Kinase Assay-Linked Phosphoproteomics: Discovery of Direct Kinase Substrates.

Dissection of direct kinase-substrate relationships provides invaluable information about phosphorylation pathways and can highlight both pathogenic mechanisms and possible drug targets for diseases in which abnormal kinase activity is linked to onset and progression. Here, we describe a mass spectrometry-based strategy to define the direct substrates of a kinase of interest. The kinase assay-linked phosphoproteomics approach examines putative kinase substrates both in vitro and in vivo to produce a list of highly confident substrates.

Quantitative chiral analysis of sugars by electrospray ionization tandem mass spectrometry using modified amino acids as chiral reference compounds.

Rapid quantitative enantiomeric analysis of mannose, glucose, galactose, and ribose is achieved using electrospray ionization and cluster ion dissociation with data analysis by the kinetic method. Several modified amino acids (N-Ac-L-Phe, N-benzoyl-L-Phe, N-t-Boc-L-Phe, N-Ac-L-Pro, N-t-Boc-L-Pro, N-Fmoc-L-Pro, N-Ac-L-Tyr, O-Me-L-Tyr) and four transition divalent metal cations (Co2+, Cu2+, Ni2+, and Zn2+) were tested to select the best system for chiral recognition and quantitation of each sugar. Quantitative determinations of the enantiomeric compositions of sugar solutions were achieved using either multiple- or two-point calibration curves; differences between the actual and experimental values were <2% enantiomeric excess (ee).

Rapid enantiomeric quantification of an antiviral nucleoside agent (D,L-FMAU, 2'-fluoro-5-methyl-beta,D,L-arabinofurano-syluracil) by mass spectrometry.

A novel mass spectrometric method is applied to rapid, accurate (<1%) quantification of chiral Clevudine (L-FMAU, 2'-fluoro-5-methyl-beta,L-arabinofuranosyluracil), a potent antiviral nucleoside agent against hepatitis B virus. Transition metal bound complex ions containing the chiral drug are generated by electrospray ionization mass spectrometry and subjected to collision-induced dissociation. The ratio of the two competitive dissociation rates is related to the enantiomeric composition of the drug mixture, allowing the determination of enantiomeric contamination in the drug.

Gas-phase SN2 reactivity of dicoordinated borinium cations using pentaquadrupole mass spectrometry.

We report gas phase ion/molecule reactions between dialkoxyborinium cations (RO-B+-OR) and small organic amides, such as N,N-dimethylformamide and N,N-diethylpropionamide. Besides direct addition at boron, the results show efficient SN2 methyl transfer from the borinium ion to the amide. Isotopic labeling and collision-induced dissociation (CID) of the methyl transfer products demonstrate O-methylation of the amide. Methyl substitution at the alpha-carbon of the amide affects the degree of alkylation and adduct formation. Direct proton abstraction via beta-elimination is a major competitive reaction for substituents other than methyl. Ab initio calculations at the B3LYP/6-31G(d) level indicate that SN2 transmethylation is highly exothermic with O-methylation favored over N-methylation by 14.8 kcal/mol.

Differentiation and quantitation of isomeric dipeptides by low-energy dissociation of copper(II)-bound complexes.

Application of the kinetic method based on the dissociation of transition metal centered cluster ions is extended from chiral analysis (Tao, W. A.; Zhang, D.; Nikolaev, E. N.; Cooks, R. G. J. Am. Chem. Soc. 2000, 122, 10598) to quantitative analysis of isomeric mixtures, including those with Leu/Ile substitutions. Copper(II)-bound complexes of pairs of peptide isomers are generated by electrospray ionization mass spectrometry and the trimeric complex [CuII(ref)2(A) - H]+ (analyte A, a mixture of isomeric peptides; reference compound ref, usually a peptide) is caused to undergo collisional dissociation. Competitive loss of the neutral reference compound or the neutral analyte yields two ionic products and the ratio of rates of the two competitive dissociations, viz. the product ion branching ratio R is shown to depend strongly on the regiochemistry of the analyte in the precursor [CuII(A)(ref)2 - H]+ complex ion. Calibration curves are constructed by relating the branching ratio measured by the kinetic method, to the isomeric composition of the mixture to allow rapid quantitative isomer analysis.

Mass spectrometric quantitation of chiral drugs by the kinetic method.

