MS-MS Spectra Research Articles

Interpretation of Tandem Mass Spectrometry (MS-MS) Spectra for Peptide Analysis.

The aim of this chapter is to give a short introduction to peptide analysis by mass spectrometry (MS) and interpretation of fragment mass spectra. Through examples and guidelines, we will demonstrate how to understand and validate search results and how to perform de novo sequencing based on the often very complex fragmentation pattern obtained by tandem mass spectrometry (also referred to as MSMS). The focus will be on simple rules for interpretation of MSMS spectra of tryptic as well as non-tryptic peptides.

Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis in Oreochromis mossambicus.

Salinity tolerance in fish involves a suite of physiological changes, but a cohesive theory leading to a mechanistic understanding at the organismal level is lacking. To examine the potential of adapting energy homeostasis theory in the context of salinity stress in teleost fish, Oreochromis mossambicus were acclimated to hypersalinity at multiple rates and durations to determine salinity ranges of tolerance and resistance. Over 3000 proteins were quantified simultaneously to analyze molecular phenotypes associated with hypersalinity. A species- and tissue-specific data-independent acquisition (DIA) assay library of MSMS spectra was created. Protein networks representing complex molecular phenotypes associated with salinity acclimation were generated. O. mossambicus has a wide "zone of resistance" from 75g/kg salinity to 120g/kg. Crossing into the zone of resistance resulted in marked phenotypic changes including blood osmolality over 400mOsm/kg, reduced body condition, and cessation of feeding. Protein networks impacted by hypersalinity consist of electron transport chain (ETC) proteins and specific osmoregulatory proteins. Cytoskeletal, cell adhesion, and extracellular matrix proteins are enriched in networks that are sensitive to the critical salinity threshold. These network analyses identify specific proteome changes that are associated with distinct zones described by energy homeostasis theory and distinguish them from general hypersalinity-induced proteome changes.

In vitro metabolite identification of acetylbenzylfentanyl, benzoylbenzylfentanyl, 3-fluoro-methoxyacetylfentanyl, and 3-phenylpropanoylfentanyl using LC-QTOF-HRMS together with synthesized references.

Acetylbenzylfentanyl, benzoylbenzylfentanyl, 3-fluoro-methoxyacetylfentanyl, and 3-phenylpropanoylfentanyl are fentanyl analogs that have been reported to the European Monitoring Centre for Drugs and Drug Addiction in recent years. The aim of this study was to identify metabolic pathways and potential biomarker metabolites of these fentanyl analogs. The compounds were incubated (5μM) with cryopreserved hepatocytes for up to 5h in vitro. Metabolites were analyzed with liquid chromatography-quadrupole time of flight-high-resolution mass spectrometry (LC-QTOF-HRMS). The experiments showed that acetylbenzylfentanyl, benzoylbenzylfentanyl, and 3-phenylpropanoylfentanyl were mainly metabolized through N-dealkylation (forming nor-metabolites) and 3-fluoro-methoxyacetylfentanyl mainly through demethylation. Other observed metabolites were formed by mono-/dihydroxylation, dihydrodiol formation, demethylation, dehydrogenation, amide hydrolysis, and/or glucuronidation. The experiments showed that a large number of metabolites of 3-phenylpropanoylfentanyl were formed. The exact position of hydroxy groups in formed monohydroxy metabolites could not be established solely based upon recorded MSMS spectra of hepatocyte samples. Therefore, potential monohydroxy metabolites of 3-phenylpropanoylfentanyl, with the hydroxy group in different positions, were synthesized and analyzed together with the hepatocyte samples. This approach could reveal that the β position of the phenylpropanoyl moiety was highly favored; β-OH-phenylpropanoylfentanyl was the most abundant metabolite after the nor-metabolite. Both metabolites have the potential to serve as biomarkers for 3-phenylpropanoylfentanyl. The nor-metabolites of acetylbenzylfentanyl, benzoylbenzylfentanyl, and 3-fluoro-methoxyacetylfentanyl do also seem to be suitable biomarker metabolites, as do the demethylated metabolite of 3-fluoro-methoxyacetylfentanyl. Identified metabolic pathways and formed metabolites were in agreement with findings in previous studies of similar fentanyl analogs.

