Analysis of deamidation artifacts induced by microwave-assisted tryptic digestion of a monoclonal antibody

The thorough characterization of biopharmaceuticals is essential for ensuring their quality and safety since many potential variations can cause changes to the properties of a drug that may be detrimental to the patient such as decreased efficacy, shorter half-life or increased immunogenicity. Prior to approval and release, protein-based drugs are subject to a battery of analyses to assess the nature of those parameters that are considered critical quality attributes. In some cases the analytical method used may itself cause modifications that are impossible to distinguish from those induced by the intended test conditions (e.g. storage time/temperature, light exposure) which are used to assess drug stability. It is therefore important to develop and utilize analytical methods which impose as few artifactual modifications as possible. Asparagine deamidation is a common protein modification and it is known to be induced during tryptic digestion. Therefore we examined common tryptic digestion protocols and compared their propensities towards asparagine modification. Since microwave assisted hydrolysis techniques are often used to shorten digestion times and the effect on deamidation is unknown we sought to compare this method against alternate digestion protocols.     

Internal amino acid sequence analysis of proteins separated by gel electrophoresis after tryptic digestion in polyacrylamide matrix

Summary A method is described for obtaining peptide fragments for sequence analysis from microquantities of proteins separated by 1- or 2-dimensional polyacrylamide gel electrophoresis. After separation by electrophoresis, the proteins were stained with Coomassie Blue and excised. Proteolytic digestion with trypsin was performed directly in the polyacrylamide matrix. The resulting peptide fragments were eluted, separated by reversed phase HPLC, collected and sequenced in a gas phase sequencer. Excellent peptide recoveries allowed generation of extensive internal sequence information from picomole amounts of protein. The method thus overcomes the problem of obtaining amino acid sequence data from N-terminally blocked proteins and provides multiple, independent stretches of sequences that can be used to generate oligonucleotide probes for molecular cloning, to design synthetic peptides for inducing antibodies, and to search sequence databases for related proteins.     

Protein identification by in-gel digestion, high-performance liquid chromatography, and mass spectrometry: Peptide analysis by complementary ionization techniques

A biologically active protein fraction was isolated from rabbit intestine, purified by one-dimensional SDS-PAGE and stained with Coomassie Brilliant Blue. A predominant band of approximately 110-130 kDa was excised and digested in-gel with trypsin. The resulting peptides were extracted then separated by microbore reversed-phase high-performance liquid chromatography (HPLC). Mass spectrometric data from one HPLC fraction obtained by two different ionization techniques proved to be complementary. Matrix-assisted laser desorption/ionization (MALDI) showed nine peptide masses, which by post source decay analysis and database searching were attributed to two proteins. Nanoflow electrospray analysis performed on a hybrid tandem mass spectrometer of quadrupole-quadrupole-orthogonal acceleration time-of-flight (QqTOF) geometry detected six additional peptide components. On the basis of the additional peptides and superior quality collision-induced dissociation spectra typical of this instrument type, two further proteins were identified. The resolution afforded by the QqTOF instrument permitted charge state determination for the fragment ions while preserving the high detection sensitivity that was essential in obtaining the composition of this mixture of proteins.     

Rapid characterization of protein chips using microwave-assisted protein tryptic digestion and MALDI mass spectrometry

We demonstrate that the microwave-assisted protein enzymatic digestion (MAPED) method can be successfully applied to the mass spectrometric characterization of proteins captured on the affinity surfaces of protein chips. The microwave-assisted on-chip tryptic digestion method was developed using a domestic microwave, completing the on-chip proteolysis reaction in minutes, whereas the previous on-chip digestion methods by incubation took hours of incubation time. For the model protein chips, antibody-presenting surfaces were prepared, where anti-α-tubulin1 and antibovine serum albumin (BSA) were immobilized on self-assembled monolayers. The resulting digestion efficiency, displaying sequence coverages of 30 and 14% for α-tubulin1 and BSA, respectively, was comparable to the previous time-consuming incubation studies. It allowed the characterization of immunosensed proteins by MASCOT search using peptide mass fingerprinting. In an example of this method for protein chip applications, BSA naturally involved in fetal bovine serum was unambiguously identified on a model protein chip by imaging mass spectrometry. This work shows that biomass spectrometry techniques can be implemented for surface mass spectrometry and biochip applications. Along with recent advances in imaging mass spectrometry, this technique will provide a new opportunity for high-speed, and thus high-throughput in the future, label-free mass spectrometric assays using protein arrays.     

