Methyl group migration during the fragmentation of singly charged ions of trimethyllysine-containing peptides: Precaution of using MS/MS of singly charged ions for interrogating peptide methylation

Core histones are susceptible to a range of post-translational modifications (PTMs), including acetylation, phosphorylation, methylation, and ubiquitination, which play important roles in the epigenetic control of gene expression. Here, we observed an unusual discrepancy between MALDI-MS/MS and ESI-MS/MS on the methylation of trimethyllysine-containing peptides with residues 9–17 from human histone H3 and residues 73–83 from yeast histone H3. It turned out that the discrepancy could be attributed to an unusual methyl group migration from the side chain of trimethyllysine to the C-terminal arginine residue during peptide fragmentation, and this methyl group transfer only occurred for singly charged ions, but not for doubly charged ions. The methyl group transfer argument received its support from the results on the studies of the fragmentation of the ESI- or MALDI-produced singly charged ions of several synthetic trimethyllysine-bearing peptides. The results presented in this study highlighted that caution should be exerted while MS/MS of singly charged ions is employed to interrogate the PTMs of trimethyllysine-containing peptides.     

MALDI mass spectrometry‐based sequence analysis of arginine‐containing glycopeptides: improved fragmentation of glycan and peptide chains by modifying arginine residue

This paper describes an improved method for the sequence analysis of Arg‐containing glycopeptide by MALDI mass spectrometry (MS). The method uses amino group derivatization (4‐aza‐6‐(2,6‐dimethyl‐1‐piperidinyl)‐5‐oxohexanoic acid N‐succinimidyl ester) and removal (carboxypeptidase B) or modification (peptidylarginine deiminase 4) of the arginine residue of the peptide. The derivatization attaches a basic tertiary amine moiety onto the peptides, and the enzymatic treatment removes or modifies the arginine residue. Fragmentation of the resulting glycopeptide under low‐energy collision‐induced dissociation yielded a simplified ion series of both the glycan and the peptide that can facilitate their sequencing. The feasibility of the method was studied using α₁‐acid glycoprotein‐derived N‐linked glycopeptides, and glycan and peptide in each glycopeptide were successfully sequenced by MALDI tandem MS (MS/MS). Copyright © 2013 John Wiley & Sons, Ltd.     

Hydrazide functionalized magnetic nanoparticles for specific extraction of N‐terminal serine and threonine peptides

In this study, we present hydrazide functionalized magnetic nanoparticles as a sorbent prepared by a new and facile method. Scanning electron microscope and Fourier transform infrared were used for characterizing the synthesized nanoparticles. The ability of the sorbent to extract N‐terminal serine and threonine peptides was evaluated. The peptides were modified by oxidation of the hydroxyl group in the 1,2‐amino alcohol structure before extraction. These aldehyde‐forms of peptides were specifically bonded to the hydrazide groups of the sorbent. The formed hydrazone bonds were cleaved in the presence of hydroxylamine reagent. Finally, the oximated peptides were released and quantified with a high‐performance liquid chromatography–diode array spectroscopy. The effects of experimental parameters including extraction time, elution time and elution volume on extraction efficiency were also investigated. The required time for the extraction process to reach equilibrium and elution time was only 8 h. The adsorption efficiency of the sorbent was 79 and 77% for peptides with N‐terminal serine and threonine, respectively. The sorbent showed good specificity for extracting the peptides. In addition, the extraction efficiency of the sorbent remained constant in the presence of a non‐N‐terminal serine and threonine peptide as interference.     

C-terminal amino acid residue loss for deprotonated peptide ions containing glutamic acid, aspartic acid, or serine residues at the C-terminus

Deprotonated peptides containing C-terminal glutamic acid, aspartic acid, or serine residues were studied by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer with ion production by electrospray ionization (ESI). Additional studies were performed by post source decay (PSD) in a matrix-assisted laser desorption ionization/time-of-flight (MALDI/TOF) mass spectrometer. This work included both model peptides synthesized in our laboratory and bioactive peptides with more complex sequences. During SORI-CID and PSD, [M - H]- and [M - 2H]2- underwent an unusual cleavage corresponding to the elimination of the C-terminal residue. Two mechanisms are proposed to occur. They involve nucleophilic attack on the carbonyl carbon of the adjacent residue by either the carboxylate group of the C-terminus or the side chain carboxylate group of C-terminal glutamic acid and aspartic acid residues. To confirm the proposed mechanisms, AAAAAD was labelled by 18O specifically on the side chain of the aspartic acid residue. For peptides that contain multiple C-terminal glutamic acid residues, each of these residues can be sequentially eliminated from the deprotonated ions; a driving force may be the formation of a very stable pyroglutamatic acid neutral. For peptides with multiple aspartic acid residues at the C-terminus, aspartic acid residue loss is not sequential. For peptides with multiple serine residues at the C-terminus, C-terminal residue loss is sequential; however, abundant loss of other neutral molecules also occurs. In addition, the presence of basic residues (arginine or lysine) in the sequence has no effect on C-terminal residue elimination in the negative ion mode.     