ИДЕНТИФИКАЦИЯ ПРИМЕСЕЙ В ФАРМАЦЕВТИЧЕСКОЙ СУБСТАНЦИИ ЛХС-1269 МЕТОДОМ ВЭЖХ-МСМС

The N.N. Blokhin Oncology Research Center synthesized indolo[2,3-a]carbazole N-glycoside, which received the laboratory cipher LСS-1269, which showed a pronounced antitumor effect during research.. During the study of LСS-1269 by HPLC, the presence of two impurities was revealed, called LСS-1269-X and LСS-1269-Y (impurities X and Y). The electronic absorption spectrum (EAS) of the impurity peak X was similar to the EAS of the indolo[2,3-a]carbazole N-glycoside obtained and described earlier under the laboratory cipher LCS-1208, and the EAS of the impurity was the spectrum of LCS–1269, which indicates that the impurities belong to indolo[2,3-a]carbazoles. In this regard, it is suggested about the structure of these impurities: impurity X is a xyloside of aglycone similar in structure to aglycone LCS-1208, which can be formed as a by-product at one of the last stages of the synthesis of LCS-1269, and impurity Y has the structure of triacetyl ester LCS-1269, which is a precursor of LCS-1269 in the synthesis process. The aim of the work was to identify impurities in the substance LHS-1C69, to confirm their structures and belonging to derivatives of indolo[2,3-a]carbazole. The identification of impurities in the substance LCS-1269 was carried out using the HPLC-MSMS method. For this purpose, X and Y impurities having the assumed structures were obtained by directed counter synthesis, which were used as reference samples. Comparison of peak retention times on extracted ion chromatograms (XIC) and MSMS spectra of impurities with XIC and MSMS spectra of samples of comparison of the alleged impurities confirmed their structure. As a result of the work carried out, the structures of impurities X and Y were identified and the affiliation of these impurities to derivatives of indolo[2,3-a]carbazole was confirmed.

Novel automated identification and quantification database using liquid chromatography quadrupole time-of-flight mass spectrometry for quick, comprehensive, cheap and extendable organic micro-pollutant analysis in environmental systems

In order to protect human health and the environment, highly efficient, low-cost, labor-saving, and green analysis of toxic chemicals are urgently required. To achieve this objective, we have developed a novel database-based automated identification and quantification system (AIQS) using LC-QTOF-MS. Since the AIQS uses retention times (RTs), exact MS and MS-MS spectra, and calibration curves of 484 chemicals registered in the database instead of the use of standards, the targets can be determined with low-cost in a short time. The AIQS uses Sequential Window Acquisition of All Theoretical Fragment-ion Spectra as an acquisition method by which we can obtain accurate MS and MS-MS spectra of all detectable substances in a sample with minimal interference from co-eluted peaks. Identification is certainly done using RTs, mass error, ion ratios (a precursor to two product ions), and accurate MS and MS-MS spectra. Consequently, the chance of misidentification is very low even in dirty samples. To examine the accuracy of the AIQS, two collaborative tests were conducted. The first test used 208 pesticide standards at two concentrations (10 and 100 ng mL−1) using 7 instruments, and showed that average trueness was 106 and 95.2%, respectively, with relative standard deviations of 90% of the test compounds below 30%. The second collaborative study involved 5 laboratories carrying out recovery tests on 200 pesticides using 10 river waters. The average recovery was 71.6%; this was 15% lower than that using purified water probably due to the matrix effects. The average relative standard deviation was 30% worse than that of measurement of the standards. Both the recovery and reproducibility, however, satisfied the criteria of Analytical Method Validity Guidelines, Ministry of Health, Labour and Welfare, Japan. Instrument detection limits of 96% of the registered compounds are below 10 pg. The AIQS allows for easy addition of new substances and retrospective analysis after their addition. The results applied to actual samples showed that the AIQS has sufficient identification and quantification performance as a target screening method for a large number of substances in environmental samples.

