Tellurium-125 NMR of Te(II) and Te(IV) dithiocarbamates

¹²⁵Te chemical shifts for Te(R₂NCS₂)₂ and Te(R₂NCS₂)₄ compounds were found to be separated by ca. 1400 ppm. When R is an alkyl group, the electronic contributions to the chemical shifts appear to be very small for both oxidation states of tellurium. The chemical shifts of these compounds display a positive temperature dependence consistent with the major contributions arising from paramagnetic shielding.     

Lactones of disialyl lactose: characterisation by NMR and mass spectra

The lactonisation of alpha-Neup5Ac-(2-->8)-alpha-Neup5Ac-(2-->3)-beta-D-Galp-(1-->4)-D-Glc (disialyl lactose) was investigated. (1)H and (13)C NMR chemical shifts of disialyl lactose and alpha-Neup5Ac-(2-->8, 1-->9)-alpha-Neup5Ac-(2-->3, 1-->2)-beta-D-Galp-(1-->4)-D-Glc (disialyl lactose-dilactone) were assigned based on 1D and 2D NMR results, including edited HSQC, HSQC-TOSCY and HMBC. The time course of lactonisation was followed by thin layer chromatography (TLC) and high-performance liquid chromatography (HPLC) with electrospray ionisation (ESI) mass spectrometry (MS) detection. The rate of lactonisation between alpha-(8)Neu5Ac and alpha-(3)Neu5Ac residues (lactonisation at the alpha-(2-->8) linkage) was faster than that of lactonisation between alpha-(3)Neu5Ac and Gal residues (lactonisation at the alpha-(2-->3) linkage). The mass spectra of disialyl lactose, its lactones, alpha-Neup5Ac-(2-->8)-alpha-Neup5Ac (alpha-(2-->8) disialic acid) and alpha-Neup5Ac-(2-->3)-beta-D-Galp-(1-->4)-D-Glc-lactone (3'-sialyllactose-lactone) showed that the alpha-(2-->8) linkage between Neu5Ac residues is difficult to cleave in the ESI-MS, compared with the alpha-(2-->3) linkage between Neu5Ac and Gal residues.     

NMR spectra of some cyanosteroids

The MMR Spectra of thirty-four cyanosteroids and of thirty-four model steroids are discussed. The chemical shifts of the protons at C-18, C-19 and C-21 are used to study the cyanosteroid structures and the specific corrections Δδ^∗ are calculated.     

NMR spectra of fluorinated carbohydrates

Recent advances in structural and conformational analysis of fluorinated carbohydrates by NMR spectroscopy are reviewed. Characteristic 1H, 13C, and 19F NMR chemical shifts and coupling constants for selected examples are given and the spectral data of a series of fluorinated carbohydrates were collected in continuation of the review of Csuk and Gl?nzer [Adv. Carbohydr. Chem. Biochem., 46 (1988) 73-177].     

Automated structure determination from NMR spectra

Automated methods for protein structure determination by NMR have increasingly gained acceptance and are now widely used for the automated assignment of distance restraints and the calculation of three-dimensional structures. This review gives an overview of the techniques for automated protein structure analysis by NMR, including both NOE-based approaches and methods relying on other experimental data such as residual dipolar couplings and chemical shifts, and presents the FLYA algorithm for the fully automated NMR structure determination of proteins that is suitable to substitute all manual spectra analysis and thus overcomes a major efficiency limitation of the NMR method for protein structure determination.     

NMR spectra of C-24 isomeric sterols

Cholesterol and four pairs of C-24 isomeric sterols, campesterol-22,23-dihydrobrassicasterol, α-spinasterol-chondrillasterol, stigmasterol-poriferasterol, and sitosterol-22,23-dihydroporiferasterol were studied by NMR spectroscopy and their spectra are presented. The NMR spectra of three of the pairs of isomeric sterols recorded at 100 MHz could be differentiated from each other, although at 60 MHz only the spectra of campesterol (24α-methylcholesterol) and 22,23-dihydrobrassicasterol (24β-methylcholesterol) showed differences. Sitosterol and 22,23-dihydroporiferasterol, the pair of sterols that showed no differences in their NMR spectra are readily differentiated by the physical properties of their acetates. The practical application of NMR spectroscopy to several problems concerning the C-24 isomeric sterols is demonstrated.     