Preparation of Oxazolidine-Containing Peptides: Unusual effects in RhIII-catalyzed acetalizations of aldehydes with urethane-protected serine and threonine esters and with dipeptides containing serine or threonine residues at the N-terminus

The cyclization reaction of aldehydes with Z- and Boc-protected β-hydroxyamino-acid esters (Tables 1 and 2), or of dipeptides containing serine or threonine at the N-terminus (Table 3), to give oxazolidine derivatives, occurs in the presence of isopropyl orthoformate and catalytic amounts of [Rh(MeCN)₃(triphos)](CF₃SO₃)₃. The reaction may be carried out under kinetic or under thermodynamic control, so that the ratio of the two possible epimeric products can be changed. The protecting group can be removed from the 3-position of the oxazolidine ring, and the resulting NH group can be coupled with another amino acid. Thus, a new method for the preparation of peptides containing β-hydroxy-amino acid-derived oxazolidines (‘pseudo-prolines’) is available. N-Neopentyl-substituted tripeptides are also described.     

苯二酚异构体双电荷离子和单电荷离子的动能谱研究

本文利用质量分析离子动能谱(MIKES)、碰撞诱导解离(CID)技术和电子捕获诱导解离(ECID)技术, 研究了邻、间、对苯二酚分子在电子轰击质谱(EIMS)中产生的双电荷离子[C6H6O2]^2^+, [C6H4O]^2^+和单电荷离子[C6H6O2]^+。根据测定的电荷分离反应动能释放值T和由此计算出的两电荷间距R, 推测出过渡态的结构。有趣的是, 可利用单电荷离子[C6H6O2]^+的MIKES/CID谱区分苯二酚异构体。     

Expansion coefficients and moments of electron momentum densities for singly charged ions

Numerical Hartree–Fock calculations of the first three coefficients of the MacLaurin expansion and the leading coefficient of the large-p asymptotic expansion of the electron momentum densities Π(p) are reported for 54 singly charged atomic cations from He⁺ (atomic number Z = 2) to Cs⁺ (Z = 55) and 43 anions from H⁻ (Z = 1) to I⁻ (Z = 53) in their experimental ground states. We also report all the finite moments <p ^k > (−2≤k≤+4) of the momentum densities Π(p) for the above-mentioned 97 ionic species. The results are compared with the previous ones for neutral atoms [Koga and Thakkar (1996) J Phys B 29: 2973], and the dependence of the expansion coefficients and moments on nuclear charge is discussed among isoelectronic species. Received: 20 November 1998 / Accepted: 15 January 1999 / Published online: 7 June 1999     

A procedure for the analysis of site‐specific and structure‐specific fucosylation in alpha‐1‐antitrypsin

A MS‐based methodology has been developed for analysis of core‐fucosylated versus antennary‐fucosylated glycosites in glycoproteins. This procedure is applied to the glycoprotein alpha‐1‐antitrypsin (A1AT), which contains both core‐ and antennary‐fucosylated glycosites. The workflow involves digestion of intact glycoproteins into glycopeptides, followed by double digestion with sialidase and galactosidase. The resulting glycopeptides with truncated glycans were separated using an off‐line HILIC (hydrophilic interaction liquid chromatography) separation where multiple fractions were collected at various time intervals. The glycopeptides in each fraction were treated with PNGase F and then divided into halves. One half of the sample was applied for peptide identification while the other half was processed for glycan analysis by derivatizing with a meladrazine reagent followed by MS analysis. This procedure provided site‐specific identification of glycosylation sites and the ability to distinguish core fucosylation and antennary fucosylation via a double digestion and a mass profile scan. Both core and antennary fucosylation are shown to be present on various glycosites in A1AT.     