Quantification of phosphatidylethanol combining dried blood spots sampling with Orbitrap-based LC-HRMS platform: Method validation and proficiency testing

Phosphatidylethanols (PEth) are phospholipids specifically synthetised by an enzymatic reaction in presence of ethanol. PEth is a mid-term direct biomarker for alcohol consumption or abstinence, leading to a growing interest for forensic toxicology purposes. Blood deposition onto a filter paper card as dried blood spots (DBS) allows PEth stabilisation which is otherwise easily degraded at room temperature. The goal of this study was to develop and validate a procedure for the quantification of PEth 16:0/18:1, the most abundant analogue, in DBS samples benefiting from the selectivity brought by Orbitrap-based high-resolution mass spectrometry (HRMS). Calibration samples and quality controls (QCs) are volumetrically spotted (10 μL) onto filter paper card (Whatman 903 protein saver) either using HemaXis DB10™ device, or using laboratory micropipette. The whole DBS is manually punched out and the PEth is then directly extracted using an in vial approach with 100 μL of PEth 16:0/18:1-D5 in methanol. Analyses are then performed by LC-HRMS in PRM mode using a QExactive Orbitrap platform. Validation was carried out on with respect to the Food and Drug Administration (FDA) criteria, using three different QC concentrations (39, 87 and 350 ng/mL) over three non-consecutive days. To assess the robustness of our method, an interlaboratory proficiency testing was carried out using 3 different commercial standards at 4 levels (50, 100, 200, and 300 ng/mL) of quality controls (QCs) provided by ACQ Science (Germany). The method was fully validated according to guidelines set forth by the FDA. Calibration curve was built using a weighting factor of 1/x. Trueness was measured between 100.1 and 103.6% for the tested concentrations. Repeatability and intermediate precision were found to be lower than 5%. Linearity was evaluated between the lower limit of quantification of 20 ng/mL and the upper limit of quantification of 2000 ng/mL with an R2 greater than 0.998. Recovery (RE) and matrix effect (ME) evaluated at 2 concentrations ranged from 76 to 99% and 8 to 10%, respectively. During the proficiency test, precision was evaluated below 8.0%, while the accuracy ranged from 93.8% to 105.9% and from 101 to 104.5% when compared with the expected concentration and the mean measured value of all the labs participating respectively. The validation results demonstrate that the use of Orbitrap-based PRM quantification present an interesting alternative over triple quadrupole platforms considered as the gold standard for LC-MS/MS quantitative approaches. Indeed, multiple reaction monitoring (MRM) and PRM provide comparable performance in terms of sensitivity, linearity, dynamic range, precision and repeatability. Moreover, the use of PRM provides access to the full fragmentation spectra without any preanalytical considerations. The proficiency testing results confirm the suitability of PRM mode showing great quantification performances. In addition, those results and especially the repeatability exhibit the precision of the volume control provided by the use of HemaXis™ device. This tool enables the standardisation of the DBS collection at the fingertip in a non-hospital environment either by minimally-trained medical staff or by the patient himself. A rapid, sensitive, and robust method was developed and fully validated for the detection and quantification of PEth 16:0/18:1 in DBS samples. The results of the validation process and the proficiency testing confirm that the use of DBS associated with HRMS PRM-based analyses does not hinder the analytical performances, while providing full information over the MS-MS spectra. The development of analytical tools enabling the use of DBS microsampling that can be performed in almost every environment opens new opportunities toward clinical and forensic toxicological applications.

Revealing Unknown Controlled Substances and New Psychoactive Substances Using High-Resolution LC-MS-MS Machine Learning Models and the Hybrid Similarity Search Algorithm.

High-resolution liquid chromatography-tandem mass spectrometry (LC--MS-MS)-based machine learning models are constructed to address the analytical challenge of identifying unknown controlled substances and new psychoactive substances (NPSs). Using a training set composed of 770 LC-MS-MS barcode spectra (with binary entries 0 or 1) obtained generally by high-resolution mass spectrometers, three classification machine learning models were generated and evaluated. The three models are artificial neural network (ANN), support vector machine (SVM) and k-nearest neighbor (k-NN) models. In these models, controlled substances and NPSs were classified into 13 subgroups (benzylpiperazine, opiate, benzodiazepine, amphetamine, cocaine, methcathinone, classical cannabinoid, fentanyl, 2C series, indazole carbonyl compound, indole carbonyl compound, phencyclidine and others). Using 193 LC-MS-MS barcode spectra as an external test set, accuracy of the ANN, SVM and k-NN models were evaluated as 72.5%, 90.0% and 94.3%, respectively. Also, the hybrid similarity search (HSS) algorithm was evaluated to examine whether this algorithm can successfully identify unknown controlled substances and NPSs whose data are unavailable in the database. When only 24 representative LC-MS-MS spectra of controlled substances and NPSs were selectively included in the database, it was found that HSS can successfully identify compounds with high reliability. The machine learning models and HSS algorithms are incorporated into our home-coded artificial intelligence screener for narcotic drugs and psychotropic substances standalone software that is equipped with a graphic user interface. The use of this software allows unknown controlled substances and NPSs to be identified in a convenient manner.