Electrochemical oxidation and cleavage of proteins with on-line mass spectrometric detection: Development of an instrumental alternative to enzymatic protein digestion

An electrochemical flow cell coupled on-line to a mass spectrometer is used to oxidize a range of proteins. Oxidation of tyrosine and tryptophan can give rise to peptide bond cleavage at their C-terminal side. This suggests the possible use of electrochemistry as an alternative protein digestion method. For the small proteins insulin and alpha-lactalbumin (6 and 14 kD) almost all potential sites are cleaved, while for the largest successfully tested protein (carbonic anhydrase, 29 kD) 7 of the 15 available sites were specifically cleaved. Several proteins did not produce peptides upon electrochemical oxidation, possibly due to problems with accessibility of tyrosine and tryptophan residues, or to competing oxidation reactions. Peptides were generally not the major oxidation products: non-cleavage oxidation products observed as protein mass + n x 16 Da, presumably by oxidation of tyrosine, tryptophan, cysteine and methionine, account for the major fraction of protein oxidation products. Nevertheless the amount and variety of cleavage products at the present conditions shows good prospects for further improvement of the system. The efficient protein oxidation also allows the use of the EC-MS system as a tool to study protein oxidation reactions in general. The preconditioning and life history and/or age of the electrochemical cell was relevant to the solvent and sample conditions needed for efficient oxidative cleavage as opposed to other oxidation reactions.     

Kinetics and mechanisms of chlorine dioxide oxidation of tryptophan

The reactions of aqueous ClO2 (*) and tryptophan (Trp) are investigated by stopped-flow kinetics, and the products are identified by high-performance liquid chromatography (HPLC) coupled with electrospray ionization mass spectrometry and by ion chromatography. The rates of ClO2 (*) loss increase from pH 3 to 5, are essentially constant from pH 5 to 7, and increase from pH 7 to 10. The reactions are first-order in Trp with variable order in ClO2 (*). Below pH 5.0, the reactions are second- or mixed-order in [ClO2 (*)], depending on the chlorite concentration. Above pH 5.0, the reactions are first-order in [ClO2 (*)] in the absence of added chlorite. At pH 7.0, the Trp reaction with ClO2 (*) is first-order in each reactant with a second-order rate constant of 3.4 x 10(4) M(-1) s(-1) at 25.0 degrees C. In the proposed mechanism, the initial reaction is a one-electron oxidation to form a tryptophyl radical cation and chlorite ion. The radical cation deprotonates to form a neutral tryptophyl radical that combines rapidly with a second ClO 2 (*) to give an observable, short-lived adduct ( k obs = 48 s(-1)) with proposed C(H)-OClO bonding. This adduct decays to give HOCl in a three-electron oxidation. The overall reaction consumes two ClO2 (*) per Trp and forms ClO2- and HOCl. This corresponds to a four-electron oxidation. Decay of the tryptophyl-OClO adduct at pH 6.4 gives five initial products that are observed after 2 min and are separated by HPLC with elution times that vary from 4 to 17 min (with an eluent of 6.3% CH 3OH and 0.1% CH 3COOH). Each of these products is characterized by mass spectrometry and UV-vis spectroscopy. One initial product with a molecular weight of 236 decays within 47 min to yield the most stable product, N-formylkynurenine (NFK), which also has a molecular weight of 236. Other products also are observed and examined.     

Nanoliter-volume protein enrichment, tryptic digestion, and partial separation based on isoelectric points by CE for MALDI mass spectral analysis

Sequence-specific proteolysis is an important part of protein identification by MS. Digestion of protein is commonly performed in-solution, in sample vials with volumes ranging from milli- to microliters. When digestion is performed with a sample volume below 1 microL, handling of solution and potential sample loss via adsorption become significant issues. In this report, a proof of concept for the digestion of a small volume protein solution inside a capillary was demonstrated using a discontinuous buffer system previously studied (Nesbitt, C. A., et al. J. Chromatogr. A 2005, 1073, 175-180). Upon voltage application, a pH junction was created by the discontinuous buffer. Using myoglobin as an example, the protein molecules were enriched at the junction with an estimated volume of a few nanoliters. A protease, trypsin, was then introduced to myoglobin at the junction by coenrichment to induce in-capillary digestion. The voltage application was then suspended to provide the necessary time (2 h) for the proteolysis to proceed. When completed, voltage application was resumed, and the discontinuous buffer reconcentrated the peptides formed from digestion. Importantly, the refocused peptides appeared to roughly elute according to their pIs, resulting in a partial separation. Direct sample deposition from capillary was performed to facilitate mass spectral analysis by MALDI. The partial separation, according to pI, offered the potential benefits of MALDI MS signal enhancement and provided supplementary pI information for peptide identity assignment.     

