Advancement in protein inference from shotgun proteomics using peptide detectability

A major challenge in shotgun proteomics has been the assignment of identified peptides to the proteins from which they originate, referred to as the protein inference problem. Redundant and homologous protein sequences present a challenge in being correctly identified, as a set of peptides may in many cases represent multiple proteins. One simple solution to this problem is the assignment of the smallest number of proteins that explains the identified peptides. However, it is not certain that a natural system should be accurately represented using this minimalist approach. In this paper, we propose a reformulation of the protein inference problem by utilizing the recently introduced concept of peptide detectability. We also propose a heuristic algorithm to solve this problem and evaluate its performance on synthetic and real proteomics data. In comparison to a greedy implementation of the minimum protein set algorithm, our solution that incorporates peptide detectability performs favorably.

Development of a multiplex non-radioactive receptor assay: the benzodiazepine receptor, the serotonin transporter and the beta-adrenergic receptor

Binding assays still form a fundamental part of modern drug development. Receptor binding assays are mostly based on radioactivity because of their speed, ease of use and reproducibility. Disadvantages, such as health hazards and production of radioactive waste, have prompted the development of non-radioactive receptor binding assays. This application therefore focuses on measuring receptor-ligand interactions using mass spectrometry. Moreover, the novelty of this approach originates in determining multiple analytes in a single assay (multiplexing). The proof of principle of a non-radioactive multiplex receptor assay is demonstrated using a pool of receptors from rat cortical tissue with flunitrazepam, MADAM and pindolol in one vial with or without their respective displacers. Flunitrazepam, MADAM and pindolol bound specifically at 73%, 30% and 40% to their respective receptors. This corresponds to specific binding sites of 0.61 pmol/mg protein, 0.07 pmol/mg protein and 0.06 pmol/mg protein, respectively. We propose to measure the bound fraction instead of the free fraction in order to reach a significant difference in measured signals (total binding versus non-specific binding). The bound fraction can be obtained after dissociating the ligand from the receptor-ligand complex using 50% methanol in water. The current setup of the assay calls for further improvement with respect to the measurement of binding constants for a multitude of receptors in one assay with sufficient accuracy and precision.

A novel quantitative proteomics reagent based on soluble nanopolymers

Bi-functionalized dendrimers leads to highly efficient quantitative proteomics and the determination of protease activities in snake venoms.

Ellagic acid glycosides fromTurpinia ternata

Bioassay-guided fractionation of the methanolic extract of Turpinia ternata stems, has led to the isolation of the new ellagic acid derivative 3,4'-di-O-methylellagic acid-4-O-alpha-L-arabinofuranoside (1), and the known compounds ellagic acid (2), 3-O-methyl ellagic acid (3), 3-O-methylellagic acid-3'-O-alpha-L-rhamnopyranoside (4), and 3,3'-di-O-methylellagic acid-4'-O-alpha-D-glucopyranoside (5). Their structures were elucidated by extensive spectroscopic methods. Compounds 1, 3, and 4 showed moderate antioxidant activity against DPPH free radical, whereas compound 1 was found to be moderately cytotoxic against Artemia salina larvae.

Putative structure and characteristics of a red water-soluble pigment secreted byPenicillium marneffei

The dimorphic fungus, Penicillium marneffei, produces and secretes a brick red pigment, during growth at temperatures below 30 degrees C. It generally diffuses into commonly used media like Sabouraud dextrose agar and malt extract agar. The pigment was purified by reverse-phase liquid chromatography and subjected to structural determination by elemental and spectral analysis using atomic absorption (AAS), ultra violet and visible (UV-VIS), fluorescence, infra red (IR), nuclear magnetic resonance (NMR) and tandem mass spectrometry (MS-MS). The pigment showed a buffering ability in aqueous solutions, maintaining an alkaline pH of 8.0. It behaved as a colorimetric pH indicator over a wide acidic and alkaline pH range, with discoloration occurring ostensibly through hydrolysis of key chemical groups at extremely acidic pH ( approximately 2.0). The pigment was found to have some structural resemblance with the copper-colored pigment (herquinone) produced by Penicillium herquei as both pigments contain the phenalene carbon framework. The notable differences between herquinone and the pigment produced by P. marneffei are (i) the latter's apparent dimerization through a sulphur-sulphur (disulfide) bond and (ii) the presence of 1,1,3,3-tetramethyl-2,3-dihydropyrrole moiety in the latter instead of 2,3,3-trimethyl-2,3-dihydrofuran moiety found in the former. The delineation of the structure of the pigment produced by Penicillium marneffei may help in understanding certain aspects of the biology of this pathogenic fungus.

Fragmentation of 3-hydroxyflavone; a computational and mass spectrometric study

In a recent study of the collision-induced dissociation of protonated and deprotonated molecules of 3-, 5-, 6-, 7-, 2'-, 3'- and 4'-hydroxyflavone, it was observed that the ratio, gamma, of the propensities for cross-ring cleavage (CRC) to ring opening (RO) varied by a factor of 660, i.e., from 0.014:1 (for deprotonated 3-hydroxyflavone) to 9.27:1 (for deprotonated 5-hydroxyflavone). An explanation for the variation of gamma was presented in terms of experimental NMR (13)C and (1)H spectra modified by computation. Deprotonated 3-hydroxyflavone exhibited the highest ion signal intensity for fragmentation following RO relative to that for CRC in that gamma = 0.014:1. Because no chemical computations of the fragmentation of protonated and deprotonated monohydroxyflavone molecules have been carried out thus far, the basis on which fragmentation mechanisms for deprotonated 3-hydroxyflavone have been proposed is principally chemical intuition. The energy states of product ions formed in the fragmentation of deprotonated 3-hydroxyflavone molecules were computed by the CBS-4M method implemented in Gaussian 03. The overly demanding calculations needed to handle diradicals reliably and directly were circumvented by a process in which each of the bond-breaking reactions was approximated by a process that gave two monoradicals. Bond energies were calculated, with one exception, from the approximation reactions as the energy of products minus the energy of reactants.

Pharmacokinetics of Darunavir (TMC114) and Atazanavir during Coadministration in HIV-Negative, Healthy Volunteers

BACKGROUND AND OBJECTIVE

To investigate the potential for pharmacokinetic interactions between the protease inhibitors darunavir (DRV, TMC114) coadministered with low-dose ritonavir (darunavir/r), and atazanavir in HIV-negative, healthy volunteers.

METHODS

This was an open-label, randomised, three-period, crossover study. Darunavir/r (400/100mg twice daily), atazanavir/r (300/100mg once daily) or darunavir/r (400/100mg twice daily) plus atazanavir (300mg once daily) were administered in three separate sessions, with a washout period of at least 7 days between regimens. The follow-up lasted 30 days. Twenty-three healthy volunteers participated. Pharmacokinetic assessments were performed at steady-state on day 7. Plasma drug concentrations were determined by liquid chromatography-tandem mass spectrometry and pharmacokinetic parameters were compared between treatments. The safety and tolerability of the study medications were monitored throughout.

RESULTS

Darunavir pharmacokinetics were unaffected by atazanavir. No change in overall exposure to atazanavir was observed during coadministration with darunavir/r. However, there was a 52% increase in minimum atazanavir plasma concentration (least squares mean ratio [90% CI 0.99, 2.34]). Mean systemic exposure to ritonavir was increased by 65% and 106%, respectively, with the combination treatment compared with darunavir/r alone or atazanavir/r alone. There were no apparent differences in mean changes in lipids between the darunavir/r, atazanavir/r or darunavir/r plus atazanavir regimens. Hyperbilirubinaemia and ocular icterus were reported with atazanavir-containing regimens.