Longibramides A-E, Peptaibols Isolated from a Mushroom Derived Fungus Trichoderma longibrachiatum Rifai DMG-3-1-1.

Five new peptaibols, longibramides A-E (1-5) with 11 amino acid residues, were isolated from a fungus Trichoderma longibrachiatum Rifai DMG-3-1-1, which was isolated from a mushroom Clitocybe nebularis (Batsch) P. Kumm collected from coniferous forest in the subboreal area of northeast China. The structures of longibramides A-E were determined by their spectroscopic data (NMR and MS-MS spectra), their absolute configurations were determined by X-ray diffractions and Marfey's analyses. The X-ray diffractions of longibramides A, B, and the similar CD spectra of A-E showed that they all had α-helix conformations. Longibramides B and E showed moderate cytotoxicities against BV2 and MCF-7 cells and also showed some inhibitory effects against methicillin-resistant Staphylococcus aureus MRSA T144. L-trans-Hyp was not commonly found in natural peptaibols, which was the 6th or 10th amino acid residue in longibramides C-E. The X-ray diffractions of longibramides A and B afforded the accuracy conformations of their secondary structures, which maybe help to interpret the structure-activity relationships of the family of peptaibols in the future.

Development and validation of a multi-residue analytical method for veterinarian and human pharmaceuticals in livestock urine and blood using UHPLC-QTOF

The aim of this work is to contribute to the assessment of multi-residue analysis of veterinarian and human pharmaceuticals using UHPLC-QTOF in livestock urine and blood (cattle, chicken, sheep and pig). Firstly, an in-house database including compound name, monoisotopic mass, chemical formula, retention time, chemical structure, and three CID MS-MS spectra of the 234 selected drugs were built for qualitative detection. Secondly, the method validation result showed that all the 234 drugs exhibited good linearity with determination coefficients (R2) higher than 0.999. Then, the distribution of the drugs recoveries, intra-day RSD and inter-day RSD results for all seven matrices were tested. Finally, after a carefully cross check, 150 veterinarian and human pharmaceuticals could meet the methodological requirements (recovery, 50–120%; intra-day RSD ≤ 15%, inter-day RSD ≤ 20%) in all seven matrices. Our results suggested that although the main applications of UHPLC-QTOF are directed towards detection and identification of the compounds, this method should be also applied for quantitative purposes.

Unique distribution of ellagitannins in ripe strawberry fruit revealed by mass spectrometry imaging

Ellagitannins (ETs) are hydrolysable tannins composed of a polyol core, primarily glucose, which is esterified with hexahydroxydiphenic acid (HHDP), and in some cases, gallic acid. ETs are the major phenolic compounds found in strawberries and may contribute to the health-related properties of strawberries, because of their strong antioxidative activity. However, their distribution in the strawberry fruit remains unclear. In this study, matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI–MSI) was used to visualize ETs in ripe strawberry fruits. Five peaks, corresponding to the m/z values of ET [M−H]− ions detected in the MALDI–MS spectrum of strawberry extracts, were identified as strictinin, pedunculagin, casuarictin, davuriicin M1, and an unknown ET using MALDI–tandem MS (MS/MS). In addition, liquid chromatography–electrospray ionization–MS/MS of the extracts revealed the presence of pedunculagin isomers and the unknown ET. Ion images of these five ETs were reconstructed using MALDI–MSI. Strictinin was widely distributed in and around the achene seed coats, while the other ETs were dispersed in and around the seed coats, and at the bottom of the receptacle; pedunculagin was distributed in the epidermis and pith, whereas casuarictin, the unknown ET, and davuriicin M1 were distributed in the pith. Moreover, MALDI–MSI of a casuarictin standard indicated that in-source fragmentation weakly affected the ion images. The results suggest that the distribution of ETs depends on the presence or absence of their constituents, namely galloyl units, HHDP, and bis-HHDP. To the best of my knowledge, this is the first report on the visualization of ETs in plant tissues using MSI, MALDI–MSI may be a useful tool for analyzing the distribution of ETs in the strawberry fruit.

