The formation of WxOy+●/-● clusters in the gas phase was studied by laser desorption ionization (LDI) and matrix assisted laser desorption ionization (MALDI) of solid WO3. LDI produced (WO3)n+ ●/- ● (n = 1-7) clusters. In MALDI, when using nano-diamonds (NDs), graphene oxide (GO), or fullerene (C60) matrices, higher mass clusters were generated. In addition to (WO3)n-● clusters, oxygen-rich or -deficient species were found in both LDI and MALDI (with the total number of clusters exceeding one hundred ≈ 137). This is the first time that such matrices have been used for the generation of(WO3)n+●/-● clusters in the gas phase, while new high mass clusters (WO3)n-● (n = 12-19) were also detected.
Among dissociation methods, negative electron transfer dissociation (NETD) has been proven the most useful for glycosaminoglycan (GAG) sequencing because it produces informative fragmentation, a low degree of sulfate losses, high sensitivity, and translatability to multiple instrument types. The challenge, however, is to distinguish positional sulfation. In particular, NETD has been reported to fail to differentiate 4-O- versus 6-O-sulfation in chondroitin sulfate decasaccharide. This raised the concern of whether NETD is able to differentiate the rare 3-O-sulfation from predominant 6-O-sulfation in heparan sulfate (HS) oligosaccharides. Here, we report that NETD generates highly informative spectra that differentiate sites of O-sulfation on glucosamine residues, enabling structural characterizations of synthetic HS isomers containing 3-O-sulfation. Further, lyase-resistant 3-O-sulfated tetrasaccharides from natural sources were successfully sequenced. Notably, for all of the oligosaccharides in this study, the successful sequencing is based on NETD tandem mass spectra of commonly observed deprotonated precursor ions without derivatization or metal cation adduction, simplifying the experimental workflow and data interpretation. These results demonstrate the potential of NETD as a sensitive analytical tool for detailed, high-throughput structural analysis of highly sulfated GAGs.
Electron transfer to doubly and triply charged heptapeptide ions containing polar residues Arg, Lys, and Asp in combination with nonpolar Gly, Ala, and Pro or Leu generates stable and metastable charge-reduced ions, (M + 2H)+●, in addition to standard electron-transfer dissociation (ETD) fragment ions. The metastable (M + 2H)+● ions spontaneously dissociate upon resonant ejection from the linear ion trap, giving irregularly shaped peaks with offset m/z values. The fractions of stable and metastable (M + 2H)+● ions and their mass shifts depend on the presence of Pro-4 and Leu-4 residues in the peptides, with the Pro-4 sequences giving larger fractions of the stable ions while showing smaller mass shifts for the metastables. Conversion of the Asp and C-terminal carboxyl groups to methyl esters further lowers the charge-reduced ion stability. Collisional activation and photodissociation at 355 nm of mass-selected (M + 2H)+● results in different dissociations that give sequence specific MS3 spectra. With a single exception of charge-reduced (LKGLADR + 2H)+●, the MS3 spectra do not produce ETD sequence fragments of the c and z type. Hence, these (M + 2H)+● ions are covalent radicals, not ion–molecule complexes, undergoing dramatically different dissociations in the ground and excited electronic states. The increased stability of the Pro-4 containing (M + 2H)+● ions is attributed to radicals formed by opening of the Pro ring and undergoing further stabilization by hydrogen atom migrations. UV–VIS photodissociation action spectroscopy and time-dependent density functional theory calculations are used in a case in point study of the stable (LKGPADR + 2H)+● ion produced by ETD. In contrast to singly-reduced peptide ions, doubly reduced (M + 3H)+ ions are stable only when formed from the Pro-4 precursors and show all characteristics of even electron ions regarding no photon absorption at 355 nm or ion-molecule reactions, and exhibiting proton driven collision induced dissociations.
Peptide cation-radical fragment ions of the z-type, [●AXAR+], [●AXAK+], and [●XAR+], where X = A, C, D, E, F, G, H, K, L, M, N, P, Y, and W, were generated by electron transfer dissociation of peptide dications and investigated by MS3-near-ultraviolet photodissociation (UVPD) at 355 nm. Laser-pulse dependence measurements indicated that the ion populations were homogeneous for most X residues except phenylalanine. UVPD resulted in dissociations of backbone CO─NH bonds that were accompanied by hydrogen atom transfer, producing fragment ions of the [yn]+ type. Compared with collision-induced dissociation, UVPD yielded less side-chain dissociations even for residues that are sensitive to radical-induced side-chain bond cleavages. The backbone dissociations are triggered by transitions to second (B) excited electronic states in the peptide ion R-CH●-CONH- chromophores that are resonant with the 355-nm photon energy. Electron promotion increases the polarity of the B excited states, R-CH+-C●(O–)NH-, and steers the reaction to proceed by transfer of protons from proximate acidic Cα and amide nitrogen positions.
