dataesr/scientific-paragraphs-categorization huggingface dataset:
Data were acquired in data-dependent mode on a Thermo Scientific TM Orbitrap Fusion Lumos TM mass spectrometer operated at a resolution of 120, 000 to 500, 000 (FWHM at m/z 200). Analysis of phosphatidylglycerol and cardiolipin molecular species showed that ultra-high resolution is a prerequisite for successful baseline separation of deuterium and 13C isotopes and therefore for accurate analysis of labeled lipid species. These results highlight the potential of ultra-high resolution MS and stable isotope labelling in establishing a more comprehensive view of lipid metabolism in vivo. The metabolic network of an organism gathers all the biochemical reactions that can occur in this organism, regardless of the conditions. In order to visualize those networks we introduce MetExploreViz, a free and open source javascript library which can easily be embedded into a webpage.
g. H20, H+. ) in order to reduce the amount of edges in the network and facilitate the visualization. Cellular compartments can be highlighted using color schemes, and a contextual menu allows displaying information from MetExplore database on compounds or reactions. MetExploreViz also enables users to save their network drawings and sessions in order to resume their work. Finally, publication ready images can be exported in various formats (jpeg, png or svg). MetExploreViz will be integrated in the e-infrastructure developed in the framework of PhenoMeNal project (EC-654241). Programme * Intervenant Géochimie / pétroéolomique / astrochimie [P156] Interactions intra-et inter-moléculaires [P157-P164] Affinity capillary electrophoresis hyphenated to mass spectrometry to study synthetic sulfated peptides and their non-covalent interactions with the chemokine SDF-1 [P157] Maud Fumex * 1 , Denis Servent , Gilles Mourier , Régis Daniel 1 , Florence Gonnet † 1 Sulfation is one of the most important post-translational modifications of proteins.
The data from sample extracts was compared to reagent blank extracts to determine the differences and potential extractables. The potential candidate markers were screened against a known library of extractables and leachables compounds which was automatically interrogated using mass accuracy, isotopic fit and fragment matching. The structural elucidation of unknown contaminants present was performed by using elemental composition, database searching and fragment identification via in-silico fragmentation of a downloaded structure compared to accurate mass fragment ion data. This application demonstrates how non-targeted screening using LC and GC workflows can be adopted on a single MS and software platform for extractable and leachable testing in food, cosmetics and pharmaceutical packaging applications.
Concerning the haematological parameters, an increase of the hematocrit was observed for all three horses but no significant results were obtained for the circulating reticulocytes. The rHuEPO concentration was measured by ELISA and was detected up to 31 days after Mircera R administration. NMR and LC-HRMS datasets were analyzed by Orthogonal Partial Least Squares (OPLS). Various models were obtained for the different biological matrices (i. e. plasma and urine) allowing a discrimination between samples collected before and after Mircera R administration up to 74 days. The results obtained by metabolomics are promising compared to the direct detection of the rHuEPO. However further studies are needed to validate the models obtained. Furthermore structure identification of some interesting ions could possibly indicate some candidate biomarkers.
The young rats were kept under standard conditions and sacrificed 30 days after the weaning and blood samples were harvested. Using LC-MS and statistical tools, we aimed to determine the effects of KI by confronting the metabolite composition of blood between KI and control groups. Using an in-house databank, we identified 67 metabolites that can be mapped in regulation pathways. Our findings suggest that many pathways -such as aminoacids, energy or lipid metabolisms -are impacted by the KI treatment. Moreover the L-tyrosine and L-Glutamine seem to be at the crossroad of regulation. Further metabolites identification will provide insight into the biological regulation impacted at middle term after birth by KI administration during the foetal period. Le développement des follicules antraux comprend des étapes essentielles d'un point de vue dynamique et fonctionnel, comprenant la croissance, la sélection et la différentiation au support final, la maturation de l'ovocyte et l'ovulation.
Depending on the total rat weight, the IONPs dose was adjusted at 10 mg/kg body weight. Liver, lung and brain proteins were extracted using the FASP (Filter Aided Sample Preparation) method combined with a Lys-C/Trypsin protease mix digestion before labelling the resulting peptides with iTRAQ 4-plex reagents for liver, lung and brain. Afterwards, the labelled peptides were fractionated in two dimensions, by OFFGEL and Reverse Phase nanoHPLC, before MALDI-TOF/TOF mass spectrometry analysis. MS and MS/MS data were analysed using ProteinPilotTM Software and quantitation was validated by the R package IsobarPTM. This proteomic approach led to the identification and quantitation of 1542 proteins in Brain and Lung, and 1124 proteins in Liver. Several proteins were dysregulated comparing treated samples to controls, in particular, proteins involved in the pathways of lipid and carbohydrate metabolism, immune system stimulation and inflammation process, response to oxidative stress, angiogenesis, and pathways related to neurodegenerative diseases.