Pseudoalteropeptide A, a novel lipopeptide from the marine bacterium Pseudoalteromonas piscicida SWA4_PA4 isolated from marine seaweed.

A new lipopeptide, pseudoalteropeptide A (1) was isolated from the marine bacterium Pseudoalteromonas piscicida SWA4_PA4. The structure was elucidated by spectroscopic analyses including NMR and MSMS spectra. It showed moderate iron chelating activity as well as cytotoxic activity against Jurkat human T lymphocyte cells. isolation/marine bacterium/natural product/structure elucidation.

Nontargeted Screening of Water Samples Using Data-Dependent Acquisition with Similar Partition Searching

A rapid screening method for the detection of nontargeted compounds in surface water samples was developed using MS-MS high-resolution mass spectrometry and data-dependent acquisition. The key parameters for the acquisition method were optimized using five model compounds with diverse chemical characteristics. The parameter selection required optimization between the total number of precursor ions that could be selected in an LC-MS run, the quality of each MS (full range) spectrum, and the quality of each MS-MS fragmentation spectrum. After the acquisition method was optimized, 18 surface water samples from rivers, reservoirs, and effluents from wastewater treatment plants were analyzed, generating 41625 MS-MS spectra in about 14 h. The raw data were then converted into two generic formats using the open-access program MSConvert. A combinatorial approach, similar partition searching (SPS), was then used to putatively identify analytes from the accurate mass of each analyte (adjusted for the adduct mass) and the corresponding MS-MS spectra were obtained. In this approach, the structures of about 250000 common compounds, stored in a large database as mathematical partitions of their exact mass, were compared directly to each MS-MS spectrum. Compounds with a similar mass and retention time were grouped together and labeled as "Analytes", using an Excel Add-In. The isotope ratio data from the MS spectrum, the corresponding MS-MS spectra, and the putative identifications were then imported into an Access relational database to facilitate sorting, searching, filtering, and querying the results. This allowed final inspection to assess confidence of the identifications made through the nontargeted screening.

Chlorpyrifos Oxon-Induced Isopeptide Bond Formation in Human Butyrylcholinesterase.

A newly recognized action of organophosphates (OP) is the ability to crosslink proteins through an isopeptide bond. The first step in the mechanism is covalent addition of the OP to the side chain of lysine. This activates OP-lysine for reaction with a nearby glutamic or aspartic acid to make a gamma glutamyl epsilon lysine bond. Crosslinked proteins are high molecular weight aggregates. Our goal was to identify the residues in the human butyrylcholinesterase (HuBChE) tetramer that were crosslinked following treatment with 1.5 mM chlorpyrifos oxon. High molecular weight bands were visualized on an SDS gel. Proteins in the gel bands were digested with trypsin, separated by liquid chromatography and analyzed in an Orbitrap mass spectrometer. MSMS files were searched for crosslinked peptides using the Batch-Tag program in Protein Prospector. MSMS spectra were manually evaluated for the presence of ions that supported the crosslinks. The crosslink between Lys544 in VLEMTGNIDEAEWEWK544AGFHR and Glu542 in VLEMTGNIDEAEWE542WK satisfied our criteria including that of spatial proximity. Distances between Lys544 and Glu542 were 7.4 and 9.5 Å, calculated from the cryo-EM (electron microscopy) structure of the HuBChE tetramer. Paraoxon ethyl, diazoxon, and dichlorvos had less pronounced effects as visualized on SDS gels. Our proof-of-principle study provides evidence that OP have the ability to crosslink proteins. If OP-induced protein crosslinking occurs in the brain, OP exposure could be responsible for some cases of neurodegenerative disease.

The Hydroxyproline Proteome of HeLa Cells with Emphasis on the Active Sites of Protein Disulfide Isomerases.

