Data requirements for protein identification using chemically-assisted fragmentation and tandem mass spectrometry

Many laboratories identify proteins by searching tandem mass spectrometry data against genomic or protein sequence databases. These database searches typically use the measured peptide masses or the derived peptide sequence and, in this paper, we focus on the latter. We study the minimum peptide sequence data requirements for definitive protein identification from protein sequence databases. Accurate mass measurements are not needed for definitive protein identification, even when a limited amount of sequence data is available for searching. This information has implications for the mass spectrometry performance (and cost), data base search strategies and proteomics research.     

A mathematical model for Modulated Differential Scanning Calorimetry

Reading and co-workers introduced a new technique a few years ago called Modulated Differential Scanning Calorimetry or MDSC. Here the first part of a theoretical analysis for this technique is given. A simple mathematical model for modulated differential scanning calorimetry in the form of an ordinary differential equation is derived. The model is analysed to find the effect of a kinetic event in the form of a chemical reaction. Some possible sources of error are discussed. A more sophisticated version of the model allowing for spatial variation in a calorimeter is developed and it is seen how it can be reduced to the earlier model. Some preliminary work on a phase change is also presented.Dedicated to Prof. Menachem Steinberg on the occasion of his 65th birthday     

Water loss from molecular protonated ions of benzyl 2-phenylethyl ether and derivatives

The skeletal rearrangement for water loss is the dominant ion reaction in the chemical ionization mass spectrum of benzyl 2-phenylethyl ether. Isotopic distributions obtained for this reaction with specifically labelled derivatives have been interpreted in terms of competing five- and six-centred skeletal rearrangements. Chemical substitution of the alternative aromatic rings strongly influences the balance of the competition.     

Density functional calculations for modeling the oxidized states of the active site of nickel-iron hydrogenases. 1. Verification of the method with paramagnetic Ni and Co complexes

ZORA relativistic DFT calculations are presented which aim to reproduce geometric structures and EPR properties of [Ni(mnt)(2)](-) (H(2)mnt = maleonitrildithiol), two other paramagnetic low-spin Ni(III) complexes, and an asymmetric paramagnetic Co(II) complex. The study tests the accuracy of the computational method as a prior step to the modeling of the geometric and electronic structure of the active site of NiFe hydrogenases in its EPR-active oxidized states Ni-A and Ni-B. Systematic deviations from experiment are found for the calculated g-values; relative differences among them are, however, well reproduced. Because no significant improvements have been achieved by using larger basis sets or more sophisticated functionals, g-values may be calculated rather rapidly at the VWN level. This is most important for the modeling of the active site of NiFe hydrogenases because its complexity does not permit calculations at high levels of theory. For [Ni(mnt)(2)](-), excellent agreement between calculated and experimental results is obtained for the (14)N quadrupole coupling, whereas the calculated hyperfine couplings are not always in good agreement with experimental data.     

An LC-MS method for the determination of pharmaceutical compounds in wastewater treatment plant influent and effluent samples

Pharmaceuticals are continually introduced into the environment as a result of industrial and domestic use. In recent years they have emerged as environmental pollutants. An analytical method has been developed allowing for simultaneous detection and identification of 20 pharmaceutical compounds from various therapeutic classes using solid phase extraction (SPE) followed by liquid chromatography-electrospray ionisation mass spectrometry (LC-MS/MS). The limits of detection and limits of quantitation for the method were in the ng/L-microg/L range. The method was applied to influent and effluent samples from three wastewater treatment plants (WWTPs). Fifteen compounds were identified in the sample matrix with salicylic acid and ibuprofen being the most abundant at 9.17 and 3.20 microg/L respectively.     

Aspergillazines A-E: novel heterocyclic dipeptides from an Australian strain of Aspergillus unilateralis

Biological and chemical profiling of an Australian strain of the fungus Aspergillus unilateralis(MST-F8675), isolated from a soil sample collected near Mount Isa, Queensland, revealed a complex array of metabolites displaying broad chemotherapeutic properties. Noteworthy among these metabolites were a unique series of highly modified dipeptides aspergillazines A-E, incorporating a selection of unprecedented and yet biosynthetically related heterocyclic systems. Co-occurring with the aspergillazines was the recently described marine-derived fungal metabolite trichodermamide A (cf. penicillazine), whereas re-fermentation of A. unilateralis in NaCl (1%) enriched media resulted in co-production of the only other known example of this structure class, the marine-derived fungal metabolite trichodermamide B. Further investigation of A. unilateralis returned the known terrestrial fungal metabolite viridicatumtoxin as the cytotoxic and antibacterial principle, together with E-2-decenedioic acid, ferulic acid, (7E,7'E)-5,5'-diferulic acid and (7E,7'E)-8,5'-diferulic acid. The aromatic diacids have previously been reported from the chemical and enzymatic (esterase) treatment of plant cell wall material, with their isolation from A. unilateralis being their first apparent reported occurrence as natural products. Structures for all metabolites were determined by detailed spectroscopic analysis and, where appropriate, comparison to literature data and/or authentic samples.     

The use of two linked scanning modes in alternation to analyse metastable peaks

Analyses of masses and relative kinetic energies for metastable peaks may be achieved by the use in alternation of two types of linked scans of the electric sector voltage and magnetic field. The method is demonstrated by an appraisal of hydrogen exchange in molecular ions of 2-methyl-[²H₃]-benzoic acid.     

The effect of lateral fluoro-substitution on the liquid crystal behaviour of some 4'-alkylphenylethyl- and trans-4'-alkylcyclohexylethyl-4,4'-disubstituted biphenyls

The preparation of several 4'-alkylphenylethyl- and trans-4'-alkylcyclohexyl-ethyl-4,4'-disubstituted biphenyls and their 2-fiuoro derivatives is described and their transition temperatures are reported. The effect on the transition temperatures caused by the replacement of a cyclohexane ring by a benzene ring and the effect of fluoro-substitution on nematic, smectic A and smectic B thermal stabilities is discussed. In these systems, and in others, when the lateral fluoro-substituent points towards the longer terminal aliphatic unit (alkyl or alkylcyclo-hexylethyl) it causes a greater depression of smectic properties.     

A simple synthesis of choline alkyl phosphates

Alkyl (2-dimethylamino)ethyl methyl phosphates are prepared and isomerize smoothly to the corresponding alkyl choline phosphates.