Low-molecular-weight human serum proteome using ultrafiltration, isoelectric focusing, and mass spectrometry

Identification of the serum proteome is a daunting analytical task due to the complex nature of the sample which has an extremely large dynamic range of protein components. This report addresses this issue by using centrifugal ultrafiltration to enrich the low-molecular-weight (LMW) serum proteome while decreasing the amount of abundant high-molecular-weight proteins. Reduction of the complex nature of the sample was achieved by fractionation of the LMW serum proteins using solution-phase isoelectric focusing (IEF). Multiple enzyme digestions are performed and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Analysis of the tandem mass spectra resulted in the identification of 262 proteins belonging to LMW serum proteome. Our results demonstrate the effectiveness of this methodology to isolate and identify LMW proteins with improved confidence in the MS data acquired. In addition, our methodology can be combined with other multidimensional chromatography techniques performed on the peptide level to increase the number of identified proteins.     

An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins

A procedure for determining the extent of phosphorylation at individual sites of multiply phosphorylated proteins was developed and applied to two polyphosphorylated proteins. The protocol, using simple chemical (Fischer methyl-esterification) and enzymatic (phosphatase) modification steps and an accessible isotopic labeling reagent (methyl alcohol-d(4)), is described in detail. Site-specific phosphorylation stoichiometries are derived from the comparison of chemically identical but isotopically distinct peptide species analyzed by microspray liquid chromatography-mass spectrometry (microLC-MS) using a Micromass Q-TOF2 mass spectrometer. Ten phosphorylation sites were unambiguously identified in tryptic digests of both proteins, and phosphorylation stoichiometries were determined for eight of the ten sites using the isotope-coded strategy. The extent of phosphorylation was also estimated from the mass spectral peak areas for the phosphorylated and unmodified peptides, and these estimates, when compared with stoichiometries determined using the isotope-coded technique, differed only marginally (within approximately 20%).     

Laboratory and field experiments used to identify<Emphasis Type="Italic"> Canis lupus</Emphasis> var. <Emphasis Type="Italic">familiaris</Emphasis> active odor signature chemicals from drugs,explosives, and humans

This paper describes the use of headspace solid-phase microextraction (SPME) combined with gas chromatography to identify the signature odors that law enforcement-certified detector dogs alert to when searching for drugs, explosives, and humans. Background information is provided on the many types of detector dog available and specific samples highlighted in this paper are the drugs cocaine and 3,4-methylenedioxy-N-methylamphetamine (MDMA or Ecstasy), the explosives TNT and C4, and human remains. Studies include the analysis and identification of the headspace "fingerprint" of a variety of samples, followed by completion of double-blind dog trials of the individual components in an attempt to isolate and understand the target compounds that dogs alert to. SPME–GC/MS has been demonstrated to have a unique capability for the extraction of volatiles from the headspace of forensic specimens including drugs and explosives and shows great potential to aid in the investigation and understanding of the complicated process of canine odor detection. Major variables evaluated for the headspace SPME included fiber chemistry and a variety of sampling times ranging from several hours to several seconds and the resultant effect on ratios of isolated volatile components. For the drug odor studies, the CW/DVB and PDMS SPME fibers proved to be the optimal fiber types. For explosives, the results demonstrated that the best fibers in field and laboratory applications were PDMS and CW/DVB, respectively. Gas chromatography with electron capture detector (GC/ECD) and mass spectrometry (GC/MS) was better for analysis of nitromethane and TNT odors, and C-4 odors, respectively. Field studies with detector dogs have demonstrated possible candidates for new pseudo scents as well as the potential use of controlled permeation devices as non-hazardous training aids providing consistent permeation of target odors.     

Comparative studies of palladium and copper-catalysed γ-arylation of silyloxy furans with diaryliodonium salts

The γ-arylation of substituted silyl-activated butenolides has been studied using a broad scope of unsymmetrical hypervalent diaryliodonium salts via a palladium- or copper-catalysed coupling reaction, yielding interesting reactivity trends. The mild catalytic conditions and coupling partner variability provide access to synthetically useful building blocks toward the pursuit of aryl-lactone containing natural products and allows for facile diversification.     

