Delineation of disease phenotypes associated with esophageal adenocarcinoma by MALDI-IMS-MS analysis of serum N-linked glycans.

N-Linked glycans, extracted from patient sera and healthy control individuals, are analyzed by Matrix-assisted laser desorption ionization (MALDI) in combination with ion mobility spectrometry (IMS), mass spectrometry (MS) and pattern recognition methods. MALDI-IMS-MS data were collected in duplicate for 58 serum samples obtained from individuals diagnosed with Barrett's esophagus (BE, 14 patients), high-grade dysplasia (HGD, 7 patients), esophageal adenocarcinoma (EAC, 20 patients) and disease-free control (NC, 17 individuals). A combined mobility distribution of 9 N-linked glycans is established for 90 MALDI-IMS-MS spectra (training set) and analyzed using a genetic algorithm for feature selection and classification. Two models for phenotype delineation are subsequently developed and as a result, the four phenotypes (BE, HGD, EAC and NC) are unequivocally differentiated. Next, the two models are tested against 26 blind measurements. Interestingly, these models allowed for the correct phenotype prediction of as many as 20 blinds. Although applied to a limited number of blind samples, this methodology appears promising as a means of discovering molecules from serum that may have capabilities as markers of disease.

Selective analysis of phosphopeptides within a protein mixture by chemical modification, reversible biotinylation and mass spectrometry.

A new method combining chemical modification and affinity purification is described for the characterization of serine and threonine phosphopeptides in proteins. The method is based on the conversion of phosphoserine and phosphothreonine residues to S-(2-mercaptoethyl)cysteinyl or beta-methyl-S-(2-mercaptoethyl)cysteinyl residues by beta-elimination/1,2-ethanedithiol addition, followed by reversible biotinylation of the modified proteins. After trypsin digestion, the biotinylated peptides were affinity-isolated and enriched, and subsequently subjected to structural characterization by liquid chromatography/tandem mass spectrometry (LC/MS/MS). Database searching allowed for automated identification of modified residues that were originally phosphorylated. The applicability of the method is demonstrated by the identification of all known phosphorylation sites in a mixture of alpha-casein, beta-casein, and ovalbumin. The technique has potential for adaptations to proteome-wide analysis of protein phosphorylation.

A chemoselective method for site-specific immobilization of peptides via aminooxy group.

Site-specific modification of peptides and proteins is an important area of basic research for preparation of well-defined biosensors and probes. The unique properties of aminooxy group present an opportunity for chemoselective site-specific immobilization of peptides to prepare well-defined biosensors. We have prepared FLAG peptide derivatives containing L-epsilon-aminooxylysine (L-epsilon-AOLys, 1a) and L-lysine units in their sequence at the C- and N-terminals via solid-phase synthesis. Site-specific modification of peptides through aminooxy group was demonstrated in the preparation of biosensors and selective conjugation in the preparation of biotinylated probes. Effect of the incorporation of L-epsilon-AOLys (1a) into the peptide sequence and its subsequent labeling on the FLAG epitopic character was measured using a surface plasmon resonance detector. It was found that incorporation of L-epsilon-AOLys (1a) into the FLAG peptide and site-specific immobilization through aminooxy group preserved the integrity of FLAG epitope.

Quantitative determination of noncovalently bound acridinium in protein conjugates by liquid chromatography/electrospray ion trap mass spectrometry.

A sensitive and robust liquid chromatography/electrospray ion trap mass spectrometry (LC/MS/MS) method has been developed for the quantitative determination of noncovalently bound acridinium free acid in protein-acridinium conjugates. The lower level of quantitation (LOQ) for acridinium free acid was determined to be 0.6 ng. The assay was validated with a linear concentration range of 0.6-60 ng. The method requires minimum sample handling and is specific, reproducible, and provides a new aspect for protein-acridinium conjugate characterization.

Evidence of nucleophilic addition to chemiluminescent N-sulfonylacridinium-9-carboxamides from electrospray ionization mass spectrometry.

Addition of nucleophiles to the chemiluminescent acridinium-9-carboxamide 1 resulted in the formation of the acridan adduct 7. The relative ratio of 1/7 present in solution could be determined by electrospray ionization mass spectrometry (ESI-MS) for a number of nucleophiles that are commonly employed during the use of 1 as a label in medical diagnostic assays.

Sequencing of anti-thyroxine monoclonal antibody fab fragment by ion trap mass spectrometry.

A comprehensive mass spectrometric strategy is described for the sequencing of anti-thyroxine monoclonal antibody Fab region (48 000 Da). After reduction and S-carboxymethylation of the Fab, the modified light chain and Fd fragment were separated and subjected to multiple proteolytic digestions. The resulting digests were characterized by on-line microbore liquid chromatography/electrospray ionization ion trap mass spectrometry. Database search against published immunoglobulins (IgGs) allowed identification of all the peptides in constant domains. The homologous framework residues in the IgGs were utilized as 'sequence maps' for the sequence determination of variable domains. S-Carboxymethylation with an isotopic-enriched moiety greatly facilitated the recognition and data elucidation of cysteinyl peptides through the unique isotopic distribution patterns specific to the modified peptides. Methylation of peptide mixtures provided additional information for the interpretation of MS/MS spectra, allowing easy differentiation of Asp/Asn and Gln/Glu pairs. This study clearly demonstrates the power of mass spectrometry for the sequencing of antibodies without knowing the corresponding DNA sequences.