Hydroxyproline-containing proteins (other than collagens) are rare and difficult to identify. Only 14 such proteins have been found in the human proteome by biochemical methods despite the fact that the list includes examples of biological importance such as hypoxia-inducible factor and the 40S ribosomal protein S23 (RPS23), both of which have significant biological function of the post-translational modification. Comparison of multinotch search software Global-PTM-Discovery to conventional proteomic database search software gave a nine-fold improvement in correctly identifying non-collagen peptides containing hydroxyproline. Manual interpretation of MS-MS spectra refined this list to discover 36 unique peptides representing 24 unique hydroxyproline sites in 21 proteins, of which only Pro62 of RPS23 had been reported previously in UniProt. Eight of the sites were found to be conserved as prolines in nine species examined, ranging from humans to yeast. These include sites 51 and 395 in protein disulfide-isomerase (PDIA1) and sites 204 and 553 in protein disulfide-isomerase A4 (PDIA4). The apparent occupancy of these sites ranged from 72-89%, suggesting a structural and possibly functional role of these PTMs. Fifteen of the sites most likely contain 4R-hydroxyproline (Pro30 of serpin H1, Pro520 of aspartyl/asparaginyl β-hydroxylase, Pro223 of neutral α-glucosidase AB, Pro977 of hypoxia upregulated protein 1, Pro378 of protein ERGIC-53, Pro252 of protein CASC4, Pro545 of bromodomain-containing protein 2, Pro488 of bromodomain-containing protein 3, Pro130 of nucleolar RNA helicase 2, Pro51 of PDIA1, Pro395 of PDIA1, Pro404 of PDIA3, Pro89 of PDIA4, Pro204 of PDIA4, and Pro553 of PDIA4). The remaining sites could be either 4R-hydroxyproline or 3S-hydroxyproline. Recommendations are made to improve automated interpretation of proteomic data to improve future proteomic research whose goal is to mine more of the remaining dark matter of the proteome.

A High Throughput Three-step Ultra-performance Liquid Chromatography Tandem Mass Spectrometry Method to Study Metabolites of Atractylenolide-III.

Atractylodes macrocephala Koidz (AMK) is a traditional Chinese medicine widely used in the treatment of various diseases, especially spleen deficiency. As the principle active constituents of AMK, however, the metabolites of Atractylenolide-III (A-lactone-III) have not been identified in rats yet. In this study, a three-step high throughput method based on UHPLC-Q-TOF-MS-MS was developed to profile and characterize the metabolites of A-lactone-III in rat feces, urine and plasma. The initial step was a full-scan that utilized a multiple mass defect filter (MMDF) combined with dynamic background subtraction (DBS). PeakView®1.2 and Metabolitepilot™1.5 software was then used to obtain data and seek possible metabolites. Finally, MS-MS spectra of the parent drug and possible metabolites were compared by the fragment ion peaks and retention times, which enabled metabolites to be identified. As a result, 53 metabolites were characterized in rats in vivo. The metabolic pathways of A-lactone-III were identified as including methylation, oxidation, hydroxylation, dihydroxylation, hydrogenation, glycosylation, sulfonation, and glucuronide, cysteine and N-acetylcysteine conjugation.

Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks (Gasterosteus aculeatus)

A data-independent acquisition (DIA) assay library for quantitative analyses of proteome dynamics has been developed for gills of threespine sticklebacks (Gasterosteus aculeatus). A raw spectral library was generated by data-dependent acquisition (DDA) and annotation of tryptic peptides to MSMS spectra and protein database identifiers. The assay library was constructed from the raw spectral library by removal of low-quality, ambiguous, and low-signal peptides. Only unique proteins represented by at least two peptides are included in the assay library, which consists of 1506 proteins, 5074 peptides, 5104 precursors, and 25,322 transitions. This assay library was used with DIA data to identify biochemical differences in gill proteomes of four populations representing different eco- and morpho-types of threespine sticklebacks. The assay library revealed unique and reproducible proteome signatures. Warm-adapted, low-plated, brackish-water fish from Laguna de la Bocana del Rosario (Mexico) show elevated HSP47, extracellular matrix, and innate immunity proteins whereas several immunoglobulins, interferon-induced proteins, ubiquitins, proteolytic enzymes, and nucleic acid remodeling proteins are reduced. Fully-plated, brackish-water fish from Westchester Lagoon (Alaska) display elevated ion regulation, GTPase signaling, and contractile cytoskeleton proteins, altered abundances of many ribosomal, calcium signaling and immunity proteins, and depleted transcriptional regulators and metabolic enzymes. Low-plated freshwater fish from Lake Solano (California) have elevated inflammasomes and proteolytic proteins whereas several iron containing and ion regulatory proteins are reduced. Gills of fully-plated, marine fish from Bodega Harbor (California) have elevated oxidative metabolism enzymes and reduced transglutaminase 2, collagens, and clathrin heavy chains. These distinct proteome signatures represent targets for testing ecological and evolutionary influences on molecular mechanisms of gill function in threespine sticklebacks. Furthermore, the gill assay library represents a model for other tissues and paves the way for accurate and reproducible network analyses of environmental context-dependent proteome dynamics in complex organisms.