Methods for the separation and quantification of arsenic species in SRM 2669: arsenic species in frozen human urine

Two independent liquid chromatography inductively coupled plasma-mass spectrometry (LC/ICP-MS) methods for the separation of arsenic species in urine have been developed with quantification by standard additions. Seven arsenic species have been quantified in a new NIST frozen human urine Standard Reference Material (SRM) 2669 Arsenic Species in Frozen Human Urine, Levels 1 and 2. The species measured were: arsenite (As(III)), arsenate (As(V)), monomethylarsonate (MMA), dimethylarsinate (DMA), arsenobetaine (AB), arsenocholine (AC), and trimethylarsine oxide (TMAO). The purity of each arsenic standard used for quantification was measured as well as the arsenic species impurities determined in each standard. Analytical method limits of detection (L _D) for the various species in both methods ranged from 0.2 to 0.8 μg L⁻¹ as arsenic. The results demonstrate that LC/ICP-MS is a sensitive, reproducible, and accurate technique for the determination of low-level arsenic species in urine. Measurements of the arsenic species 3 years after initial production of the SRM demonstrate the stability of the arsenic species in the urine reference material.     

Genome-based deletion analysis reveals the prenyl xanthone biosynthesis pathway in Aspergillus nidulans

Xanthones are a class of molecules that bind to a number of drug targets and possess a myriad of biological properties. An understanding of xanthone biosynthesis at the genetic level should facilitate engineering of second-generation molecules and increasing production of first-generation compounds. The filamentous fungus Aspergillus nidulans has been found to produce two prenylated xanthones, shamixanthone and emericellin, and we report the discovery of two more, variecoxanthone A and epishamixanthone. Using targeted deletions that we created, we determined that a cluster of 10 genes including a polyketide synthase gene, mdpG, is required for prenyl xanthone biosynthesis. mdpG was shown to be required for the synthesis of the anthraquinone emodin, monodictyphenone, and related compounds, and our data indicate that emodin and monodictyphenone are precursors of prenyl xanthones. Isolation of intermediate compounds from the deletion strains provided valuable clues as to the biosynthetic pathway, but no genes accounting for the prenylations were located within the cluster. To find the genes responsible for prenylation, we identified and deleted seven putative prenyltransferases in the A. nidulans genome. We found that two prenyltransferase genes, distant from the cluster, were necessary for prenyl xanthone synthesis. These genes belong to the fungal indole prenyltransferase family that had previously been shown to be responsible for the prenylation of amino acid derivatives. In addition, another prenyl xanthone biosynthesis gene is proximal to one of the prenyltransferase genes. Our data, in aggregate, allow us to propose a complete biosynthetic pathway for the A. nidulans xanthones.     

Anti-inflammatory and antimalarial meroterpenoids from the New Zealand ascidian Aplidium scabellum

Bioassay-directed fractionation of an extract of the New Zealand ascidian Aplidium scabellum has afforded the anti-inflammatory secondary metabolite 2-geranyl-6-methoxy-1,4-hydroquinone-4-sulfate (1) and a family of pseudodimeric meroterpenoids scabellones A (2)-D (5). The benzo[c]chromene-7,10-dione scaffold contained within scabellones A-D is particularly rare among natural products. The structures were elucidated by interpretation of NMR data. Scabellone B was also identified as a moderately potent, nontoxic inhibitor of Plasmodium falciparum.     

Testing of microorganisms for ω-transaminase activity

Various bacterial cells were tested to identify ω-transaminase activity. For this purpose, the kinetic resolution of a rac-amine was chosen as an assay reaction transforming, in the ideal case, one enantiomer into the corresponding ketone and leaving the other enantiomer untouched. Sodium pyruvate was employed as an amino acceptor. To test also for the amination of the prochiral ketone various amino donors were investigated. Alanine proved to be the most suitable amino donor especially when coupled with a pyruvate decarboxylase to shift the reaction equilibrium; however, much lower conversions were achieved compared to the kinetic resolution. Janibacter terrae DSM 13953 was identified as the most suitable microorganism to possess ω-transaminase activity.     

The interlaboratory comparison "IMEP-19 trace elements in rice"—a new approach for measurement performance evaluation

The aim of IMEP is to present objectively the quality of chemical measurements. Participants in IMEP compare their reported measurement results with independent external certified reference values with demonstrated traceability and uncertainty, as evaluated according to international guidelines. IMEP-19 focused on measurements of trace elements in rice aiming to support the Commission Regulation (EC) No. 466/2001 on maximum levels for certain contaminants in foodstuff. Measurement results for the elements Cd, Cu, Pb and Zn were reported by 267 field laboratories involved in food analysis from 43 countries. Performance criteria for the evaluation of the reported measurement results in IMEP-19 are suggested. The chosen performance indicators not only take into account the deviation of the reported measurement value from the certified reference value, but also set criteria for maximum and minimum acceptable uncertainty. The IMEP-19 participants' performance is reviewed by means of using new simple graphical tools, called "Naji plots".