We report a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-rich and hydrogen-deficient types. Stable, long-lived, hydrogen-rich peptide cation radicals, such as [AAAYR + 2H]+● and several of its sequence and homology variants, were generated by electron transfer dissociation (ETD) of peptide-crown-ether complexes, and their CID-MS3 dissociations were found to be dramatically different from those upon ETD of the respective peptide dications. All of the hydrogen-rich peptide cation radicals contained major (77%–94%) fractions of species having radical chromophores created by ETD that underwent photodissociation at 355 nm. Analysis of the CID and UVPD spectra pointed to arginine guanidinium radicals as the major components of the hydrogen-rich peptide cation radical population. Hydrogen-deficient peptide cation radicals were generated by intramolecular electron transfer in CuII(2,2′:6′,2″-terpyridine) complexes and shown to contain chromophores absorbing at 355 nm and undergoing photodissociation. The CID and UVPD spectra showed major differences in fragmentation for [AAAYR]+● that diminished as the Tyr residue was moved along the peptide chain. UVPD was found to be superior to CID in localizing Cα-radical positions in peptide cation radical intermediates.
Peptide cation radicals of the z-type were produced by electron transfer dissociation (ETD) of peptide dications and studied by UV-Vis photodissociation (UVPD) action spectroscopy. Cation radicals containing the Asp (D), Asn (N), Glu (E), and Gln (Q) residues were found to spontaneously isomerize by hydrogen atom migrations upon ETD. Canonical N-terminal [z4 + H]+● fragment ion-radicals of the R-C●H-CONH- type, initially formed by N?Cα bond cleavage, were found to be minor components of the stable ion fraction. Vibronically broadened UV-Vis absorption spectra were calculated by time-dependent density functional theory for several [●DAAR + H]+ isomers and used to assign structures to the action spectra. The potential energy surface of [●DAAR + H]+ isomers was mapped by ab initio and density functional theory calculations that revealed multiple isomerization pathways by hydrogen atom migrations. The transition-state energies for the isomerizations were found to be lower than the dissociation thresholds, accounting for the isomerization in non-dissociating ions. The facile isomerization in [●XAAR + H]+ ions (X = D, N, E, and Q) was attributed to low-energy intermediates having the radical defect in the side chain that can promote hydrogen migration along backbone Cα positions. A similar side-chain mediated mechanism is suggested for the facile intermolecular hydrogen migration between the c- and [z + H]●-ETD fragments containing Asp, Asn, Glu, and Gln residues.
We investigate the tandem mass spectrometry of regiospecifically labeled, deprotonated sucrose analytes. We utilize density functional theory calculations to model the pertinent gas-phase fragmentation chemistry of the prevalent glycosidic bond cleavages (B1-Y1 and C1-Z1 reactions) and compare these predictions to infrared spectroscopy experiments on the resulting B1 and C1 product anions. For the C1 anions, barriers to interconversion of the pyranose [α-glucose-H]?, C1 anions to entropically favorable ring-open aldehyde-terminated forms were modest (41 kJ mol?1) consistent with the observation of a band assigned to a carbonyl stretch at ~?1680–1720 cm?1. For the B1 anions, our transition structure calculations predict the presence of both deprotonated 1,6-anhydroglucose and carbon 2-ketone ((4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one) anion structures, with the latter predominating. This hypothesis is supported by our spectroscopic data which show diagnostic bands at 1600, 1674, and 1699 cm?1 (deprotonated carbon 2-ketone structures), and at ~?1541 cm?1 (both types of structure) and RRKM rate calculations. The deprotonated carbon 2-ketone structures are also the lowest energy product B1 anions.
Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L*nLm)K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X?H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific 13C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)+ ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H]+ ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide–peptide ion interactions in the gas phase.