Refining Transcriptome Gene Catalogs by MS-Validation of Expressed Proteins.

Protein sequence identification by tandem mass spectroscopy (LC-MS/MS) identifies thousands of protein sequences even in complex mixtures, and provides valuable insight into the biological functions of different cells. For non-model organisms, transcriptomes are generally used to allow peptide identification, an important addition to their use as a gene catalog allowing the potential metabolic activities of cells to be determined. We used LC-MS/MS data to identify which of the six possible reading frames in the transcriptome was actually used by the cell to make protein, and asked whether this would have an impact on downstream analyses using the dataset. We combined results from several LC-MS/MS experiments designed to identify peptide sequences in extracts from the dinoflagellate Lingulodinium polyedra using a 74 655-sequence transcriptome. We compiled a list of 6628 translated nucleic acid sequences that contained the ensemble of peptide matches (termed MS-validated sequences) and assessed the similarity in downstream analyses between this data set and the 6628 nucleic acid sequences from which they were derived. When compared with BLASTx analyses of the DNA sequences, the MS-validated protein-sequences-analyzed using BLASTp showed differences in gene ontology, had more identified BLAST hits, and contained more KEGG pathway enzymes. The MS-validated protein sequences also differ from datasets containing longest open reading frame (ORF) protein sequences. We also note a poor correlation between the levels of protein and mRNA abundance, a comparison not previously performed for dinoflagellates. The differences observed between analyses of MS-validated protein sequence and nucleic acid sequence datasets suggest use of the former may provide a more accurate representation of cellular capacity than the latter. Developing MS-validated protein sequence datasets may also speed interpretation of MS-MS spectra in bottom up proteomics experiments.

Structure determination of disease associated peak AAA from l-Tryptophan implicated in the eosinophilia-myalgia syndrome

The eosinophilia-myalgia syndrome (EMS) outbreak of 1989 that occurred in the USA and elsewhere was caused by the ingestion of l-Tryptophan (L-Trp) solely manufactured by the Japanese company Showa Denko K.K. (SD). Six compounds present in the SD L-Trp were reported to be case-associated contaminants. However, “one” of these compounds, Peak AAA has remained structurally uncharacterized, despite the fact that it was described as “the only statistically significant (p=0.0014) contaminant”. Here, we employ on-line microcapillary-high performance liquid chromatography-electrospray ionization mass spectrometry (LC–MS), and tandem mass spectrometry (MS/MS) to determine that Peak AAA is in fact two structurally related isomers. Peak AAA1 and Peak AAA2 differed in LC retention times, and were determined by accurate mass-LC–MS to both have a protonated molecular ion (MH+) of mass 343.239Da (Da), corresponding to a molecular formula of C21H30N2O2, and possessing eight degrees of unsaturation (DoU) for the non-protonated molecule. By comparing the LC–MS and LC–MS-MS retention times and spectra with authentic synthetic standards, Peak AAA1 was identified as the intermolecular condensation product of L-Trp with anteiso 7-methylnonanoic acid, to afford (S)-2-amino-3-(2-((S,E)-7-methylnon-1-en-1-yl)-1H-indol-3-yl)propanoic acid. Peak AAA2 was determined to be a condensation product of L-Trp with decanoic acid, which produced (S)-2-amino-3-(2-((E)-dec-1-en-1-yl)-1H-indol-3-yl)propanoic acid.