Optimization of in-gel protein digestion system in combination with thin-gel separation and negative staining in 96-well plate format

Improvement of in-gel digestion efficiency is highly desirable for one- or two-dimensional gel electrophoretic separation and mass spectrometric (MS) analysis in proteomics, because the resultant increases in sequence coverage and MS signal intensity lead to higher confidence in protein identification. Here an optimized in-gel digestion system, in combination with thin-gel separation and negative staining in a high-throughput format using 96-well plates, is described. The combination of negative staining and protein separation on a 0.9 mm thick gel showed a clear improvement in in-gel digestion efficiency in comparison with the more typical protocols such as the combination of silver staining and a 1.0 mm gel. In addition, the use of 96-well plates to increase throughput did not decrease the efficiency of this strategy when the stirring of the gel pieces in processes such as destaining, washing, gel-shrinking and peptide extraction was performed by sonication instead of shaking the plates. This procedure was optimized and applied to identify proteins of the postsynaptic density fraction; 105 proteins were identified after SDS-PAGE separation.     

Peptide bond formation mediated by 4,5-dimethoxy-2-mercaptobenzylamine after periodate oxidation of the N-terminal serine residue

[reaction in text] A thiol linker-attached peptide was prepared from a nonprotected peptide via an N(alpha)()-alpha-oxoacyl peptide. Selective oxidation of the N-terminal serine with sodium periodate gave the N(alpha)-glyoxyloyl peptide, reductive amination of which with 4,5-dimethoxy-2-(triphenylmethylthio)benzylamine gave an N(alpha)-4,5-dimethoxy-2-mercaptobenzyl glycyl peptide after removal of the trityl group. The N(alpha)-4,5-dimethoxy-2-mercaptobenzyl peptide can be condensed with a peptide thioester, and the linker is removable. This strategy provides a useful method for the synthesis of peptides using recombinant proteins.     

Identification of oxidation products and free radicals of tryptophan by mass spectrometry

New oxidation products and free radicals derived from tryptophan (Trp) oxidation under Fenton reaction conditions were identified using mass spectrometry. After the oxidation of tryptophan using hydrogen peroxide and iron (II) system (Fenton reaction), mono- and dihydoxy tryptophans and N-formylkynurenine were identified using electrospray mass spectrometry (ES-MS) and ES-MS/MS. Besides these products, new products resulting from the reaction of tryptophan and oxidized tryptophan and 3-methyl indole derivatives were also identified. The 3-methyl indole derivatives resulted, most probably, from the oxidation process and not from in-source processes. A dimer formed by cross-linking between two Trp radicals (Trp-Trp), similar to the previously described tyrosine dimer was observed, as well as the corresponding monohydroxy-dimer (Trp-Trp-OH). Tandem mass spectrometry was used to identify the structures of these new oxidation products. Free radicals derived from tryptophan oxidation under Fenton reaction were detected using as spin trap the DMPO. The free radical species originated during the oxidation reaction formed stable adducts with the spin trap, and these adducts were identified by ES-MS. New adducts of oxidized tryptophan radicals, namely monohydroxy-tryptophan and dihydroxy-Trp dimer radicals, with one and two DMPO spin trap molecules where identified. Tandem mass spectrometry was used to confirm the proposed structure of the observed adducts.     

Fragmentation of peptides with N-terminal dimethylation and imine/methylol adduction at the tryptophan side-chain

The reaction between formaldehyde and the side-chain of tryptophan results in a methylol adduct. This methylol adduct formation also occurs during reductive methylation reactions. In the current study, we investigate the fragmentation pattern of peptides with N-terminal dimethylation and methylol adduction at the tryptophan side-chain. Once formed, the methylol group can easily undergo water loss to form an imine. The peptides with imine or methylol adduct on tryptophan exhibit similar MS/MS fragmentation patterns. We observed ions resulting from an intramolecular reaction between the dimethylamino group at the peptide N-terminus or the lysine side-chain and the imine group. This reaction reduces the imine to a methyl group. We also observed the loss of the imine adduct on tryptophan. This reaction is likely to occur through the reaction of an amino or hydroxyl group with the imine adduct followed by subsequent loss of methylenimine or formaldehyde.     