An ion of m/z 110.06036 (ion formula [C6H8NO]+; error: 0.32 mDa) was observed in the collision induced dissociation tandem mass spectrometry experiments of protonated N-(3-aminophenyl)benzamide, which is a rearrangement product ion purportedly through nitrogen-oxygen (N–O) exchange. The N–O exchange rearrangement was confirmed by the MS/MS spectrum of protonated N-(3-aminophenyl)-O18-benzamide, where the rearranged ion, [C6H8NO18]+ of m/z 112 was available because of the presence of O18. Theoretical calculations using Density Functional Theory (DFT) at B3LYP/6-31 g(d) level suggest that an ion-neutral complex containing a water molecule and a nitrilium ion was formed via a transition state (TS-1), followed by the water molecule migrating to the anilide ring, eventually leading to the formation of the rearranged ion of m/z 110. The rearrangement can be generalized to other protonated amide compounds with electron-donating groups at the meta position, such as, –OH, –CH3, –OCH3, –NH(CH3)2, –NH-Ph, and –NHCOCH3, all of which show the corresponding rearranged ions in MS/MS spectra. However, the protonated amide compounds containing electron-withdrawing groups, including –Cl, –Br, –CN, –NO2, and –CF3, at the meta position did not display this type of rearrangement during dissociation. Additionally, effects of various acyl groups on the rearrangement were investigated. It was found that the rearrangement can be enhanced by substitution on the ring of the benzoyl with electron-withdrawing groups.
A method is developed for the prediction of mass spectral ion counts of drug-like molecules using in silico calculated chemometric data. Various chemometric data, including polar and molecular surface areas, aqueous solvation free energies, and gas-phase and aqueous proton affinities were computed, and a statistically significant relationship between measured mass spectral ion counts and the combination of aqueous proton affinity and total molecular surface area was identified. In particular, through multilinear regression of ion counts on predicted chemometric data, we find that log10(MS ion counts) = –4.824 + c1?PA + c2?SA, where PA is the aqueous proton affinity of the molecule computed at the SMD(aq)/M06-L/MIDI!//M06-L/MIDI! level of electronic structure theory, SA is the total surface area of the molecule in its conjugate base form, and c1 and c2 have values of –3.912 × 10–2 mol kcal–1 and 3.682 × 10–3 Å–2. On a 66-molecule training set, this regression exhibits a multiple R value of 0.791 with p values for the intercept, c1, and c2 of 1.4 × 10–3, 4.3 × 10–10, and 2.5 × 10–6, respectively. Application of this regression to an 11-molecule test set provides a good correlation of prediction with experiment (R = 0.905) albeit with a systematic underestimation of about 0.2 log units. This method may prove useful for semiquantitative analysis of drug metabolites for which MS response factors or authentic standards are not readily available.
As a reagent gas for positive- and negative-mode chemical ionization mass spectrometry (CI-MS), isobutane (i-C4H10) produces superior analyte signal abundance to methane. Isobutane has never been widely adopted for CI-MS because it fouls the ion source more rapidly and produces positive CI spectra that are more strongly dependent on reagent gas pressure compared with methane. Isobutane was diluted to various concentrations in argon for use as a reagent gas with an unmodified commercial gas chromatograph-mass spectrometer. Analyte spectra were directly compared using methane, isobutane, and isobutane/argon mixtures. A mixture of 10% i-C4H10 in argon produced twice the positive-mode analyte signal of methane, equal to pure isobutane, and reduced spectral dependence on reagent gas pressure. Electron capture negative chemical ionization using 1% i-C4H10 in argon tripled analyte signal compared with methane and was reproducible, unlike pure isobutane. The operative lifetime of the ion source using isobutane/argon mixtures was extended exponentially compared with pure isobutane, producing stable and reproducible CI signal throughout. By diluting the reagent gas in an inert buffer gas, isobutane CI-MS experiments were made as practical to use as methane CI-MS experiments but with superior analytical performance.
Laser desorption ionization using time-of-flight mass spectrometer afforded with quadrupole ion trap was used to study As2Ch3 (Ch = S, Se, and Te) bulk chalcogenide materials. The main goal of the study is the identification of species present in the plasma originating from the interaction of laser pulses with solid state material. The generated clusters in both positive and negative ion mode are identified as 10 unary (Sp+/– and Asm+/–) and 34 binary (AsmSp+/–) species for As2S3 glass, 2 unary (Seq+/–) and 26 binary (AsmSeq+/–) species for As2Se3 glass, 7 unary (Ter+/–) and 23 binary (AsmTer+/–) species for As2Te3 material. The fragmentation of chalcogenide materials was diminished using some polymers and in this way 45 new, higher mass clusters have been detected. This novel approach opens a new possibility for laser desorption ionization mass spectrometry analysis of chalcogenides as well as other materials.