CONCLUSION

Atazanavir at a dose of 300mg once daily can be coadministered with a darunavir/r twice-daily regimen without any dose adjustment if there is a clinical need to combine darunavir/r and atazanavir in HIV-1-infected patients.

Lipid composition of membranes of Escherichia coli by liquid chromatography/tandem mass spectrometry using negative electrospray ionization

A liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method using reversed-phase chromatography was developed for the analysis of phospholipids from bacterial extracts of a wild-type strain of Escherichia coli. Product ion mass spectra from [M--H](-) precursor ions allowed an identification of individual phospholipid species that includes both fatty acid composition and fatty acyl location on the glycerol backbone using diagnostic product ions. Thus, complete assignment, including sn-1/sn-2 fatty acyl position, was achieved for this strain of E. coli. In addition, the phospholipids were quantified relative to one another using an internal standard method.

Simplifying sample handling for protein identification by peptide mass fingerprint using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

An ultrasonic bath, an ultrasonic probe and a sonoreactor were used to speed up the kinetics of the reactions involved in each step of the sample handling for in-gel protein identification by peptide mass fingerprint, PMF, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The following steps were successfully accelerated using ultrasonic energy: gel washing, protein reduction, and protein alkylation. As a result, a reduction comprising 80% to 90% of the total time involved in the classic approach was achieved. In addition the sample handling was also drastically simplified. The number of peptides identified and the protein sequence coverage obtained for the new procedure were comparable to those obtained with the traditional sample treatment for the following protein standards: glycogen phosphorylase b, BSA, ovalbumin, carbonic anhydrase, trypsin inhibitor and alpha-lactalbumin. Finally, as a proof of the procedure, specific proteins were identified from complex protein mixtures obtained from three different sulphate-reducing bacteria: Desulfovibrio desulfuricans G20, Desulfuvibrio gigas NCIB 9332, and Desulfuvibrio desulfuricans ATCC 27774.

Liquid chromatography–tandem mass spectrometry method for identification and quantification of two biologically active polyisoprenylated benzophenones, isoxanthochymol and camboginol, inGarcinia species

A sensitive liquid chromatography/electrospray ionization tandem mass spectrometrical (LC/ESI-MS/MS) method was developed for simultaneous identification and quantification of two polyisoprenylated benzophenones, isoxanthochymol and camboginol, in the extracts of the fruit rinds, stem bark, seed and leaves of Garcinia indica and in the fruit rinds of Garcinia cambogia. The separation of isoxanthochymol and camboginol was achieved on an RP-8 column using the solvent system consisting of a mixture of acetonitrile-water (80:20) and methanol-acetic acid (99.0:1.0) as a mobile phase in a gradient elution mode. A multiple reaction monitoring (MRM) method was developed for quantification of isoxanthochymol and camboginol in the above extracts of Garcinia species. Based on a signal-to-noise ratio of 3, the limits of detection in MRM mode for isoxanthochymol and camboginol were 2.0 and 5.0 ng/mL respectively. The method was validated in terms of linearity, accuracy and precision for 6 days. The method developed was found to be useful for identification and quantification of isoxanthochymol and camboginol in the extracts of the fruit rinds, stem bark, seed and leaves of Garcinia indica and in the fruit rinds of Garcinia cambogia.

Studies on Neurosteroids XXI: An Improved Liquid Chromatography-Tandem Mass Spectrometric Method for Determination of 5.ALPHA.-Androstane-3.ALPHA.,17.BETA.-diol in Rat Brains

A sensitive liquid chromatography-electrospray ionization-tandem mass spectrometric (LC-ESI-MS/MS) method for the determination of the rat brain 5alpha-androstane-3alpha,17beta-diol (3alpha,5alpha-Adiol) has been developed and validated. The brain extract was purified using solid-phase extraction cartridges, derivatized with isonicotinoyl azide, and subjected to LC-MS/MS. The method was accurate and reproducible, and the limit of quantitation was 0.1 ng/g tissue when a 100-mg tissue sample was used. The change in the brain 3alpha,5alpha-Adiol level by immobilization stress was also analyzed using the developed method.

Acrylamide content in heat-treated carbohydrate-rich foods in Poland

The objective of the study was to determine the content of acrylamide in randomly selected samples of potato crisps and French fries using GC/MS/MS. The mean content of acrylamide in tested crisps amounted to 998 microg/kg (range from 352 to 3647 microg/kg) and was almost three times higher than in French fries--337 microg/kg (range from 88 to 799 microg/kg). Differences (even ten times) in the level of acrylamid in individual product samples, testifying the impact of raw materials and technological process running conditions on the content of acrylamide in the final product. The results of our study were close to those obtained in other countries.

Sub parts-per-million mass measurement accuracy of intact proteins and product ions achieved using a dual electrospray ionization quadrupole fourier transform ion cyclotron resonance mass spectrometer

High mass measurement accuracy (MMA) is demonstrated for intact proteins and subsequent collision-induced dissociation product ions using internal calibration. Internal calibration was accomplished using a dual electrospray ionization source coupled with a hybrid quadrupole Fourier transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer. Initially, analyte ions generated via the first electrospray (ESI) emitter are isolated and dissociated in the external quadrupole. This event is followed by a simultaneous switch to the calibrant ion ESI emitter and a disablement of the isolation and activation of the external quadrupole such that a broad m/z range of calibrant ions are accumulated before injecting the analyte/calibrant ion mixture into the ICR cell. Two different internal calibrant solutions were utilized in these studies to evaluate this approach for the top-down characterization of melittin and ubiquitin. While external calibration of protein fragments resulted in absolute MMA greater than 16 ppm, internal standardization significantly improved upon the MMA of both the intact proteins and their products ions which ranged from -2.0 ppm to 1.1 ppm, with an average of -0.9 ppm. This method requires limited modification to ESI-FT-ICR mass spectrometers and is applicable for both positive and negative ionization modes.

[Novel tumor marker discovery of gastrointestinal cancers using various proteomic approaches]

Cancer has been the disease with the highest cause of death for a decade. This is partly due to the lack of ideal tumor markers for early diagnosis, which causes cancer found at the advanced stage where no curative treatment is available. Therefore, development of tumor markers with higher sensitivity and specificity is waiting to emerge. The ideal source for the tumor markers are serum, plasma or urine samples that are routinely used as clinical laboratory test. They contain a number of proteins that could be useful for cancer diagnosis. Recent advances in proteomic technology made it possible to identify the low abundant proteins in the clinical samples and thus extensive efforts are now attempted to search for the tumor markers across the country. There are two prominent types of proteomic approaches, 2D gel-based (2DE) and MS/MS based approach. 2DE is favorable to analyze relatively high moleculer weight proteins (MW > 20kD) and MS is superior to detect low molecular proteins or peptides. In this article, we introduce our recent studies on tumor marker discovery using various proteomic approaches and will discuss future application for cancer

Highly sensitive assay for tiotropium, a quaternary ammonium, in human plasma by high-performance liquid chromatography/tandem mass spectrometry

Tiotropium bromide, a long-acting inhaled bronchodilator analogous to ipratropium bromide, is currently undergoing development for the treatment of chronic obstructive pulmonary disease. To evaluate its systemic absorption in humans, we have developed a rapid and sensitive method for its determination in human plasma based on high-performance liquid chromatography with tandem mass spectrometric detection (HPLC/MS/MS). Reversed-phase chromatography of tiotropium and the internal standard clenbuterol was carried out using acetonitrile/10 mM ammonium acetate (1% formic acid) 40:60 as mobile phase in a run time of 3.0 min. The sample preparation involved deproteination with acetonitrile, extraction into dichloromethane and back-extraction into hydrochloric acid. The assay was linear over the concentration range 0.500-50.0 pg/mL with intra- and inter-day precision (as relative standard deviation) both <or=7.34%. The method was successfully applied to a pharmacokinetic study of systemic absorption in healthy male volunteers given a single 18 microg inhaled dose.