A novel mass spectrometric method for rapid, accurate (2-4% ee) quantitation of chiral drugs is described. Copper(II)-bound complexes of seven model drugs (atenolol, DOPA, ephedrine, pseudoephedrine, isoproterenol, norepinephrine, propranolol) with chiral reference compounds (L-amino acids) are generated by electrospray ionization mass spectrometry. The trimeric complex ions (three chiral ligands--one of the analyte and two of the reference compound) are collisionally activated, and they undergo dissociation by competitive loss of either the neutral reference or the neutral drug molecule. The ratio of the two competitive dissociation rates, viz. the product ion branching ratio, is related via the kinetic method to the enantiomeric composition of the drug mixture. A two-point calibration curve, derived from the kinetic method, allows rapid quantitation of enantiomeric excess of drug mixtures. The chiral sensitivity of the method is such as to allow determination of mixtures with a few percent enantiomeric contamination.

Liquid chromatographic studies of the effect of phosphate on the binding properties of silica-immobilized bovine serum albumin.

High-performance liquid chromatography has been used to examine how phosphate ions affect the binding properties of bovine serum albumin (BSA) immobilized to porous silica. In doing this, the time dependence of the protein to reach conformational equilibrium is measured as a function of the concentration of phosphate in the eluent using the D- and L-isomers of tryptophan and kynurenine as solutes. The overall binding and chiral selectivity (alphaD,L) of the protein toward these solutes appear to be related to two types of effects: one being those that are site-selective and only influence the retention of the L-isomers and the other being those that are nonselective and influence the retention of both enantiomers. An interesting feature of the concentration-dependent data is a maximum in alphaD,L at intermediate phosphate concentrations (i.e., 10 to 50mM phosphate) indicative of both cooperative and antagonistic binding effects. Phosphate eluents within this concentration range provide selectivity advantages, and those at higher concentrations decrease the time required for the protein or column to reach equilibrium. A final set of studies has also been carried out using four alternate buffer systems (i.e., borate, carbonate, acetate, and arsenate eluents). Although the borate eluents affect the BSA's binding properties and alphaD,L similar to the phosphate eluents, the other buffers result in poor separations. Observations from this study are useful in helping to optimize separations carried out on immobilized BSA as well as addressing biological and mechanistic questions related to how anions influence the native binding properties of serum albumins.

Metal-assisted esterification: glutaric acid-iron(II) complexes in the gas phase.

Transition metal ions are routinely used to assist organic reactions; however, direct detection of the intermediates in such reactions is uncommon. Here, we demonstrate a transition metal ion-assisted reaction between glutaric acid (L) and methanol, using electrospray ionization mass spectrometry (ESI-MS). Esterification of glutaric acid does not occur in aqueous methanol solution under ESI conditions, but the FeII-bound acid cluster, [FeII L2 - H]+, adds methanol and dehydrates to give rise to an abundant product ion with a 14 Da increased mass. The occurrence of methyl esterification is supported by collision-induced dissociation and isotopic labeling data, which indicate that the sequence by which the product ion is generated is loss of water, followed by the addition of methanol. Electrospray ionization conditions, specifically the tube lens offset voltage, strongly affect the reaction efficiency, presumably through control of the dehydration process. Other transition metal ions, such as NiII, ZnII, CoII and CuII, also show distinctive metal-assisted reactions.

Kinetic Resolution of d,l-Amino Acids Based on Gas-Phase Dissociation of Copper(II) Complexes.

Chiral recognition of d- and l-amino acids is achieved in the gas phase on the basis of the kinetics of competitive fragmentations of trimeric Cu(II)-bound complexes. The singly charged copper(II)-amino acid trimeric cluster ions [A(2)BCu(II) - H](+) dissociate to form [A(2)Cu(II) - H](+) and [ABCu(II) - H](+) upon collision-induced dissociation (CID) in a quadrupole ion trap. The abundance ratios of these fragments depend strongly on the stereochemistry of the ligands in the [A(2)BCu(II) - H](+) complex ion. The kinetic method was used to calculate relative Cu ion affinities (ΔCu(II)') for homo- and heterochiral copper(II)-bound dimeric cluster ions as the indicator of chiral discrimination. Six amino acids of four different types showed chiral distinctions which ranged from 0 to 6.5 kJ/mol in terms of values of ΔCu(II)' with abundance ratios, referenced to the other enantiomer, ranging from 1 to 9.2. Amino acids with aromatic substituents displayed the largest chiral distinction, which correlates well with reported chromatographic results. The methodology presented here provides a sensitive means to study enantiomers by mass spectrometry, and initial results show that it is applicable to measurement of enantiomeric excess.