7±0. 7 µg/kg) was injected to 10 young men (22±2 years) with a regular sport activity (between 5 to 10h/week). Urine and blood were collected at days -60, -53, -39, -18 and 0 before administration and at days  2, 4, 7, 10, 17, 24, 31, 45, 56  after administration. Haematological parameters and total EPO concentration were monitored meanwhile urine samples were analyzed by untargeted LC-HRMS metabolomics. After a simple sample preparation, urine metabolic fingerprints were recorded by LCHRMS in positive and negative modes. Raw data was preprocessed with XCMS package and multivariate statistical methods were conducted by Orthogonal Partial Least Squares (OPLS). The aim was to develop models allowing sample discrimination between before and after Mircera R administration and to find out interesting candidate biomarkers.
Human haematological parameters showed significant variations with an increase of the reticulocytes percentage (%ret) and a decrease of the OFF-score with a peak at day 10 after administration. Total EPO concentrations (endogenous and exogenous) were measured by ELISA and were detected superior to endogenous levels up to 17 days after Mircera R administration. OPLS models were constructed by combining ESI positive and negative LC-HRMS datasets. The models obtained allowed discrimination between samples collected before and after Mircera R administration up to 56 days. Background: Nonalcoholic Fatty Liver Disease (NAFLD) encompass a wide spectrum of lesions including steatosis (nonalcoholic fatty liver, NAFL), steatohepatitis (NASH), fibrosis/cirrhosis, that may progress to cancer. Detailed mechanisms underlying disease progression remain poorly understood; in particular the potential relationship between in situ lipotoxicity and disease patterns.
The cohort was composed of 160 patients and control samples. Moreover, samples were collected just before and after haemodialysis, to evaluate potential metabolome variations due to the latter. Each sample and quality control (QC) was analysed by RPLC and HILIC coupled to QTOF-MS in negative and positive ESI mode. Low-level data fusion was carried out using multiblock approaches to combine signals from the different data blocks, evaluate the complementary of the techniques and eliminate redundant information. Data fusion strategies were investigated based on (i) unambiguous metabolite identification based on authentic chemical standard analysis of more than 600 metabolites (in house database) and (ii) automatic annotation without standard using chemical classes and biochemical pathways (public databases).
Cellular FN was among the major ECM glycoproteins produced by CAFs and TIFs. Other matrix glycoproteins include transforming growth factor-ß-induced (TGFBI), Emilin-1 and Tenascin C (TNC). Both matrisomes contained a similar set of core matrix components and matrisomeassociated proteins with comparable relative abundance. Conclusions This dataset of ECM components present in the stroma of HNSCC provides valuable insights into the adhesion-dependent events that take place in the microenvironment of these tumours. The ECM of human TIFs and CAFs display a similar composition, thus TIF-derived ECM can be utilized for functional studies, including ECM-tumour cell interactions and interactions between the ECM immune cells. Mots-Clés : Matrisome, HNSCC, FN, tandem MS/MS, Label, free Background: Environmental exposure to allergens plays an important role in the exacerbation of allergic diseases such as asthma.
Peptide mapping was performed with Mascot and the in-house-developed software Proline, allowing raw MS signal extraction of identified neo N-terminal peptides across samples treated with different allergens. Results: We found that all allergen proteases analyzed (9 distinct allergens, including fungi, house dust mite, cockroach and pollens) cleave IL-33 in the central "sensor" domain and generate mature forms containing the C-terminal IL-1 cytokine domain. Some of these forms can also be produced by inflammatory proteases from mast cells and neutrophils, while others are uniquely generated by allergen proteases. Maturated forms were shown to be potent inducers of type-2 innate immune responses in vivo.
Label-free quantification of T-cell proteome in nephrotic syndrome [P206] Cérina Chhuon * 1 , Guerrera Chiara CMIP is overexpressed in lymphocytes of idiopathic nephrotic syndrome (INS) patients. To dissect its role in INS pathogenesis, we generated a transgenic mouse overexpressing CMIP in peripheral mature T-cells. We aimed to evaluate the impact of CMIP on T-cell proteome in basal and stimulating conditions. T-cells from transgenic (Tg) and control (Wt) mice (n=3) were purified by negative immunoselection, and subjected to anti-CD3/anti-CD28 stimulation. At 0 and 60min post-activation, total proteins were extracted, digested, and peptides analyzed by nano-RSLC Q-Exactive-Plus MS. Protein quantification was performed by label-free using MaxQuant and Perseus softwares on three parallel technical replicates per sample.
The untargeted analysis was performed with Full scan data processed with Progenesis thanks to a new dynamic steroids database based on retention time compound annotation. Retention time are predicted for any gradient conditions at fixed temperature, stationary phase and mobile phase type using linear solvent strength theory (LSS) parameters. The database facilitates level 2+ and 2 annotations, obtained by recalculating retention times from experimental data and by predicting LSS parameters using a QSRR model, respectively. SIM data were processed with the Quan Browser software from Thermo and quantified using the isotope dilution quantification method. The Q-Exactive allows enhanced selectivity of ions through the SIM mode while the Orbitrap detector displays high resolution mass spectra, leading to stronger identification and more accurate quantification.