Occurrence of perfluorooctane sulfonate and other perfluorinated alkylated substances in harbor porpoises from the Black Sea

Perfluorooctane sulfonate (PFOS) and other perfluorinated alkylated substances (PFAS) were determined in liver, kidney, muscle, brain, and blubber samples of 31 harbor porpoises (Phocoena phocoena relicta) of different age and sex stranded along the Ukrainian coast of the Black Sea. In all individuals and in all tissues, PFOS was the predominant PFAS, accounting for on average 90% of the measured PFAS load. PFOS concentrations were the highest in liver (327+/-351 ng/g wet wt) and kidney (147 +/-262 ng/g wet wt) tissue, and lower in blubber (18+/-8 ng/g wet wt), muscle (41+/-50 ng/g wet wt), and brain (24 +/-23 ng/g wetwt). No significant differences could be determined between males and females, nor between juvenile and adult animals (p > 0.05). Perfluorononanoic acid, perfluorodecanoic acid, perfluoroundecanoic acid, and perfluorododecanoic acid could be detected in liver tissue of approximately 25% of the individuals. Perfluorobutane sulfonate, perfluorobutanoic acid, and perfluorooctanoic acid were not detected in any of the porpoise livers. Although we investigated a potential intraspecies segregation according to the source of prey, using stable isotopes, no statistically significant correlation between PFOS concentrations and stable isotopes could be determined. It is, however, noteworthy that the contamination by PFOS in the Black Sea harbor porpoises is comparable to levels found in porpoises from the German Baltic Sea and from coastal areas near Denmark and, therefore, might pose a threat to this population.

Organismal differences in post-translational modifications in histones H3 and H4

Post-translational modifications (PTMs) of histones play an important role in many cellular processes, notably gene regulation. Using a combination of mass spectrometric and immunobiochemical approaches, we show that the PTM profile of histone H3 differs significantly among the various model organisms examined. Unicellular eukaryotes, such as Saccharomyces cerevisiae (yeast) and Tetrahymena thermophila (Tet), for example, contain more activation than silencing marks as compared with mammalian cells (mouse and human), which are generally enriched in PTMs more often associated with gene silencing. Close examination reveals that many of the better-known modified lysines (Lys) can be either methylated or acetylated and that the overall modification patterns become more complex from unicellular eukaryotes to mammals. Additionally, novel species-specific H3 PTMs from wild-type asynchronously grown cells are also detected by mass spectrometry. Our results suggest that some PTMs are more conserved than previously thought, including H3K9me1 and H4K20me2 in yeast and H3K27me1, -me2, and -me3 in Tet. On histone H4, methylation at Lys-20 showed a similar pattern as H3 methylation at Lys-9, with mammals containing more methylation than the unicellular organisms. Additionally, modification profiles of H4 acetylation were very similar among the organisms examined.

N-formylation of lysine in histone proteins as a secondary modification arising from oxidative DNA damage

The posttranslational modification of histone and other chromatin proteins has a well recognized but poorly defined role in the physiology of gene expression. With implications for interfering with these epigenetic mechanisms, we now report the existence of a relatively abundant secondary modification of chromatin proteins, the N(6)-formylation of lysine that appears to be uniquely associated with histone and other nuclear proteins. Using both radiolabeling and sensitive bioanalytical methods, we demonstrate that the formyl moiety of 3'-formylphosphate residues arising from 5'-oxidation of deoxyribose in DNA, caused by the enediyne neocarzinostatin, for example, acylate the N(6)-amino groups of lysine side chains. A liquid chromatography (LC)-tandem mass spectrometry (MS) method was developed to quantify the resulting N(6)-formyl-lysine residues, which were observed to be present in unperturbed cells and all sources of histone proteins to the extent of 0.04-0.1% of all lysines in acid-soluble chromatin proteins including histones. Cells treated with neocarzinostatin showed a clear dose-response relationship for the formation of N(6)-formyl-lysine, with this nucleosome linker-selective DNA-cleaving agent causing selective N(6)-formylation of the linker histone H1. The N(6)-formyl-lysine residue appears to represent an endogenous histone secondary modification, one that bears chemical similarity to lysine N(6)-acetylation recognized as an important determinant of gene expression in mammalian cells. The N(6)-formyl modification of lysine may interfere with the signaling functions of lysine acetylation and methylation and thus contribute to the pathophysiology of oxidative and nitrosative stress.

Proteomic alteration in gastic adenocarcinomas from Japanese patients

Background

Gastric adenocarcinomas comprise one of the common types of cancers in Asian countries including Japan. Comprehensive protein profiling of paired surgical specimens of primary gastric adenocarcinomas and nontumor mucosae derived from Japanese patients was carried out by means of two-dimensional gel electrophoresis (2D-EP) and liquid chromatography-electrospray ionic tandem mass spectrometry (LC-ESI-MS) to establish gastric cancer-specific proteins as putative clinical biomarkers and molecular targets for chemotherapy.

Results

Relatively common alterations in protein expression were revealed in the tumor tissues. Increases in manganese dismutase and nonhistone chromosomal protein HMG-1 (HMG-1) were observed, while decreases in carbonic anhydrases I and II, glutatione-S-transferase and foveolin precursor (gastrokine-1) (FOV), an 18-kDa stomach-specific protein with putative tumor suppressor activity, were detected. RT-PCR analysis also revealed significant down-regulation of FOV mRNA expression in tumor tissues.

Conclusion

A possible pathological role for down-regulation of FOV in gastric carcinogenesis was demonstrated. Evaluation of the specific decreases in gene and protein expression of FOV in patients may be utilized as clinical biomarkers for effective diagnosis and assessment of gastric cancer.

A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein

The platelet surface is poorly characterized due to the low abundance of many membrane proteins and the lack of specialist tools for their investigation. In this study we identified novel human platelet and mouse megakaryocyte membrane proteins using specialist proteomics and genomics approaches. Three separate methods were used to enrich platelet surface proteins prior to identification by liquid chromatography and tandem mass spectrometry: lectin affinity chromatography, biotin/NeutrAvidin affinity chromatography, and free flow electrophoresis. Many known, abundant platelet surface transmembrane proteins and several novel proteins were identified using each receptor enrichment strategy. In total, two or more unique peptides were identified for 46, 68, and 22 surface membrane, intracellular membrane, and membrane proteins of unknown subcellular localization, respectively. The majority of these were single transmembrane proteins. To complement the proteomics studies, we analyzed the transcriptome of a highly purified preparation of mature primary mouse megakaryocytes using serial analysis of gene expression in view of the increasing importance of mutant mouse models in establishing protein function in platelets. This approach identified all of the major classes of platelet transmembrane receptors, including multitransmembrane proteins. Strikingly 17 of the 25 most megakaryocyte-specific genes (relative to 30 other serial analysis of gene expression libraries) were transmembrane proteins, illustrating the unique nature of the megakaryocyte/platelet surface. The list of novel plasma membrane proteins identified using proteomics includes the immunoglobulin superfamily member G6b, which undergoes extensive alternate splicing. Specific antibodies were used to demonstrate expression of the G6b-B isoform, which contains an immunoreceptor tyrosine-based inhibition motif. G6b-B undergoes tyrosine phosphorylation and association with the SH2 domain-containing phosphatase, SHP-1, in stimulated platelets suggesting that it may play a novel role in limiting platelet activation.