Electron capture dissociation (ECD) and electron transfer dissociation (ETD) in metal-peptide complexes are dependent on the metal cation in the complex. The divalent transition metals Ni2+, Cu2+, and Zn2+ were used as charge carriers to produce metal-polyhistidine complexes in the absence of remote protons, since these metal cations strongly bind to neutral histidine residues in peptides. In the case of the ECD and ETD of Cu2+-polyhistidine complexes, the metal cation in the complex was reduced and the recombination energy was redistributed throughout the peptide to lead a zwitterionic peptide form having a protonated histidine residue and a deprotonated amide nitrogen. The zwitterion then underwent peptide bond cleavage, producing a and b fragment ions. In contrast, ECD and ETD induced different fragmentation processes in Zn2+-polyhistidine complexes. Although the N–Cα bond in the Zn2+-polyhistidine complex was cleaved by ETD, ECD of Zn2+-polyhistidine induced peptide bond cleavage accompanied with hydrogen atom release. The different fragmentation modes by ECD and ETD originated from the different electronic states of the charge-reduced complexes resulting from these processes. The details of the fragmentation processes were investigated by density functional theory.
Energy-resolved collision-induced dissociation (ER-CID) experiments of sodium cationized glycosyl phosphate complexes, [GPx+Na]+, are performed to elucidate the effects of linkage stereochemistry (α versus β), the geometry of the leaving groups (1,2-cis versus 1,2-trans), and protecting groups (cyclic versus non-cyclic) on the stability of the glycosyl phosphate linkage via survival yield analyses. A four parameter logistic dynamic fitting model is used to determine CID50% values, which correspond to the level of rf excitation required to produce 50% dissociation of the precursor ion complexes. Present results suggest that dissociation of 1,2-trans [GPx+Na]+ occurs via a McLafferty-type rearrangement that is facilitated by a syn orientation of the leaving groups, whereas dissociation of 1,2-cis [GPx+Na]+ is more energetic as it involves the formation of an oxocarbenium ion intermediate. Thus, the C1?C2 configuration plays a major role in determining the stability/reactivity of glycosyl phosphate stereoisomers. For 1,2-cis anomers, the cyclic protecting groups at the C4 and C6 positions stabilize the glycosidic bond, whereas for 1,2-trans anomers, the cyclic protecting groups at the C4 and C6 positions tend to activate the glycosidic bond. The C3 O-benzyl (3 BnO) substituent is key to determining whether the sugar or phosphate moiety retains the sodium cation upon CID. For 1,2-cis anomers, the 3 BnO substituent weakens the glycosidic bond, whereas for 1,2-trans anomers, the 3 BnO substituent stabilizes the glycosidic bond. The C2 O-benzyl substituent does not significantly impact the glycosidic bond stability regardless of its orientation.
Carboxamides bearing an N–H functionality are known to undergo deprotonation under negative-ion-generating mass spectrometric conditions. Herein, we report that N–H bearing carboxamides with acidities lower than that of the hydroperoxyl radical (HO-O?) preferentially form superoxide radical-anion (O2-?) adducts, rather than deprotonate, when they are exposed to the glow discharge of a helium-plasma ionization source. For example, the spectra of N-alkylacetamides show peaks for superoxide radical-anion (O2-?) adducts. Conversely, more acidic amides, such as N-alkyltrifluoroacetamides, preferentially undergo deprotonation under similar experimental conditions. Upon collisional activation, the O2-? adducts of N-alkylacetamides either lose the neutral amide or the hydroperoxyl radical (HO-O?) to generate the superoxide radical-anion (m/z 32) or the deprotonated amide [m/z (M – H)?], respectively. For somewhat acidic carboxamides, the association between the two entities is weak. Thus, upon mildest collisional activation, the adduct dissociates to eject the superoxide anion. Superoxide-adduct formation results are useful for structure determination purposes because carboxamides devoid of a N–H functionality undergo neither deprotonation nor adduct formation under HePI conditions.