Substituent effects on the gas‐phase fragmentation reactions of protonated peptides containing benzylamine‐derivatized lysyl residues

Motivated by the need for chemical strategies designed to tune peptide fragmentation to selective cleavage reactions, benzyl ring substituent influence on the relative formation of carbocation elimination (CCE) products from peptides with benzylamine‐derivatized lysyl residues has been examined using collision‐induced dissociation (CID) tandem mass spectrometry. Unsubstituted benzylamine‐derivatized peptides yield a mixture of products derived from amide backbone cleavage and CCE. The latter involves side‐chain cleavage of the derivatized lysyl residue to form a benzylic carbocation [C₇H₇]⁺ and an intact peptide product ion [(MH_n)ⁿ⁺ – (C₇H₇)⁺]^(n‐1)+. The CCE pathway is contingent upon protonation of the secondary ε‐amino group (N_ε) of the derivatized lysyl residue. Using the Hammett methodology to evaluate the electronic contributions of benzyl ring substituents on chemical reactivity, a direct correlation was observed between changes in the CCE product ion intensity ratios (relative to backbone fragmentation) and the Hammett substituent constants, σ, of the corresponding substituents. There was no correlation between the substituent‐influenced gas‐phase proton affinity of N_ε and the relative ratios of CCE product ions. However, a strong correlation was observed between the π orbital interaction energies (ΔE_int) of the eliminated benzylic carbocation and the logarithm of the relative ratios, indicating the predominant factor in the CCE pathway is the substituent effect on the level of hyperconjugation and resonance stability of the eliminated benzylic carbocation. This work effectively demonstrates the applicability of σ (and ΔE_int) as substituent selection parameters for the design of benzyl‐based peptide‐reactive reagents which tune CCE product formation as desired for specific applications. Copyright © 2012 John Wiley & Sons, Ltd.     

Structural properties of reciprocal form factor in neutral atoms and singly charged ions

Structural characteristics of the spherically averaged internally folded density or reciprocal form factor Br are studied within the Hartree-Fock framework for 103 neutral atoms, 54 singly charged cations, and 43 anions in their ground state. The function Br is classified throughout the Periodic Table into three types: (i) monotonic decrease from the origin, (ii) maximum at r=0 and a negative minimum at r>0, and (iii) a local maximum at r=0 and a pair maximum-minimum out of the origin. A detailed study of the corresponding properties for individual subshells as well as their relative weight for the total Br is also carried out. For completeness, the analytical Br for hydrogenlike atoms in both ground and excited states is also analyzed.     

phosphate hydrate complexes of singly and doubly charged magnesium ions: Structure,energies, and spin states

For mixed magnesium phosphate hydrate complexes containing Mg²⁺ and Mg⁺ cations and HPO₄²⁻, HPO₄⁻, and H₂P₂O₇²⁻ anions, theoretical analysis of the electronic structure and energies has been performed at the model level in order to predict the actual role of these systems in various reactions that occur in the catalytic sites of ATP synthesizing enzymes. The calculations (DFT/B3LYP, MP2 with the 6–31G* basis set) of isolated aqua complexes Mg(H₂O) _n ^p (n = 1−6, p = 0, +1, +2) show that their relative stability monotonically increases with increasing n in each series and sharply decreases at a given n in going from the charged systems of Mg²⁺ (4–16 eV) and Mg⁺ (2–7 eV) to the neutral systems of Mg (<2 eV). An even higher stability is predicted for mixed magnesium complexes. The energies of fragmentation of mixed Mg²⁺ complexes into singlet phosphate and Mg²⁺-containing fragments at n = 0–4 are within 6–27 eV, and the energies of fragmentation into the corresponding radical ions are within 3–10 eV; for the Mg⁺ complexes, the fragmentation energies are also high (6–14 eV). The reasons for the enhanced stability of the complexes of both types have been analyzed with allowance for the predicted specific features of the electron density redistribution upon complex formation. Typical changes in the geometry of the P- and Mg-containing fragments caused by formation of mixed complexes have been discussed in the framework of the vibronic model of heteroligand systems. The high stability of all mixed magnesium complexes relative to various fragmentation products presumably rules out any dissociative processes in them in the course of ATP synthesis with the participation of phosphorylating enzymes.     