SpecAlign--processing and alignment of mass spectra datasets

SUMMARY: Pre-processing of chromatographic profile or mass spectral data is an important aspect of many types of proteomics and biomarker discovery experiments. Here we present a graphical computational tool, SpecAlign, that enables simultaneous visualization and manipulation of multiple datasets. SpecAlign not only provides all common processing functions, but also uniquely implements an algorithm that enables the complete alignment of each mass spectrum within a loaded dataset. We demonstrate its utility by aligning two datasets each containing six spectra; one set was acquired prior to instrument calibration and the other following calibration. AVAILABILITY: The software is free of charge and available for download from http://ptcl.chem.ox.ac.uk/~jwong/specalign. Supports Windows operating systems including Windows 9X/NT/2000/XP.     

The 220 MHz NMR spectra of phytosterols

The 220MHz NMR spectra of forty two steroids are reported. Eight pairs of C-24 epimers (24α- and 24β) and two pairs of double bond isomers (cis and trans) can be distinguished by this technique. The influence of substituents, solvents and stereochemistry on methyl group chemical shifts is discussed.     

Prediction of peak overlap in NMR spectra

Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.     

Recognition of D-homoannulation by proton and carbon NMR spectra

One-and two dimensional proton and carbon NMR spectra of the D-homoannulated rearrangement product of triamcinolone (9 alpha-fluoro-11 beta,16 alpha,17 alpha, 21-tetrahydroxy-pregna-1,4-diene-3,20-dione) establish its structure as that of 9 alpha-fluoro-11 beta,16 alpha,17 alpha-trihydroxy-17 beta-hydroxy-methyl-D-homoandrosta-1,4-diene-3,17 alpha-dione. These methods accord ready recognition of D-homoannulation of C21-17-hydroxy-20-ketosteroids.     

Fast-atom-bombardment mass spectra of enkephalins.

The positive- and negative-ion mass spectra of [methionine]enkephalin and [leucine]enkephalin have been obtained by using a fast-atom-bombardment source described previously by Barber, Bordoli, Sedgwick & Tyler [(1981) J. Chem. Soc. Chem. Commun., in the press]. This technique has allowed the spectra to be obtained without conversion of the enkephalins into volatile derivatives. The fast-atom-bombardment spectra show good pseudo-molecular-ion sensitivity and fragmentation that can be interpreted on the basis of the known molecular structure.     

Clustering millions of tandem mass spectra

Tandem mass spectrometry (MS/MS) experiments often generate redundant data sets containing multiple spectra of the same peptides. Clustering of MS/MS spectra takes advantage of this redundancy by identifying multiple spectra of the same peptide and replacing them with a single representative spectrum. Analyzing only representative spectra results in significant speed-up of MS/MS database searches. We present an efficient clustering approach for analyzing large MS/MS data sets (over 10 million spectra) with a capability to reduce the number of spectra submitted to further analysis by an order of magnitude. The MS/MS database search of clustered spectra results in fewer spurious hits to the database and increases number of peptide identifications as compared to regular nonclustered searches. Our open source software MS-Clustering is available for download at http://peptide.ucsd.edu or can be run online at http://proteomics.bioprojects.org/MassSpec.     