Raman, infrared and XPS study of bamboo phytoliths after chemical digestion

Many phosphate containing minerals are found in the Jenolan Caves. Such minerals are formed by the reaction of bat guano and clays from the caves. Among these cave minerals is the mineral taranakite (K,NH(4))Al(3)(PO(4))(3)(OH)·9(H(2)O) which has been identified by X-ray diffraction. Jenolan Caves taranakite has been characterised by Raman spectroscopy. Raman and infrared bands are assigned to H(2)PO(4), OH and NH stretching vibrations. By using a combination of XRD and Raman spectroscopy, the existence of taranakite in the caves has been proven.     

Conformational control of oxidation sites, spin states and orbital occupancy in nickel porphyrins

Ni(II) porphyrin π cation radicals are known to undergo an internal electronic isomerization to L₂Ni(III) cations upon complexation with ligands (L). Additional examples of the Ni(II) to Ni(III) conversion are presented for flexible, 'planar' NiOEP (2,3,7,8,12,13,17,18-octaethylporphyrin) and NiT(Pr)P (5,10,15,20-tetra-n-propylporphyrin) in which the Ni(III) orbital occupancy, d _z2 or d _x2-y2, is determined by the ligand field strength of the axial ligands (pyridine, imidazole, or cyanide). In contrast to these results, the nonplanar NiOETPP (2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetraphenylporphyrin), which is easily oxidized because of its saddle-shape, yields a complex postulated to be a high spin Ni(II) π cation radical, based on crystallographic and optical data for (imidazole)2NiOETPP⁺ClO^4-, in which the electron of high spin Ni(II) in the d _x2-y2 orbital is antiferromagnetically coupled to the unpaired electron of the porphyrin radical leaving one electron in the Ni(II) d _z2 orbital, i.e. a pseudo Ni(III). The sterically encumbered, nonplanar NiT(t-Bu)P (5,10,15,20-tetra-tertiary-butylporphyrin) yields Ni(III) complexes when ligated by pyridine, imidazole or cyanide, but in all cases only the Ni(III) d _z2 orbital is occupied as evidenced by EPR spectroscopy. This anomalous chemistry is attributed to the fact that the macrocycle of NiT(t-Bu)P is so sterically constrained that it cannot readily expand to accommodate the longer equatorial Ni—N distances required by population of the d _x2-y2 orbital in Ni(III) or high spin Ni(II). Further support for this postulate derives from NiD(t-Bu)P (5,10-di-tertiary-butylporphyrin) which is less sterically constrained and in which the Ni(III) d _x2-y2 orbital is indeed occupied upon complexation with cyanide. These results thus illustrate the significant effects that the conformations, plasticity or rigidity of Ni porphyrin macrocycles can have on sites of oxidation (metal or porphyrin), spin states (low spin Ni(III) or high spin Ni(II)), and orbital occupancies (d _z2 or d _x2-y2 in Ni(III)).     

Inhibiting the photosensitized oxidation of anthracene and tryptophan by means of natural antioxidants

It is shown that model reactions of photosensitized oxidation of anthracene and tryptophan can be used for evaluation and comparison of antioxidant activity of various classes of compounds. Inhibition of the oxidation of substrates in the presence of the familiar antioxidants tocopherol (vitamin E), ascorbic acid (vitamin C), and mixtures of these vitamins with methionine, and in the presence of reputed antioxidants dihydroquercetin and taurine, are considered. It is concluded that all of the above compounds except for taurine have antioxidant properties; i.e., they reduce the rate constants of the photosensitized oxidation of anthracene and tryptophan. It is found that the inhibition of oxidation is associated with the interaction between antioxidants and singlet oxygen. Analysis of the kinetic dependences of the photosensitized oxidation of substrates in the presence of antioxidants reveals that a mixture of vitamins inhibits the process most efficiently, and inhibition occurs at the initial stages due to more active interaction between singlet oxygen and vitamin C     

Electrochemical oxidation and cleavage of peptides analyzed with on-line mass spectrometric detection