Nonlinear optical polyimides consisting of chromophore‐containing dendrons with site‐isolation effect

To investigate the dendritic structure effects on the electro‐optical (EO) coefficients and thermal stability of the nonlinear optical (NLO) active materials, a bifunctional compound, IDD (4‐isocyanato‐4′(3,3‐dimethyl‐ 2,4‐dioxo‐acetidino)‐diphenylmethane) was used as a building block to synthesize a series of novel NLO chromophore‐containing dendritic structures including Generation 0.5 (G0.5) to Generation 3 (G3). The glass transition temperatures (T_g) of G1–G3 dendrons were in the range of 76–116°C, whereas only the G0.5 dendron exhibited a melting temperature (T_m), 98°C. Moreover, a series of NLO‐active guest–host systems ranging from polyimide‐G0.5 (PI‐G0.5) to polyimide‐G3 (PI‐G3) were prepared by blending 20 wt% chromophore‐containing dendron with a high T_g polyimide. EO coefficients ranged from 6.1 to 12.9 pm/V. The r₃₃/dye content ratio increased with increasing generation of dendron‐containing polyimide samples. Particularly, the improvement in r₃₃/dye content ratio of PI‐G2.5 sample tripled as compared to that of the guest–host sample with Disperse Red 1. Excellent temporal stability of PI‐G0.5 and PI‐G1.5 at 80°C was obtained. Moreover, waveguide properties for NLO polymers containing higher generation dendrons (3.1–3.6 dB/cm at 830 nm) were also obtained. Copyright © 2008 John Wiley & Sons, Ltd.     

Interaction of vanadyl (VO2+) with ligands containing serine, tyrosine, and threonine

Reaction of vanadyl sulfate with an aldehyde (2-hydroxy-1-naphthaldehyde (nap); 3-methoxysalicylaldehyde = o-vanillin (van)) and an amino acid carrying an OH group (L-tyrosine (L-tyr); L-serine (L-ser), L-threonine (L-thr)) yielded the complexes [VO(nap-D-Tyr)(H2O)] 1a, [VO(van-D,L-Tyr)(H2O)] 1c, [VO(nap-Ser)(H2O)] 2a, [VO(van-D,L-Ser)(H2O)] 2b, [VO(nap-Thr)(H2O)] 3a, and [VO(van-Thr)(H2O)] 3b. [VO(nap-L-tyr(H2O)], 1b, was obtained from the reaction between [VO(nap)(2)] and l-TyrOMe. The crystal and molecular structures of 1a.CH3OH, 1b.CH3OH, 1c.H2O, 2b.2H2O, and the Schiff base nap-D,L-TyrOMe (4) are reported. The ligands coordinate in a tridentate manner through the phenolate component of nap or van, the imine nitrogen, and the carboxylate of the amino acid. Direct coordination of the (deprotonated) OH amino acid functionality is not observed in these complexes. Instead, the OH groups are involved in hydrogen bonding, leading, along with pi-pi stacking, to extended one- and three-dimensional supramolecular networks. The relevance for the interaction between oxovanadium(IV,V) and proteins having serine, threonine, or tyrosine at their reactive sites is addressed.     

Electron impact fragmentation of pyranocoumarin derivatives. Tandem mass spectrometric study of abundant singly and doubly charged fragment ions at high and low collision energy

A series of novel pyranocoumarin derivatives were analysed by electron impact mass spectrometry and tandem mass spectrometry at low aud high collision energy. The collision-induced decomposition tandem mass spectra of the [M ? CH₃]⁺ ions yielded several structurally valuable fragments and those of the [M ? CH₃]²⁺ ions allowed some charge-separation reactions to be recognized.     

A chemoenzymatic approach enables the site‐specific conjugation of recombinant proteins

Many biotechniques including protein microarray, drug screening, biosensors rely on the immobilization of recombinant proteins on the solid supports. It is well known that random orientation of the immobilized proteins could impair their biologic functions. Thus, it is very important to develop new site‐specific immobilization approach. In this study, we presented a chemoenzymatic approach for site‐specific conjugation of recombinant proteins onto solid support. In this strategy, the affinity tag on recombinant protein was enzymatically cleaved to expose the N‐terminal serine, which was oxidized to carry an aldehyde group and was then covalently coupled to hydrazide resin through hydrazone ligation. As this approach takes advantage of the most frequently used TEV protease, it requires no further sequence design on recombinant protein. This method was validated by site specific coupling of a synthetic peptide and a recombinant protein onto solid supports. It was found that the site specific immobilized SH2 domain is functional and could be used to enrich tyrosine phosphorylated peptides.