Parallel acquisition of multi-dimensional spectra in protein NMR

We introduce the use of multiple receivers applied in parallel for simultaneously recording multi-dimensional data sets of proteins in a single experiment. The utility of the approach is established through the introduction of the 2D (15)N,(1)H(N)||(13)CO HSQC experiment in which a pair of two-dimensional (15)N,(1)H(N) and (15)N,(13)CO spectra are recorded. The methodology is further extended to higher dimensionality via the 3D (1)H(N)||(13)CO HNCA in which a pair of data sets recording (13)C(α),(15)N,(1)H(N) and (13)C(α),(15)N,(13)CO chemical shifts are acquired. With the anticipated increases in probe sensitivity it is expected that multiple receiver experiments will become an important approach for efficient recording of NMR data.     

The mass spectra of acetylated and propanoylated aldofuranosylamines

The mass spectra of six N-acetylaldofuranosylamine acetates and propanoates were recorded. The spectra are more complicated than those of the corresponding pyranoid compounds. As in that case, the spectra are rich in long-lived fragments, in agreement with the stabilizing influence of the nitrogen atom on the positive charge. Several fragmentation series are similar to those of the aldopyranosylamine derivatives, and others agree better with those of the aldofuranose acetates, thus allowing identification of the furanoid ring.     

The mass spectra of diethylstilbestrol and related compounds

The low resolution mass spectra of E-3,4-bis-(p-hydroxyphenyl)-hex-3-ene (diethylstilbestrol), E-[1,1,1-3H3]3,4-bis-(p-hydroxyphenyl)-hex-3-ene, E-2,3-bis-(p-hydroxyphenyl)-but-2-ene (dimethylstilbestrol), E,E-3,4-bis-(p-hydroxyphenyl)hexa-2,4-diene (dienestrol) and 3,4-bis-(p-hydroxyphenyl)-hexane (hexestrol) were examined as the parent compounds, their diacetates, dimethyl ethers, and bis-trimethylsilyl ethers. In addition, the mass spectra of the diethyl ether and the hexadeuteriodimethyl ether of E-3,4-bis-(p-hydroxyphenyl)-hex-3-ene were studied. Each compound gives rise to several sets of characteristic fragment ions associated with loss of alkyl groups, loss of aryl groups and rearrangements. An ion of m/e 165 (C13H9) was found in the spectra of all the compounds studied. With the aid of high resolution mass spectrometry empirical formulae were assigned to major ions of the free diphenols.     

Study of patulin by NMR and mass spectroscopy

Patulin was studied by NMR and mass spectrometry. On the basis of the 1H and 13C NMR spectral analysis and experiments on double homo-(1H NMR) and heteronuclear (13C NMR) resonances complete assigning of the proton and carbon signals was achieved. Patulin was studied mass spectrometrically with using high performance mass spectrometry and the DADI technique. It was shown that formation of the [M--C2H4O]+ ion was due to rearrangement of the molecular ion (M+).     

Synthesis and NMR spectra of 13C-labeled coenzyme A esters

The synthesis of coenzyme A thioesters of 13C-labeled acetate, propionate, succinate, and methyl malonate is described. The average yields were 94%. The 13C-NMR spectra were determined to provide a reference for the resonance positions of these metabolites. The synthesis of coenzyme thioesters of small-molecular-weight acids labeled with 13C has not been described previously, nor have the resonance positions been previously reported.     

Interpreting peptide mass spectra by VEMS

Most existing Mass Spectra (MS) analysis programs are automatic and provide limited opportunity for editing during the interpretation. Furthermore, they rely entirely on publicly available databases for interpretation. VEMS (Virtual Expert Mass Spectrometrist) is a program for interactive analysis of peptide MS/MS spectra imported in text file format. Peaks are annotated, the monoisotopic peaks retained, and the b-and y-ion series identified in an interactive manner. The called peptide sequence is searched against a local protein database for sequence identity and peptide mass. The report compares the calculated and the experimental mass spectrum of the called peptide. The program package includes four accessory programs. VEMStrans creates protein databases in FASTA format from EST or cDNA sequence files. VEMSdata creates a virtual peptide database from FASTA files. VEMSdist displays the distribution of masses up to 5000 Da. VEMSmaldi searches singly charged peptide masses against the local database.