Plasma protein distribution and its impact on pharmacokinetics of liposomal amphotericin B in paediatric patients with malignant diseases

OBJECTIVE

This study investigates the association of liposomal amphotericin B (L-AmB) with plasma proteins and its impact on the pharmacokinetics of L-AmB in paediatric patients with malignant diseases.

METHODS

Paediatric oncology patients (n = 39) who received multiple-doses of L-AmB were recruited into this study. The association of the drug with plasma lipoprotein was investigated using single vertical spin density gradient ultracentrifugation and quantitated with a validated HPLC assay. The unbound amphotericin B (AmB) in the plasma was separated by ultrafiltration and determined with a validated LC/MS/MS assay.

RESULTS

The ex vivo lipoprotein distribution of L-AmB found that 68.3 +/- 11.8% of the drug was associated with the high density lipoprotein (HDL) fraction, which demonstrated a significant inverse correlation with posterior Bayesian estimates of L-AmB clearance (r = -0.690, p < 0.01). The average of unbound fraction of AmB in plasma of patients administered with L-AmB was 0.005, but its relationship with L-AmB clearance did not reach a statistical significance.

CONCLUSION

L-AmB displays different lipoprotein distribution profile from that of the conventional AmB formulation, with L-AmB preferentially associated with HDL in plasma. The inverse correlation of L-AmB clearance to its HDL distribution contributes to the difference in the pharmacokinetic profile of L-AmB.

Site-Selective Modifications of Arginine Residues in Human Hemoglobin Induced by Methylglyoxal

Methylglyoxal (MG) is an important glycating agent produced under physiological conditions. MG could react with DNA and proteins to generate advanced glycation end products. Human hemoglobin, the most abundant protein in blood cells, has not been systematically investigated as the target protein for methylglyoxal modification. Here we examined carefully, by using HPLC coupled with tandem mass spectrometry (LC-MS/MS), the covalent modifications of human hemoglobin induced by methylglyoxal. Our results revealed that hemoglobin could be modified by methylglyoxal, and the major form of modification was found to be the hydroimidazolone derivative of arginine residues. In addition, Arg-92 and Arg-141 in the alpha chain as well as Arg-40 and Arg-104 in the beta chain were modified, whereas two other arginine residues, that is, Arg-31 in the alpha chain and Arg-30 in the beta chain, were not modified. Semiquantitative measurement for adduct formation, together with the analysis of the X-ray structure of hemoglobin, showed that the extents of arginine modification were highly correlated with the solvent accessibilities of these residues. The facile formation of hydroimidazolone derivatives of arginine residues in hemoglobin by methylglyoxal at physiologically relevant concentrations suggested that this type of modification might occur in vivo. The unambiguous determination of the sites and extents of methylglyoxal modifications of arginines in hemoglobin provided a basis for understanding the implications of these modifications and for employing this type of hemoglobin modification as molecular biomarkers for clinical applications.

Recovery of drugs of abuse from the Immunalysis Quantisal oral fluid collection device

Drug recovery from a new oral fluid collection device was assessed. The evaluation was performed in vitro at three physiologically relevant concentrations for the following substances: amphetamine, methamphetamine, morphine, codeine, cocaine, benzoylecgonine, methadone, oxazepam, and Delta(9)-tetrahydrocannabinol (THC). Drug-free and drug-fortified controls were prepared and their concentration verified by liquid chromatography-tandem mass spectrometry. Aliquots of the controls were then "collected" with the device (n=3) using the manufacturer's recommended procedure. Collected samples were stored for 12 h to simulate shipping before analysis. Fresh, non-"collected" aliquots of each pool (n=3) were concurrently analyzed. The drug recoveries from the Quantisal were expressed as a mean percentage of the concurrently analyzed aliquots that were not subjected to device collection. Recoveries for oxazepam exceeded 97%, for amphetamine and methamphetamine exceeded 93%, and for opioids all exceeded 91%. The recoveries of cocaine were >91% and >82% for its polar metabolite, benzoylecgonine. Especially noteworthy was the recovery of THC from the Quantisal collector (81.3-91.4%). When compared with recoveries reported from other collection devices, the Quantisal was clearly superior.

Titanium dioxide as a chemo-affinity solid phase in offline phosphopeptide chromatography prior to HPLC-MS/MS analysis

We have developed a new offline chromatographic approach for the selective enrichment of phosphorylated peptides that is directly compatible with subsequent analysis by online nano electrospray ionization tandem mass spectrometry. In this technique, a titanium dioxide (TiO2)-packed pipette tip is used as a phosphopeptide trap that acts as an offline first-dimension separation step in a two-dimensional chromatography system. This is followed by online nano reversed-phase high-performance liquid chromatography. Here, we present suitable methods for enrichment, optimized separately for each step: sample loading, washing and elution from the TiO2-filled tips. To increase the trapping selectivity of the TiO2 column, we used the sodium salt of 1-octanesulfonic acid combined with 2,5-dihydroxybenzoic acid as ion-pairing agents and displacers for acidic peptides. These agents also improve the binding of phosphorylated peptides and block the binding of non-phosphorylated ones. This enrichment procedure takes 30 min, followed by a 100-min HPLC program, including washing and an elution gradient.

EBP, a program for protein identification using multiple tandem mass spectrometry datasets

MS/MS combined with database search methods can identify the proteins present in complex mixtures. High throughput methods that infer probable peptide sequences from enzymatically digested protein samples create a challenge in how best to aggregate the evidence for candidate proteins. Typically the results of multiple technical and/or biological replicate experiments must be combined to maximize sensitivity. We present a statistical method for estimating probabilities of protein expression that integrates peptide sequence identifications from multiple search algorithms and replicate experimental runs. The method was applied to create a repository of 797 non-homologous zebrafish (Danio rerio) proteins, at an empirically validated false identification rate under 1%, as a resource for the development of targeted quantitative proteomics assays. We have implemented this statistical method as an analytic module that can be integrated with an existing suite of open-source proteomics software.

Mechanism for Covalent Binding of Rofecoxib to Elastin of Rat Aorta

We have previously reported that oral administration of [(14)C]rofecoxib to rats resulted in the long retention of radioactivity by the aorta as a consequence of covalent binding to elastin. Treatment of rats with alpha-phenyl-alpha-propylbenzeneacetic acid 2-[diethylamino]-ethyl ester hydrochloride (SKF-525A), a cytochrome P450 inhibitor, significantly decreased the systemic exposure of 5-hydroxyrofecoxib, one of the main metabolites of rofecoxib, whereas there was no statistically significant change in the retention of radioactivity from [(14)C]rofecoxib in the aorta. On the other hand, the aortic retention of radioactivity closely correlated to the systemic exposure of unchanged rofecoxib in the dose range between 2 and 10 mg/kg. A covalent binding study of [(14)C]rofecoxib in vitro using rat aorta homogenate in the presence of d-penicillamine, hydralazine, beta-aminopropionitrile, and sodium borohydride suggested that the aldehyde group of allysine in elastin was relevant to the covalent binding. In a model reaction using benzaldehyde, rofecoxib but not 5-hydroxyrofecoxib reacted with the aldehyde group of benzaldehyde in a manner of condensation reaction under a physiological pH condition. A histopathological examination using an electron microscope demonstrated that multiple oral administration of rofecoxib to rats caused marked degradation of the elastic fiber system of the aorta. These results suggested that rofecoxib as such is reactive in vivo, undergoing a condensation reaction with allysine, thereby preventing the formation of cross-linkages in elastin, i.e., desmosine and isodesmosine, and causing the degradation of the elastic fibers.