Evaluation of chemiluminescent estradiol conjugates by using a surface plasmon resonance detector.

A series of chemiluminescent 17beta-estradiol probes were synthesized. Relative equilibrium dissociation constants (K(D)) for the interaction of an anti-E(2) Fab fragment for the probes in solution were evaluated using a single E(2)-analog biosensor surface on a BIAcore surface plasmon resonance instrument. The results show the antibody fragment binds all chemiluminescent conjugates tested with high affinity showing only minor preferences for site of substitution (C6 versus C7), stereochemistry (alpha versus beta), or linker moiety.

Papain digestion of different mouse IgG subclasses as studied by electrospray mass spectrometry.

On-line liquid chromatography-electrospray ionization mass spectrometry (LC/ESI-MS) has been utilized to monitor the papain digestion of mouse monoclonal antibodies (mAb) of different subclasses (IgG1, IgG2a, IgG2b, and IgG3). The method is simple, rapid, sensitive, and allows for simultaneous determination of digestion products and the identification of microheterogenous fragments. The results provide important insight into the mechanism of papain digestion of mouse IgGs of different subclasses.

A simple method to identify cysteine residues by isotopic labeling and ion trap mass spectrometry.

A simple method was developed to facilitate the identification of cysteine-containing peptides based on S-carboxymethylation of cysteine residues with isotopically enriched bromoacetic acid. An ion trap mass spectrometer with high-resolution scan functionality allows identification of the unique isotopic distribution patterns specific to the modified peptides.

Charge derivatization of peptides to simplify their sequencing with an ion trap mass spectrometer.

The low energy collision-induced dissociation of fixed-charge derivatives [tris(2,4,6-trimethoxyphenyl)phosphonium] of peptides was investigated using an electrospray ion trap mass spectrometer. The fixed charge directed the fragmentation pattern and generated solely N-terminal fragments with minimal internal rearrangement, regardless of the presence and position of basic amino acids in the peptide chain. Generally only b-type ions, accompanied by less intense a-type ions, were observed, depending on the collision energy. It was observed that the fixed charge controlled the fragmentation beyond typical MS/MS, and thus the capacity of the ion trap to perform multiple stage fragmentation (MS(n)) was found particularly useful for obtaining the complete sequence information of the peptides.

Electrospray mass spectrometry of alpha and beta chains of selected hemoglobins and their TNBA and TNB conjugates.

The molecular weights of alpha and beta hemoglobin chains from 15 different vertebrate animal sources and 2 common human variants were determined by electrospray mass spectrometry and compared to the calculated masses based on published amino acid sequences. Conjugates were prepared for 14 of the globins using 2 traditional colorimetric derivatizing reagents, 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) and trinitrobenzenesulfonic acid (TNBS), and the mass of each conjugate was determined by mass spectrometry.

Immunoassay reagents for thyroid testing. 2. Binding properties and energetic parameters of a T4 monoclonal antibody and its Fab fragment with a library of thyroxine analog biosensors using surface plasmon resonance.

A library of 16 thyroxine analog biosensors were prepared for use on the BIAcore surface plasmon resonance instrument. An anti-thyroxine monoclonal antibody and its Fab fragment were tested with each biosensor to generate the association and dissociation rate constants, equilibrium association constants, and Gibbs free energy values for characterizing the binding event.

Characterization of protein-hapten conjugates. 2. Electrospray mass spectrometry of bovine serum albumin-hapten conjugates.

Fifteen hapten-bovine serum albumin (BSA) conjugates were prepared from five commercially available activated haptens. Each hapten was coupled to BSA at three different ratios. The conjugates were characterized by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two mass spectrometry (MS) methods: matrix-assisted laser desorption ionization (MALDI) and liquid chromatography-electrospray ionization (LC-ESI). SDS-PAGE was useful in detecting protein cross-linking, but not assessing hapten density. MALDI-MS and LC-ESI-MS gave comparable qualitative results, but LC-ESI-MS provided a clearer representation of the distribution of hapten-protein species present in the conjugates. Conjugate species substitute with up to 25 haptens per BSA were recorded by LC-ESI-MS.

Substrate-induced inactivation of a crippled beta-glucosidase mutant: identification of the labeled amino acid and mutagenic analysis of its role.