Ion mobility/mass spectrometry techniques are employed to investigate the binding of Zn2+ to the nine-residue peptide hormone oxytocin (OT, Cys1-Tyr2-Ile3-Gln4-Asn5-Cys6-Pro7-Leu8-Gly9-NH2, having a disulfide bond between Cys1 and Cys6 residues). Zn2+ binding to OT is known to increase the affinity of OT for its receptor [Pearlmutter, A. F., Soloff, M. S.: Characterization of the metal ion requirement for oxytocin-receptor interaction in rat mammary gland membranes. J. Biol. Chem. 254, 3899–3906 (1979)]. In the absence of Zn2+, we find evidence for two primary OT conformations, which arise because the Cys6–Pro7 peptide bond exists in both the trans- and cis-configurations. Upon addition of Zn2+, we determine binding constants in water of KA = 1.43 ± 0.24 and 0.42 ± 0.12 μM?1, for the trans- and cis-configured populations, respectively. The Zn2+ bound form of OT, having a cross section of Ω = 235 Å2, has Pro7 in the trans-configuration, which agrees with a prior report [Wyttenbach, T., Liu, D., Bowers, M. T.: Interactions of the hormone oxytocin with divalent metal ions. J. Am. Chem. Soc. 130, 5993–6000 (2008)], in which it was proposed that Zn2+ binds to the peptide ring and is further coordinated by interaction of the C-terminal, Pro7-Leu8-Gly9-NH2, tail. The present work shows that the cis-configuration of OT isomerizes to the trans-configuration upon binding Zn2+. In this way, the proline residue regulates Zn2+ binding to OT and, hence, is important in receptor binding.
Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔHo, ΔSo, and ΔGo, for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data.
Percolator is a widely used software tool that increases yield in shotgun proteomics experiments and assigns reliable statistical confidence measures, such as q values and posterior error probabilities, to peptides and peptide-spectrum matches (PSMs) from such experiments. Percolator’s processing speed has been sufficient for typical data sets consisting of hundreds of thousands of PSMs. With our new scalable approach, we can now also analyze millions of PSMs in a matter of minutes on a commodity computer. Furthermore, with the increasing awareness for the need for reliable statistics on the protein level, we compared several easy-to-understand protein inference methods and implemented the best-performing method—grouping proteins by their corresponding sets of theoretical peptides and then considering only the best-scoring peptide for each protein—in the Percolator package. We used Percolator 3.0 to analyze the data from a recent study of the draft human proteome containing 25 million spectra (PM:24870542). The source code and Ubuntu, Windows, MacOS, and Fedora binary packages are available from http://percolator.ms/ under an Apache 2.0 license.
Radical-driven dissociation (RDD) of hydrogen-deficient peptide ions [M???H?+?H]·+ has been examined using matrix-assisted laser dissociation/ionization in-source decay mass spectrometry (MALDI-ISD MS) with the hydrogen-abstracting matrices 4-nitro-1-naphthol (4,1-NNL) and 5-nitrosalicylic acid (5-NSA). The preferential fragment ions observed in the ISD spectra include N-terminal [a]?+?ions and C-terminal [x]+, [y?+?2]+, and [w]+ ions which imply that β-carbon (Cβ)-centered radical peptide ions [M???Hβ?+?H]·+ are predominantly produced in MALDI conditions. RDD reactions from the peptide ions [M???Hβ?+?H]·+ successfully explains the fact that both [a]+ and [x]+ ions arising from cleavage at the Cα-C bond of the backbone of Gly-Xxx residues are missing from the ISD spectra. Furthermore, the formation of [a]+ ions originating from the cleavage of Cα-C bond of deuterated Ala(d3)-Xxx residues indicates that the [a]+ ions are produced from the peptide ions [M???Hβ?+?H]·+ generated by deuteron-abstraction from Ala(d3) residues. It is suggested that from the standpoint of hydrogen abstraction via direct interactions between the nitro group of matrix and hydrogen of peptides, the generation of the peptide radical ions [M???Hβ?+?H]·+ is more favorable than that of the α-carbon (Cα)-centered radical ions [M???Hα?+?H]·+ and the amide nitrogen-centered radical ions [M???HN?+?H]·+, while ab initio calculations indicate that the formation of [M???Hα?+?H]·+ is energetically most favorable.
Trajectory calculations are used to investigate peak shapes and ion transmission with a proposed new method of mass analysis with a quadrupole mass filter. Dipole excitation is applied to either the x or the y electrodes, or both, to create bands of instability within the first stability region. With excitation between the y electrodes (near βy?=?0), ions are removed from the low mass side of a peak, and with ion excitation in x (near βx?=?1), ions are removed from the high mass side. The mass resolution can be approximately doubled with comparatively little loss in ion transmission. Ion motion in an ideal quadrupole field and in the field of a quadrupole constructed with round rods has been studied. With an ideal quadrupole field, excitation in y is found to give better peak shape and resolution than excitation in x. With quadrupoles constructed with round rods, excitation in y is found to remove ions from both the low and high mass sides of a peak. The additional higher order multipoles introduced to the quadrupole potential by the use of round rods couple the x motion to the y motion so that exciting the y motion also excites ions in x. Thus, only excitation in y is necessary. Both with an ideal quadrupole field and quadrupoles constructed with round rods, the resolution can be increased ca. ×2 with little loss of transmission.