Proteomic analysis of outer membranes and vesicles from wild-type serogroup B Neisseria meningitidis and a lipopolysaccharide-deficient mutant

Current experimental vaccines against serogroup B Neisseria meningitidis are based on meningococcal outer membrane (OM) proteins present in outer membrane vesicles (OMV) in which toxic lipopolysaccharide is depleted by detergent extraction. Knowledge of the composition of OM and OMV is essential for developing new meningococcal vaccines based on defined antigens. In the current study, sodium dodecyl sulfate-polyacrylamide gel electrophoresis and nanocapillary liquid chromatography-tandem mass spectrometry were used to investigate the proteomes of OM and OMV from meningococcal strain MC58 and OM from a lipopolysaccharide-deficient mutant. The analysis of OM revealed a composition that was much more complex than the composition that has been reported previously; a total of 236 proteins were identified, only 6.4% of which were predicted to be located in the outer membrane. The most abundant proteins included not only the well-established major OM proteins (PorA, PorB, Opc, Rmp, and Opa) but also other proteins, such as pilus-associated protein Q (PilQ) and a putative macrophage infectivity protein. All of these proteins were also present in OMV obtained by extraction of the OM with deoxycholate. There were markedly increased levels of some additional proteins in OM from the lipopolysaccharide-deficient mutant, including enzymes that contribute to the tricarboxylic acid cycle. In all the preparations, the proteins not predicted to have an OM location were predominantly periplasmic or cytoplasmic or had an unknown location, and relatively few cytoplasmic membrane proteins were detected. However, several proteins that have previously been identified as potential vaccine candidates were not detected in either OM preparations or in OMV. These results have important implications for the development and use of vaccines based on outer membrane proteins.

Analysis of the oxidative damage-induced conformational changes of apo- and holocalmodulin by dose-dependent protein oxidative surface mapping

Calmodulin (CaM) is known to undergo conformational and functional changes on oxidation, allowing CaM to function as an oxidative stress sensor. We report the use of a novel mass spectrometry-based methodology to monitor the structure of apo- and holo-CaM as it undergoes conformational changes as a result of increasing amounts of oxidative damage. The kinetics of oxidation for eight peptides are followed by mass spectrometry, and 12 sites of oxidation are determined by MS/MS. Changes in the pseudo-first-order rate constant of oxidation for a peptide after increasing radiation exposure reveal changes in the accessibility of the peptide to the diffusing hydroxyl radical, indicating conformational changes as a function of increased oxidative damage. For holo-CaM, most sites rapidly become less exposed to hydroxyl radicals as the protein accumulates oxidative damage, indicating a closing of the hydrophobic pockets in the N- and C-terminal lobes. For apo-CaM, many of the sites rapidly become more exposed until they resemble the solvent accessibility of holo-CaM in the native structure and then rapidly become more buried, mimicking the conformational changes of holo-CaM. At the most heavily damaged points measured, the rates of oxidation for both apo- and holo-CaM are essentially identical, suggesting the two assume similar structures.

Mapping the dimer interface in the C-terminal domains of the yeast MLH1-PMS1 heterodimer

Yeast MutLalpha is a heterodimer of MLH1 and PMS1 that participates in a variety of DNA transactions, including DNA mismatch repair. Formation of the MutLalpha heterodimer requires that the C-terminal domains of MLH1 and PMS1 interact in a manner that is not yet fully understood. Here we investigate the interactions involved in heterodimerization. Using protein surface modification and mass spectrometry, we identify numerous lysine residues that are exposed to solvent in monomeric MLH1. A corresponding analysis of the MLH1-PMS1 heterodimer reveals that three of these exposed residues, K665, K675, and K704, are no longer solvent accessible in the heterodimer, suggesting that they are within the dimer interface. We refine secondary structure predictions and sequence alignments of C-terminal residues of seven eukaryotic MutL homologues and then develop homology models for the N- and C-terminal domains of MLH1. On the basis of this information, we present a model for interaction of the C-terminal domains of MLH1 and PMS1.

Sequencing of oligoarabinosyl units released from mycobacterial arabinogalactan by endogenous arabinanase: identification of distinctive and novel structural motifs

The mycobacterial D-arabinofuran is a common constituent of both cell wall mycolyl-arabinogalactan (AG) and the associated lipoarabinomannan (LAM), and is thus accorded critical structural and immunological roles. Despite a well-recognized importance, progress in understanding its full structural characteristics beyond the nonreducing terminal motifs has hitherto been limited by available analytical tools. An endogenous arabinanase activity recently isolated from Mycobacterium smegmatis was previously shown to be capable of releasing large oligoarabinosyl units from AG. Advanced tandem mass spectrometry utilizing both low and high energy collision induced dissociation now afforded a facile way to map and directly sequence the digestion products which were dominated by distinctive Ara18 and Ara19 structural units, together with Ara7 and lesser amount of Ara11 and Ara12. Significantly, evidence was obtained for the first time which validated the linkages and branching pattern of the previously inferred Ara22 structural motif of AG, on which the preferred cleavage sites of the novel arabinanase could be localized. The established linkage-specific MS/MS fragmentation characteristics further led to identification of a galactosamine substituent on the C2 position of a portion of the internal 3,5-branched Ara residue of the AG of Mycobacterium tuberculosis, but not that of the nonpathogenic, fast growing M. smegmatis.

Structural organization of the 19S proteasome lid: insights from MS of intact complexes

The 26S proteasome contains a 19S regulatory particle that selects and unfolds ubiquitinated substrates for degradation in the 20S catalytic particle. To date there are no high-resolution structures of the 19S assembly, nor of the lid or base subcomplexes that constitute the 19S. Mass spectra of the intact lid complex from Saccharomyces cerevisiae show that eight of the nine subunits are present stoichiometrically and that a stable tetrameric subcomplex forms in solution. Application of tandem mass spectrometry to the intact lid complex reveals the subunit architecture, while the coupling of a cross-linking approach identifies further interaction partners. Taking together our results with previous analyses we are able to construct a comprehensive interaction map. In summary, our findings allow us to identify a scaffold for the assembly of the particle and to propose a regulatory mechanism that prevents exposure of the active site until assembly is complete. More generally, the results highlight the potential of mass spectrometry to add crucial insight into the structural organization of an endogenous, wild-type complex.

Tandem mass spectrometry coupled with structural cross-linking enabled a depiction of how components of the 19S proteasome lid interact and the active site remains hidden until assembly is complete.

Light-induced changes in protein nitration in photoreceptor rod outer segments

PURPOSE

Light has been shown to modulate protein nitration in rat retinas. To better understand the role of protein nitration in photoreceptor cell death induced by intense light, we examined retinal protein nitration and identified target proteins in rod outer segments (ROS).

METHODS

Cyclic light-reared rats, treated or not with the antioxidant, dimethylthiourea (DMTU), were exposed to intense green light for 8 h. A subset of these rats was kept in the dark for 24 h after 8 h of light exposure. Western analysis of ROS proteins with an anti-nitrotyrosine antibody was performed to examine changes in protein nitration. 2D-immunoblots with anti-nitrotyrosine antibody followed by liquid chromatography tandem mass spectrometry was used to identify nitrated proteins in ROS. The expression levels of three nitric oxide synthase (NOS) isoforms, inducible, neuronal-, and endothelial-NOS were semi-quantified by immunoblot analysis.