The beta-glucosidase from Agrobacterium sp. catalyzes the hydrolysis of beta-glucosides via a covalent alpha-D-glucopyranosyl-enzyme intermediate involving Glu358. Hydrolysis of 2,4-dinitrophenyl beta-D-glucopyranoside by the low activity Glu358Asp mutant of Agrobacterium beta-glucosidase is accompanied by time-dependent inactivation of the enzyme. Through kinetic studies, labeling, and sequence analysis, inactivation is shown to be a consequence of the occasional (1 time in 1100) attack of Tyr298 on the anomeric center of the substrate, in place of the catalytic nucleophile, with formation of a stable alpha-D-glucopyranosyl tyrosine residue. Tyr298 is conserved throughout family 1 of glycoside hydrolases, an indication of a possible role in catalysis. Results of a kinetic analysis of the Tyr298Phe mutant are consistent with a function of Tyr298 in both orienting the nearby nucleophile Glu358 and stabilizing its deprotonated state in the free enzyme.

The Claviceps purpurea gene encoding dimethylallyltryptophan synthase, the committed step for ergot alkaloid biosynthesis.

The first pathway-specific step of ergot alkaloid biosynthesis in the fungus, Claviceps purpurea, is catalyzed by the prenyltransferase, 4-(gamma,gamma-dimethylallyl)tryptophan synthase. Partial sequence information was obtained for the purified enzyme and a degenerate oligonucleotide mixture was used to identify and amplify segments of the gene, dmaW. The complete gene and near-full-length cDNA were cloned and sequenced. The cDNA was cloned in a yeast expression vector in sense and antisense orientations relative to the inducible GAL1 promoter. Extracts of yeast transformants with the sense constructs, but not antisense constructs or cloning vector, catalyzed production of 4-(gamma,gamma-dimethylallyl)tryptophan. The sequence of dmaW and its cDNA indicated that it encoded a 455 amino acid polypeptide with a predicted molecular mass of 51,824 Da and a putative prenyl diphosphate binding motif.

Characterization of protein-hapten conjugates. 1. Matrix-assisted laser desorption ionization mass spectrometry of immuno BSA-hapten conjugates and comparison with other characterization methods.

Several different low molecular weight haptens were conjugated to BSA to produce immunogens useful for antibody development. The extent of BSA modification due to covalent attachment of hapten was estimated by matrix-assisted laser desorption ionization mass spectrometry. The average number of hapten incorporated to immunogen was determined from the difference in the measured molecular weights of the conjugate from nonmodified BSA. The results from mass spectrometry were compared with results obtained from other more traditional methods of immunogen characterization (UV analysis, trinitrobenzenesulfonic acid titrations, and gel electrophoresis). In each case we were able to calculate the average number of hapten covalently bound to BSA for each synthetically prepared immunogen using matrix-assisted laser desorption ionization mass spectrometry. The other methods presented limitations in certain cases.

Purification and characterization of dimethylallyl tryptophan synthase from Claviceps purpurea.

Dimethylallyl tryptophan synthase (DMAT synthase) catalyzes the alkylation of L-tryptophan by dimethylallyl diphosphate to form 4-(gamma,gamma-dimethylallyl)-L-tryptophan. The enzyme from mycelia of Claviceps purpurea was purified approximately 125-fold to apparent homogeneity by chromatography on n-butyl Sepharose, Q Sepharose, phenyl Sepharose, and Protein Pak as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Analysis by gel filtration chromatography and SDS-PAGE indicated that DMAT synthase is an alpha 2 dimer with a molecular mass of 105 kDa. The purified enzyme was active in metal-free buffer containing EDTA. However, activity was enhanced upon addition of divalent calcium or magnesium ions to the buffer. Values for KM and Vmax were determined in the metal-free EDTA buffer (KMDMAPP, 14 microM; KML-tryptophan, 40 microM; Vmax, 215 nmol min-1 mg-1), 4 mM CaCl2 (KMDMAPP, 8.0 microM; KML-tryptophan, 17 microM; Vmax, 504 nmol min-1 mg-1), and 4 mM MgCl2 (KMDMAPP, 8.0 microM; KML-tryptophan, 12 microM; Vmax, 455 nmol min-1 mg-1). The product was isolated and characterized by 1H NMR, uv, and FAB mass spectrometry.

Glu-537, not Glu-461, is the nucleophile in the active site of (lac Z) beta-galactosidase from Escherichia coli.

The covalent intermediate formed during catalysis by the lac Z beta-galactosidase from Escherichia coli can be trapped by reaction of the enzyme with 2',4'-dinitrophenyl 2-deoxy-2-fluoro-beta-D-galactopyranoside, thereby inactivating the enzyme. Kinetic parameters for this inactivation process with the holo- and apo-enzymes have been determined. The intermediate so formed turns over only very slowly (t1/2 = 11.5 h) resulting in reactivation of the enzyme. The nucleophilic amino acid involved has been identified as Glu-537 by using a tritium-labeled inactivator to label the enzyme, then cleaving the labeled protein into peptides and purifying and sequencing the labeled peptide. This residue is conserved in five homologous beta-galactosidases and is different from that (Glu-461) proposed to be the nucleophile (Herrchen, M., and Legler, G. (1984) Eur. J. Biochem. 138, 527-531) on the basis of affinity labeling studies with conduritol C cis-epoxide. A role for glutamic acid residue 461 as the acid/base catalyst is proposed and justified.