a strong dependence on the position of Arg; complexes of des-Arg¹-Pep (which contains a C-terminal Arg) produce primarily y_n ions whereas those of des-Arg⁹-Pep generate exclusively a_n and b_n ions. These trends are consistent with Cu⁺ ligation by Arg’s guanidine group. The [Pep + Cs⁺]⁺ ions mainly yield Cs⁺; a second significant fragmentation occurs only if a C-terminal arginine is present and involves elimination of this arginine’s side chain plus water. This reaction is rationalized through a salt bridge mechanism. The most prominent PSD products from [Pep − H⁺ + Co²⁺]⁺ and [Pep − H⁺ + Ni²⁺]⁺ contain at least one phenylalanine residue, revealing a marked preference for these divalent metal ions to bind to aromatic rings; the fragmentation patterns of the complexes further suggest that Co²⁺ and Ni²⁺ bind to deprotonated amide nitrogens. The coordination chemistry of Zn²⁺ combines features found with the divalent Co²⁺/Ni²⁺ as well as the monovalent Cu⁺/Ag⁺ transition metal ions. Generally, the structure and fragmentation behavior of each complex reflects the intrinsic coordination preferences of the corresponding metal ion.     

Synthesis of 4-substituted 3-(indol-3-yl)maleimides and azepines with annelated indole and maleimide nuclei

A series of 4-substituted 3-(indole-3-yl)maleimides has been synthesized. Upon the action of CH₃SO₃H in TFA, the 3-(indole-3-yl)-4-(arylalkylamino)-maleimides undergo cyclization to give 12b,13-dihydro-4bH-indolo[3,2-d]pyrrolo[3,4-b][1]benzazepine-5,7(6H,8H)-dione derivatives.     

Collision-activated dissociation mass spectra of crown ethers,perfluorinated crown ethers and related macrocycles

The collision-activated dissociation (CAD) mass spectra for a series of crown ethers, perfluoro crown ethers, cryptands and several dicyclohexano substituted crown ethers are reported. The CAD spectra were acquired with a triple quadrupole mass spectrometer, and in some cases spectra were recorded as a function of collision energy. In general, the protonated crown ethers dissociate via a series of losses of C₂H₄O units. The perfluoro crown ethers dissociate predominantly via losses of C₂F₄O units. The dicyclohexano ethers fragment in analogous ways in conjunction with cleavage of the cyclohexano rings. CAD spectra are also reported for acyclic ether systems.     

LC-DAD-ESI-MS Characterization of Carbohydrates Using a New Labeling Reagent

A novel labeling reagent 1-(2-naphthyl)-3-methyl-5-pyrazolone (NMP) coupling to liquid chromatography with electrospray ionization mass spectrometry for the detection of carbohydrates from the derivatized rape bee pollen samples is reported. Carbohydrates are derivatized to their bis-NMP-labeled derivatives. Derivatives showed an intense protonated molecular ion at m/z [M+H]⁺ in positive-ion detection mode. The mass-to-charge ratios of characteristic fragment ions at m/z 473.0 could be used for the accurately qualitative analysis of carbohydrates. This characteristic fragment ion is from the cleavage of C2–C3 bond in carbohydrate chain giving the specific fragment ions at m/z [MH-C _m H_2m+1O _m -H₂O]⁺ for pentose, hexose and glyceraldehydes and at m/z [MH-C _m H_2m-1O _m+1-H₂O]⁺ for alduronic acids such as galacturonic acid and glucuronic acid (m = n ? 2, n is carbon number of carbohydrate). No interferences for all aliphatic and aromatic aldehydes presented in natural environmental samples were observed due to the highly specific parent mass-to-charge ratio and the characteristic fragment ions. The method, in conjunction with a gradient elution, offered a baseline resolution of carbohydrate derivatives on a reversed-phase Hypersil ODS-2 column. The carbohydrates such as mannose, galacturonic acid, glucuronic acid, rhamnose, glucose, galactose, xylose, arabinose and fucose can successfully be detected.     

Tandem mass spectrometry of low solubility polyamides

The structural characterization of polyamides (PA) was achieved by tandem mass spectrometry (MS/MS) with a laser induced dissociation (LID) strategy. Because of interferences for precursor ions selection, two chemical modifications of the polymer end groups were proposed as derivatization strategies. The first approach, based on the addition of a trifluoroacetic acid (TFA) molecule, yields principally to complementary b_n and y_n product ions. This fragmentation types, analogous to those obtained with peptides or other PA, give only poor characterization of polymer end-groups [1]. A second approach, based on the addition of a basic diethylamine (DEA), permits to fix the charge and favorably direct the fragmentation. In this case, b_n ions were not observed. The full characterization of ω end group structure was obtained, in addition to the expected y_n and consecutive fragment ions.     

Using Gas-Phase Guest–Host Chemistry to Probe the Structures of b Ions of Peptides

Middle-sized b _n (n????5) fragments of protonated peptides undergo selective complex formation with ammonia under experimental conditions typically used to probe hydrogen?Cdeuterium exchange in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Other usual peptide fragments like y, a, a*, etc., and small b _n (n????4) fragments do not form stable ammonia adducts. We propose that complex formation of b _n ions with ammonia is characteristic to macrocyclic isomers of these fragments. Experiments on a protonated cyclic peptide and N-terminal acetylated peptides fully support this hypothesis; the protonated cyclic peptide does form ammonia adducts while linear b _n ions of acetylated peptides do not undergo complexation. Density functional theory (DFT) calculations on the proton-bound dimers of all-Ala b ₄ , b ₅ , and b ₇ ions and ammonia indicate that the ionizing proton initially located on the peptide fragment transfers to ammonia upon adduct formation. The ammonium ion is then solvated by N⁺-H??O H-bonds; this stabilization is much stronger for macrocyclic b _n isomers due to the stable cage-like structure formed and entropy effects. The present study demonstrates that gas-phase guest?Chost chemistry can be used to selectively probe structural features (i.e., macrocyclic or linear) of fragments of protonated peptides. Stable ammonia adducts of b ₉ , b ₉ -A, and b ₉ -2A of A₈YA, and b ₁₃ of A₂₀YVFL are observed indicating that even these large b-type ions form macrocyclic structures.