RESULTS

Western analysis revealed that the level of ROS protein nitration increased during the dark recovery period after 8 h of light treatment in both DMTU treated and untreated rats. However, DMTU effectively reduced protein nitration in ROS during light exposure and during the subsequent dark recovery period. Using 2D-immunoblotting followed by liquid chromatography tandem mass spectrometry analysis, we identified ten ROS proteins as nitration targets. Most of these proteins were glycolytic enzymes. The level of inducible-NOS in the retina was increased by light exposure.

CONCLUSIONS

The effect of DMTU in reducing ROS protein nitration during and after light suggests the involvement of protein nitration during light-induced photoreceptor cell death. Nitration of glycolytic enzymes specifically may alter their activities. Increased levels of iNOS during and after intense light exposure suggest that this isoform is responsible for intense light induced protein nitration in ROS during the dark recovery period. The limited nitration seen in ROS during light exposure may reflect a quenching effect by endogenous antioxidants on the generation of reactive oxygen and nitrogen species.

Proteomic identification of proteins associated with the osmoregulatory transcription factor TonEBP/OREBP: functional effects of Hsp90 and PARP-1

Hypertonicity (e.g., high NaCl) activates the transcription factor tonicity-responsive enhancer/osmotic response element-binding protein (TonEBP/OREBP), increasing transcription of protective genes. In the present studies, by stably expressing amino acids 1-547 of TonEBP/OREBP in HEK 293 cells and immunoprecipitating it plus associated proteins from the nuclei of cells exposed to high NaCl, we identify 14 proteins that are physically associated with TonEBP/OREBP. The associated proteins fall into several classes: 1) DNA-dependent protein kinase, both its catalytic subunit and regulatory subunit, Ku86; 2) RNA helicases, namely RNA helicase A, nucleolar RNA helicase II/Gu, and DEAD-box RNA helicase p72; 3) small or heterogeneous nuclear ribonucleoproteins (snRNPs or hnRNPs), namely U5 snRNP-specific 116 kDa protein, U5 snRNP-specific 200 kDa protein, hnRNP U, hnRNP M, hnRNP K, and hnRNP F; 4) heat shock proteins, namely Hsp90beta and Hsc70; and 5) poly(ADP-ribose) polymerase-1 (PARP-1). We confirm identification of most of the proteins by Western analysis and also demonstrate by electrophoretic mobility-shift assay that they are present in the large complex that binds specifically along with TonEBP/OREBP to its cognate DNA element. In addition, we find that PARP-1 and Hsp90 modulate TonEBP/OREBP activity. PARP-1 expression reduces TonEBP/OREBP transcriptional activity and the activity of its transactivating domain. Hsp90 enhances those activities and sustains the increased abundance of TonEBP/OREBP protein in cells exposed to high NaCl.

Effect of fish skin mucus on the soluble proteome of Vibrio salmonicida analysed by 2-D gel electrophoresis and tandem mass spectrometry

Vibrio salmonicida is the causative agent of cold-water vibriosis in farmed marine fish species. Adherence of pathogenic bacteria to mucosal surfaces is considered to be the first steps in the infective processes, and proteins involved are regarded as virulence factors. The global protein expression profile of V. salmonicida, grown with and without the presence of fish skin mucus in the synthetic media, was compared. Increased levels of proteins involved in motility, oxidative stress responses, and general stress responses were demonstrated as an effect of growth in the presence of mucus compared to non-mucus containing media. Enhanced levels of the flagellar proteins FlaC, FlaD and FlaE indicate increased motility capacity, while enhanced levels of the heat shock protein DnaK and the chaperonin GroEL indicate a general stress response. In addition, we observed that peroxidases, TPx.Grx and AhpC, involved in the oxidative stress responses, were induced by mucus proteins. The addition of mucus to the culture medium did not significantly alter the growth rate of V. salmonicida. An analysis of mucus proteins suggests that the mucus layer harbours a protein species that potentially possesses catalytic activity against DNA, and a protein with iron chelating activity. This study represents the first V. salmonicida proteomic analysis, and provides specific insight into the proteins necessary for the bacteria to challenge the skin mucus barrier of the fish.

Identification of siderophores ofPseudomonas stutzeri

We have identified two types of siderophores produced by Pseudomonas, one of which has never before been found in the genus. Twelve strains of Pseudomonas stutzeri belonging to genomovars 1, 2, 3, 4, 5, and 9 produced proferrioxamines, the hydroxamate-type siderophores. Pseudomonas stutzeri JM 300 (genomovar 7) and DSM 50238 (genomovar 8) and Pseudomonas balearica DSM 6082 produced amonabactins, catecholate-type siderophores. The major proferrioxamines detected were the cyclic proferrioxamines E and D2. Pseudomonas stutzeri KC also produced cyclic (X1and X2) and linear (G1and G2a-c) proferrioxamines. Our data indicate that the catecholate-type siderophores belong to amonabactins P 750, P 693, T 789, and T 732. A mutant of P. stutzeri KC (strain CTN1) that no longer produced the secondary siderophore pyridine-2,6-dithiocarboxylic acid continued to produce all other siderophores in its normal spectrum. Siderophore profiles suggest that strain KC (genomovar 9) belongs to the proferrioxamine-producing P. stuzeri. Moreover, a putative ferrioxamine outer membrane receptor gene foxA was identified in strain KC, and colony hybridization showed the presence of homologous receptor genes in all P. stutzeri and P. balearica strains tested.Key words: siderophore, Pseudomonas stutzeri, ferrioxamine, amonabactin.

Retinal Penetration of Calpain Inhibitors in Rats After Oral Administration

Calpain-mediated proteolysis has been involved in neuronal cell death of retinal neurological degeneration. An aldehyde-based calpain inhibitor, SJA6017 (1), was effective following oral administration in a rat retinal ischemia model but had low oral bioavailability. The aim of this study was to identify calpain inhibitors with good retinal penetration after oral dosing. The orally bioavailable inhibitors, hemiacetal 3 (SNJ-1715), amphipathic ketoamide 5 (SNJ-1945), and pyridine ketoamide 6 (SNJ-2008), were evaluated for their retinal pharmacokinetic (PK) profiles. The retinal drug exposure of these inhibitors was more than tenfold higher than 1. Among these compounds, 5 exhibited the most favorable retinal PK properties, such as good penetration and long half-life. Comparisons of 5 and the structurally related ketoamide 6 suggested that the presence of a methoxy diethylene glycol moiety resulted in the inhibitor with high penetration into the retina and the sustained high retinal levels. Ketoamide 5 was selected as the development candidate for the treatment of retinal diseases.

Strategies for analysis of glycoprotein glycosylation

Glycoproteins are known to exhibit multiple biological functions. In order to assign distinct functional properties to defined structural features, detailed information on the respective carbohydrate moieties is required. Chemical and biochemical analyses, however, are often impeded by the small amounts of sample available and the vast structural heterogeneity of these glycans, thus necessitating highly sensitive and efficient methods for detection, separation and structural investigation. The aim of this article is to briefly review suitable strategies for characterization of glycosylation at the levels of intact proteins, glycopeptides and free oligosaccharides. Furthermore, methods commonly used for isolation, fractionation and carbohydrate structure analysis of liberated glycoprotein glycans are discussed in the context of potential applications in glycoproteomics.