An on-line electrochemistry/electrospray mass spectrometry system (EC/MS) is described that allows fast analysis of the oxidation products of peptides. A range of peptides was oxidized in an electrochemical cell by application of a potential ramp from 0 to 1.5 V during passage of the sample. Electrochemical oxidation of peptides was found to occur readily when tyrosine was present. Tyrosine was found to be oxidized between 0.5 and 1.0 V to various oxidation products, including peptide fragments formed by hydrolysis at the C-terminal side of tyrosine. The results confirm earlier knowledge on the mechanisms and reaction products of chemical and electrochemical peptide oxidation. Methionine residues are also readily oxidized, but do not induce peptide cleavage. At potentials higher than about 1.1 V, additional oxidation products were observed in some peptides, including loss of 28 Da from the C-terminus and dimerization. The tyrosine-specific cleavage reaction suggests a possible use of the EC/MS system as an on-line protein digestion and peptide mapping system. In addition, the system can be used to distinguish phosphorylated from unphosphorylated tyrosine residues. Four forms of the ZAP-70 peptide ALGADDSYYTAR with both, either or neither tyrosine phosphorylated were subjected to a 0-1.5 V potential ramp. Oxidation of, and cleavage adjacent to, tyrosine was observed exclusively at unphosphorylated tyrosine residues.     

The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode

The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H(+)) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H(3)O(+)). Using the computed solvation free energy of H(+) as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pK(a) and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pK(a), NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent.     

Anodic oxidation of a tetrasubstituted cyclooctatetraene. Multiple carbon-carbon bond cleavage and aromatization

Anodic oxidation of 1,2-,5,6-bis[trimethylene]cyclooctaetraene in methanol affords as the major product a substance formed by a complex sequence of carbon-carbon bond cleavages and concomitant aromatization.     

Preparation, structure characterization, and oxidation activity of ruthenium complexes with tripodal ligands bearing noncovalent interaction sites

Ruthenium(II/III) complexes with tripodal tris(pyridylmethyl)amine ligands bearing one, two, or three pivalamide groups (MPPA, BPPA, TPPA: amide-series ligands) or neopentylamine ones (MNPA, BNPA, TNPA: amine-series ligands) at the 6-position of the pyridine ring have been synthesized and structurally characterized. The X-ray structure analyses of the single crystals of these complexes reveal that they complete an octahedral geometry with the tripodal ligand and some monodentate ligands. The amide-series ligands prefer to form a Ru(II) complex, while the amine-series ones give a Ru(III) complex. In the presence of PhIO oxidant, the catalytic activities for epoxidation of olefins, hydroxylation of alkane, and dehydrogenation of alcohol have been investigated using the six ruthenium complexes [Ru(II)(tppa)Cl(2)] (1), [Ru(III)(tnpa)Cl(2)]PF(6) (2), [Ru(II)(bppa)Cl]PF(6) (3), [Ru(III)(bnpa)Cl(2)]PF(6) (4), [Ru(II)(mppa)Cl]PF(6) (5), and [Ru(III)(mnpa)Cl(2)]PF(6) (6). Among them, the amide-series complexes, 1, 3, and 5, showed a higher epoxidation activity in comparison with the amine-series ones, 2, 4, and 6. On the other hand, the latter showed a higher reactivity for hydroxylation, allylic oxidation, and C=C bond cleavage reactions compared with the former. Such a complementary reactivity is interpreted by the character of the ruthenium-oxo species involving electronically equivalent formulas, Ru(V)=O and Ru(IV)-O.     

Synthesis, crystal structures, DNA binding and cleavage studies of two oxovanadium(IV) complexes of 1,10-phenanthroline and Schiff bases derived from tryptophan

Two new V(IV) complexes, [VO(Naph?Ctrp)(phen)]·CH₃OH (1) and [VO(o-Van?Ctrp)(phen)]·CH₃OH·H₂O (2) (Naph?CTrp?=?Schiff base derived from 2-hydroxy-1-naphthaldehyde and l-tryptophan, o-Van?Ctrp?=?Schiff base derived from o-vanillin and l-tryptophan, phen?=?1,10-phenanthroline), have been synthesized and characterized by physicochemical methods. The V(IV) atoms in both complexes are six-coordinated in a distorted octahedral environment. In the crystals of complex 1, the C?CH···?? and ?ШC?? stacking interactions form a 1D chain structure, whereas for complex 2, hydrogen bonds connect the molecular units into a 2D plane structure. The DNA binding properties and cleavage efficiencies of the complexes have been investigated by spectroscopic methods, viscosity measurements and agarose gel electrophoresis. The results suggest that both complexes can bind to CT-DNA in an intercalative mode and can also cleave pBR322 DNA.