Peptidomic analysis of the venom of the solitary bee Xylocopa appendiculata circumvolans

BackgroundAmong the hymenopteran insect venoms, those from social wasps and bees – such as honeybee, hornets and paper wasps – have been well documented. Their venoms are composed of a number of peptides and proteins and used for defending their nests and themselves from predators. In contrast, the venoms of solitary wasps and bees have not been the object of further research. In case of solitary bees, only major peptide components in a few venoms have been addressed. Therefore, the aim of the present study was to explore the peptide component profile of the venom from the solitary bee Xylocopa appendiculata circumvolans by peptidomic analysis with using LC-MS.MethodsA reverse-phase HPLC connected to ESI-OrbiTrap MS was used for LC-MS. On-line mass fingerprinting was made from TIC, and data-dependent tandem mass spectrometry gave MSMS spectra. A major peptide component was isolated by reverse-phase HPLC by conventional way, and its sequence was determined by Edman degradation, which was finally corroborated by solid phase synthesis. Using the synthetic specimen, biological activities (antimicrobial activity, mast cell devaluation, hemolysis, leishmanicidal activity) and pore formation in artificial lipid bilayer were evaluated.ResultsOn-line mass fingerprinting revealed that the crude venom contained 124 components. MS/MS analysis gave 75 full sequences of the peptide components. Most of these are related to the major and novel peptide, xylopin. Its sequence, GFVALLKKLPLILKHLH-NH2, has characteristic features of linear cationic α-helical peptides; rich in hydrophobic and basic amino acids with no disulfide bond, and accordingly, it can be predicted to adopt an amphipathic α-helix secondary structure. In biological evaluation, xylopin exhibited broad-spectrum antimicrobial activity, and moderate mast cell degranulation and leishmanicidal activities, but showed virtually no hemolytic activity. Additionally, the peptide was able to incorporate pores in artificial lipid bilayers of azolectin, confirming the mechanism of the cytolytic activity by pore formation in biological membranes.ConclusionsLC-ESI-MS and MS/MS analysis of the crude venom extract from a solitary bee Xylocopa appendiculata circumvolans revealed that the component profile of this venom mostly consisted of small peptides. The major peptide components, xylopin and xylopinin, were purified and characterized in a conventional manner. Their chemical and biological characteristics, belonging to linear cationic α-helical peptides, are similar to the known solitary bee venom peptides, melectin and osmin. Pore formation in artificial lipid bilayers was demonstrated for the first time with a solitary bee peptide.

Anti-inflammatory and anticancer effects of flavonol glycosides from Diplotaxis harra through GSK3β regulation in intestinal cells

Context and objective: Diplotaxis harra (Forssk.) Boiss. (Brassicaceae) is traditionally used as an antidiabetic, anti-inflammatory or anticancer agent. In these pathologies, the glycogen synthase kinase 3 β (GSK3β) is overactivated and represents an interesting therapeutic target. Several flavonoids can inhibit GSK3β and the purpose of this study was to search for the compounds in Diplotaxis harra which are able to modulate GSK3β.Materials and methods: Methanol extracts from D. harra flowers were prepared and the bio-guided fractionation of their active compounds was performed using inflammatory [protease-activated receptor 2 (PAR2)-stimulated IEC6 cells] and cancer (human Caco-2 cell line) intestinal cells. 50–100 μg/mL of fractions or compounds purified by HPLC were incubated with cells whose inhibited form of GSK3β (Pser9 GSK3β) and survival were analyzed by Western blot at 1 h and colorimetric assay at 24 h, respectively. LC-UV-MS profiles and MS-MS spectra were used for the characterization of extracts and flavonoids-enriched fractions, and the identification of pure flavonoids was achieved by MS and NMR analysis.Results: The methanol extract from D. harra flowers and its flavonoid-enriched fraction inhibit GSK3β in PAR2-stimulated IEC6 cells. GSK3β inhibition by the flavonoid-enriched D. harra fraction was dependent on PKC activation. The flavonoid-enriched D. harra fraction and its purified compound isorhamnetin-3,7-di-O-glucoside induced a 20% decrease of PAR2-stimulated IEC6 and Caco-2 cell survival. Importantly, normal cells (non-stimulated IEC6 cells) were spared by these treatments.Conclusion: This work indicates that flavonoids from D. harra display cytotoxic activity against inflammatory and cancer intestinal cells which could depend on GSK3β inhibition.