Post-translational modification accounts for the presence of varied forms of nerve growth factor in Australian elapid snake venoms

The Australian elapid snakes are amongst the most venomous snakes in the world, but much less is known about the overall venom composition in comparison to Asian and American snakes. We have used a combined approach of cDNA cloning and 2-DE with MS to identify nerve growth factor (NGF) in venoms of the Australian elapid snakes and demonstrate its neurite outgrowth activity. While a single 730 nucleotide ORF, coding for a 243 amino acid precursor protein was detected in all snakes, use of 2-DE identified NGF proteins with considerable variation in molecular size within and between the different snakes. The variation in size can be explained at least in part by N-linked glycosylation. It is possible that these modifications alter the stability, activity and other characteristics of the snake NGFs. Further characterisation is necessary to delineate the function of the individual NGF isoforms.

A Review of Nanoelectrospray Ionization Applications for Drug Metabolism and Pharmacokinetics

Although traditionally reserved for proteomic analysis, nanoESI has found increased use for small molecule applications related to drug metabolism/pharmacokinetics (DMPK). NanoESI, which refers to ESI performed at flow rates in the range of 200 to 1000 nL/min using smaller diameter emitters (10 to 100 microm id), produces smaller droplets than conventional ESI resulting in more efficient ionization. Benefits include greater sensitivity, enhanced dynamic range, and a reduced competition for ionization. These advantages may now be harnessed largely due to the introduction of a commercial system for automated nanoESI infusion. This development in turn has allowed ADME (absorption, distribution, metabolism, and excretion) scientists to consider novel approaches to mass spectrometric analysis without direct LC interfacing. While it is freely acknowledged that nanoESI infusion is not likely to supplant LC-MS as the primary analytical platform for ADME, nanoESI infusion has been successfully applied to both quantitative (bioanalysis) and qualitative (metabolite identification) applications. This review summarizes published applications of this technology and offers a perspective on where it fits best into the DMPK laboratory.

Global Comparison of the Membrane Subproteomes between a Multidrug-ResistantAcinetobacterbaumanniiStrain and a Reference Strain

Acinetobacter baumannii causes severe infections in compromised patients. We combined SDS-PAGE, two-dimensional gel electrophoresis and mass spectrometry (LC-MS/MS and MALDI-TOF) to separate and characterize the proteins of the cell envelope of this bacterium. In total, 135 proteins (inner and outer membrane proteins) were identified. In this analysis, we described the expression by this bacterium of RND-type efflux systems and some potential virulence factors. We then compared the membrane subproteome of a clinical multidrug-resistant (MDR) isolate with that of a reference strain. We found that the MDR strain expressed lower levels of the penicillin-binding-protein 1b, produced a CarO protein having different primary and quaternary structures to that of the reference strain, and expressed OmpW isoforms. We also showed that the clinical strain has a high ability to form biofilms consistent with the accumulation of some outer membrane proteins (OMPs) such as NlpE or CsuD that have already been described as involved in bacterial adhesion. These features may partly explain the MDR emergence of the clinical isolate.

Protein clusters associated with carcinogenesis, histological differentiation and nodal metastasis in esophageal cancer

We examined the proteomic background of esophageal cancer. We used laser microdissection to obtain tumor tissues from 72 esophageal squamous cell carcinoma cases and adjacent normal tissues in 57 of these cases. The 2D-DIGE generated quantitative expression profiles with 1730 protein spots. Based on the intensity of the protein spots, unsupervised classification distinguished the tumor tissues from their normal counterparts, and subdivided the tumor tissues according to their histological differentiation. We identified 498 protein spots with altered intensity in the tumor tissues, which protein identification by LC-MS/MS showed to correspond to 217 gene products. We also found 41 protein spots that were associated with nodal metastasis, and identified 33 proteins corresponding to the spots, including cancer-associated proteins such as alpha-actinin 4, hnRNP K, periplakin, squamous cell carcinoma antigen 1 and NudC. The identified cancer-associated proteins have been previously reported to be individually involved in a range of cancer types, and our study observed them collectively in a single type of malignancy, esophageal cancer. As the identified proteins are involved in important biological processes such as cytoskeletal/structural organization, transportation, chaperon, oxidoreduction, transcription and signal transduction, they may function in a coordinate manner in carcinogenesis and tumor progression of esophageal cancer.

Trace mycotoxin analysis in complex biological and food matrices by liquid chromatography–atmospheric pressure ionisation mass spectrometry

Mycotoxins are toxic secondary metabolites produced by filamentous fungi that are growing on agricultural commodities. Their frequent presence in food and their severe toxic, carcinogenic and estrogenic properties have been recognised as potential threat to human health. A reliable risk assessment of mycotoxin contamination for humans and animals relies basically on their unambiguous identification and accurate quantification in food and feedstuff. While most screening methods for mycotoxins are based on immunoassays, unambiguous analyte confirmation can be easily achieved with mass spectrometric methods, like gas chromatography/mass spectrometry (GC/MS) or liquid chromatography/mass spectrometry (LC/MS). Due to the introduction of atmospheric pressure ionisation (API) techniques in the late 80s, LC/MS has become a routine technique also in food analysis, overcoming the traditional drawbacks of GC/MS regarding volatility and thermal stability. During the last few years, this technical and instrumental progress had also an increasing impact on the expanding field of mycotoxin analysis. The aim of the present review is to give an overview on the application of LC-(API)MS in the analysis of frequently occurring and highly toxic mycotoxins, such as trichothecenes, ochratoxins, zearalenone, fumonisins, aflatoxins, enniatins, moniliformin and several other mycotoxins. This includes also the investigation of some of their metabolites and degradation products. Suitable sample pre-treatment procedures, their applicability for high sample through-put and their influence on matrix effects will be discussed. The review covers literature published until July 2006.

Protein processing and other modifications analyzed by diagonal peptide chromatography

Diagonal peptide chromatography consists of two consecutive, identical peptide separations with in between an enzymatic or chemical alteration of the side-chain structure of selected peptides. Such selected and altered peptides acquire different chromatographic properties thereby segregating from non-altered peptides in a series of secondary peptide separations. Originally described by Brown and Hartley in 1966, we have modified the technique such that it can be used for higher throughput gel-free proteomics. Our technique is termed COmbined FRActional DIagonal Chromatography (COFRADIC) and exploits evoked differences of the hydrophobicity of peptides in reverse-phase liquid chromatography. One important advantage of COFRADIC is its versatility: by changing the alteration reaction, different classes of peptides are sorted and finally analyzed. We previously published protocols and applications for separating methionyl, cysteinyl, amino terminal and phosphorylated peptides. In this review, we assess the potential of COFRADIC for the analysis of several posttranslational modifications emphasizing on in vivo protein processing events. Additional modifications that can be analyzed include phosphorylation and N-glycosylation. The potential of COFRADIC for isolating peptides holding such modified amino acids are discussed here.

Proteome analysis of bronchoalveolar lavage in lung diseases

The proteomic approach is complementary to genomics and enables protein composition to be investigated under various clinical conditions. Its application to the study of bronchoalveolar lavage (BAL) is extremely promising. BAL proteomic studies were initially based on two-dimensional electrophoretic separation of complex protein samples and subsequent identification of proteins by different methods. With the techniques available today it is possible to attain many different research objectives. BAL proteomics can contribute to the identification of proteins in alveolar spaces with possible insights into pathogenesis and clinical application for diagnosis, prognosis and therapy. Many proteins with different functions have already been identified in BAL. Some could be biomarkers that need to be individually confirmed by correlation with clinical parameters and validation by other methods on larger cohorts of patients. The standardization of BAL sample preparation and processing for proteomic studies is an important goal that would promote and facilitate clinical applications. Here, we review the principal literature on BAL proteomic analysis applied to the study of lung diseases.

Enhanced biodegradation of iopromide and trimethoprim in nitrifying activated sludge

Iopromide (an X-ray contrast agent) and trimethoprim (an antibacterial drug) are frequently detected pharmaceuticals in effluents of wastewater treatment plants (WWTPs) and in surface waters due to their persistence and high usage. Laboratory-scale experiments showed that a significantly higher removal rate in nitrifying activated sludge as compared to conventional activated sludge was observed for both iopromide and trimethoprim. When the activity of the nitrifying bacteria was inhibited, the percent removal of iopromide decreased from 97 to 86% while trimethoprim removal decreased from 70 to 25%. The metabolite of iopromide identified when nitrification was not inhibited was a dehydroxylated iopromide at the two side chains. However, when the nitrifying bacteria were inhibited the metabolite identified was a carboxylate, formed during the oxidation of the primary alcohol on the side chain of iopromide. These results suggest that the nitrifying bacteria are important in the observed biodegradation of iopromide in the activated sludge with higher solid retention time (SRT). Results from the laboratory-scale study were corroborated by the observed removal efficiencies in a full-scale municipal WWTP, which showed that iopromide (ranging from 0.10 to 0.27 microg/L) and trimethoprim (ranging from 0.0.08 to 0.53 microg/L) were removed more effectively in the nitrifying activate sludge which has a higher SRT (49 days) than in the conventional activated sludge (SRT of 6 days). In nitrifying activated sludge, the percent removal of iopromide in the WWTP reached 61%, while in conventional activated sludge, average removal was negligible. For trimethoprim, removal was limited to about 1% in the conventional activated sludge, while in the nitrifying activated sludge, the removal was increased to 50%.

Study of posttranslational modifications in lenticular αA-Crystallin of mice using proteomic analysis techniques

In the present work the complexity in the 2D-gel protein pattern of murin lenticular alphaA-Crystallin was analyzed. An in depth study of the different protein isoforms was done combining different proteomic tools. Lens proteins of four different ages, from embryo to 100-week-old mice, were separated by large 2D-PAGE, revealing an increase in the number and intensity of the spots of alphaA-Crystallin during the process of aging. For further analyses the oldest mice were chosen. Comparison and evaluation of two different staining methods proved Imidazole-Zinc to be a good alternative to the generally used Coomassie stain. The characterization of the different alphaA-Crystallin protein species was done using nanoLC-ESI-MS/MS (liquid chromatography electrospray ionisation tandem mass spectrometry). Data interpretation was done by database searching, manual validation and a new MS/MS-interpretation tool for posttranslational modifications--the PTM-Explorer. Using this way, eight different phosphorylation sites were identified and localized; the identification of four of them was not published so far. Furthermore, quantitative N-terminal acetylation of alphaA-Crystallin and variable C-terminal truncation was observed, also not published in this extent yet. The results of the mass spectrometric analysis were validated by immunoblotting experiments using two different alphaA-Crystallin specific antibodies. In addition, a fluorescent phospho-specific stain was used to detect the protein spots including phosphorylation groups. Re-separation 2D-PAGE was done to round off the present study and explain the appearance of some of the protein spots in the gel as artifacts of the 2D-PAGE separation.

Occurrence and fate of the cytostatic drugs cyclophosphamide and ifosfamide in wastewater and surface waters

The two oxazaphosphorine compounds cyclophosphamide and ifosfamide are important cytostatic drugs used in the chemotherapy of cancer and in the treatment of autoimmune diseases. Their mechanism of action, involving metabolic activation and unspecific alkylation of nucleophilic compounds, accounts for genotoxic effects described in the literature and is reason for environmental concern. The occurrence and fate of cyclophosphamide and ifosfamide were studied in wastewater treatment plants (WWTPs) and surface waters in Switzerland, using a highly sensitive analytical method based on solid-phase extraction and liquid chromatography tandem mass spectrometry. The compounds were detected in untreated and treated wastewater at concentrations of <0.3-11 ng/L, which corresponded well with concentrations predicted from consumption data and typical renal excretion rates. Weekly loads determined in influent and effluent wastewater were comparable and suggested a high persistence in WWTPs. Furthermore, no degradation was observed in activated sludge incubation experiments within 24 h at concentrations of approximately 100 ng/L. Processes that may be relevant for elimination in natural waterbodies were studied with a set of incubation experiments in the laboratory. After extrapolation to natural conditions in surface waters, a slow dark-chemical degradation (half-lives on the order of years) is the most important transformation process. Degradation by photochemically formed HO* radicals may be of some relevance only in shallow, clear, and nitrate-rich waterbodies but could be further exploited for elimination of these compounds by advanced oxidation processes, i.e., in a treatment of hospital wastewater. In surface waters, concentrations ranged from < or =50 to 170 pg/L and were thus several orders of magnitude lower than the levels at which acute ecotoxicological effects have been reported in the literature (mg/L range). However, due to a lack of studies on chronic effects on aquatic organisms and data on occurrence and effects of metabolites, a final risk assessment cannot be made.

Detection in human saliva of different statherin and P-B fragments and derivatives

Statherin is a multifunctional polypeptide specific of human saliva involved in oral calcium homeostasis, phosphate buffering and formation of protein networks. Salivary P-B peptide is usually included into the basic proline-rich protein family but it shows some similarities with statherin and its specific biological role is still undefined. In this study, various fragments and derivatives of statherin and P-B peptide were consistently detected by RP-HPLC ESI-IT MS in 23 samples of human saliva. They were: statherin mono- and non-phosphorylated, statherin Des-Phe(43) (statherin SV1), statherin Des-Thr(42),Phe(43), statherin Des-Asp(1), statherin Des(6-15) (statherin SV2), statherin Des(1-9), statherin Des(1-10), statherin Des(1-13) and P-B Des(1-5). Statherin SV3 (statherin Des(6-15), Phe(43)) was detected only in one sample. Identity of the fragments was confirmed either by MS/MS experiments or by enzymatic digestion or by Edman sequencing. Detection of the fragments suggests that statherin and P-B peptide are submitted to post-translational proteolytic cleavages that are common to other classes of salivary proteins.

The Tetrahymena thermophila phagosome proteome

In vertebrates, phagocytosis occurs mainly in specialized cells of the immune system and serves as a primary defense against invading pathogens, but it also plays a role in clearing apoptotic cells and in tissue remodeling during development. In contrast, unicellular eukaryotes, such as the ciliate Tetrahymena thermophila, employ phagocytosis to ingest and degrade other microorganisms to meet their nutritional needs. To learn more about the protein components of the multistep process of phagocytosis, we carried out an analysis of the Tetrahymena phagosome proteome. Tetrahymena cells were fed polystyrene beads, which allowed for the efficient purification of phagosomes. The protein composition of purified phagosomes was then analyzed by multidimensional separation coupled with tandem mass spectrometry. A total of 453 peptides were identified that resulted in the identification of 73 putative phagosome proteins. Twenty-eight of the proteins have been implicated in phagocytosis in other organisms, indicating that key aspects of phagocytosis were conserved during evolution. Other identified proteins have not previously been associated with phagocytosis, including some of unknown function. Live-cell confocal fluorescence imaging of Tetrahymena strains expressing green fluorescent protein-tagged versions of four of the identified phagosome proteins provided evidence that at least three of the proteins (including two with unknown functions) are associated with phagosomes, indicating that the bulk of the proteins identified in the analyses are indeed phagosome associated.