In this context, the aim of our study presented in this poster is to develop an untargeted lipidomic approach by using supercritical fluid chromatography high resolution mass spectrometry to be able to propose a relative quantification of main lipids class in various biological sample. To develop the method, the optimization of the separation and the detection of lipid species were performed on pure standards and then on liver lipid extract from 12-weeks-old C57BL6/J mice exposed to a control or an HFD (60% lipids in the diet) during 14 weeks. These analyses allowed the building of a homemade lipid data bank. An automatic process was then developed to produce the relative quantification of lipids species belonging to the 6 main class of lipids. The optimization of this method will be present with the first results obtained on liver disease model.
The objective of the present study was to evaluate modifications in serum composition in animals infected by E. ruminantium and define new diagnostic biomarkers. For this, sera from goats experimentally infected by intravenous injection of E. ruminantium cultured in bovine aortic endothelial cells in vitro were sampled. Sera at Day 0 and Day 14 post-infection (occurrence of clinical signs) were pre-fractionated by SDS-PAGE and analysed by shotgun next-generation proteomics by means of high-throughput analysis of peptides with a Q-Exactive HF mass spectrometer incorporating an ultra-high-field Orbitrap analyzer. Preliminary data obtained against the Capra hircus and Ehrlichia ruminantium theoretical molecular databases evidenced 6 and 2 proteins of interest for which abundances were increased or decreased, respectively, at Day 14.
Cela semble indiquer une redondance d'information, le mode positif ayant une plus grande richesse d'information. Une première analyse statistique par ACP présente une classification des échantillons en fonction du niveau d'inhibition par le phénol. Ensuite, une sparse PCA (package mixOmics) a permis de ne sélectionner que les variables les plus influentes sur chaque axe de l'ACP afin d'affiner la discrimination entre les groupes d'échantillons. La même classification est obtenue avec seulement 200 et 100 variables au lieu de 1033 initialement. Trois groupes d'échantillons se distinguent de façon plus nette en cohérence avec les niveaux d'inhibitions mesurés par les indicateurs de performance. L'objectif suivant sera d'assigner les molécules associées à cette classification afin d'identifier les voies métaboliques les plus sensibles à une inhibition par le phénol.
Many of the identified proteins are connected to basic cell functions but some are related to the temperature adaptation. Among the thermoregulated proteins, some are particularly overexpressed at 37•C, the temperature at which L. monocytogenes is virulent, and others at low-temperature condition, as those prevailing in food workshops. These comparisons of protein expression throughout several conditions (temperatures, mode/phase of growth) will enrich databases and help to model regulatory circuitry that drives adaptation of L. monocytogenes to environments. MALDI-TOF IMS is a surface-sampling technology that can determine spatial information and relative abundance of analytes directly from biological samples. IMS has broad applications in clinical and pharmaceutical research, food science and microbiology.
C. Virgiliou, I. Sampsonidis, H. G. Gika, N, Raikos, G. A. Theodoridis, Development and validation of a HILIC-MS/MS multitargeted method for metabolomics applications, Electrophoresis 36 (2015) 2215-2225. (2) A. Periat, I. S. Krull, D. Guillarme, Applications of hydrophilic interaction chromatography to amino acids, peptides, and proteins, Review Article, J. Sep. Sci. 38 (2015) 357-367. Mots-Clés : Metabolomics, LC, HRMS, RPLC, HILIC, Database * Intervenant † Auteur correspondant: Serge. Rudaz@unige. ch An in-solution digestion method to improve Proteome coverage from small samples of Extracellular Matrix and Membrane extracts [P27] Haddad Iman * † 1 , Anne Joutel 2,3 , Joelle Vinh 1 Spectrométrie de Masse Biologique et Protéomique (SMBP) -CNRS : USR3149, ESPCI Paris, PSL Research University : USR3149 -10 rue vauquelin 75005 Paris, France 2 Genetics and Pathogenesis of Cerebrovascular Diseases (UMR 1161 INSERM) -Université Paris Diderot -Paris 7 -10 avenue de Verdun 75010 Paris, France 3 Hôpital Lariboisière (APHP) -DHU NeuroVasc Sorbonne -10 avenue de Verdun; 75010 Paris, France.
Using the generated datasets, extraction and integration performed by four programs, Spectronaut (Reiter et al. , 2011), PeakView (Gillet et al. , 2012), Skyline (MacLean et al. , 2010) and DIA-Umpire (Tsou et al. , 2015), were evaluated, regarding key parameters: extraction window width, XIC width, transition number and FDR threshold.
Ce travail a bénéficié d'une aide de l'Agence Nationale de la Recherche au titre du programme Investissement d'avenir portant la référence ANR-15-CE21-0016. Mots-Clés : Lipides, Identification, micro, organismes, MALDI, TOF * Intervenant † Auteur correspondant: Morgane. Barthelemy@cnrs. fr Caractérisation des protéines du système BAC impliqué dans la formation de biofilms et la production de rhamnolipides chez Pseudomonas aeruginosa [P248] Brahim Saffiedine * 1 , Mohamed Amine Ben Mlouka , Rémy Agniel , Julie Hardouin , Emmanuelle Dé , Patrick Di Martino , Thierry Jouenne , Pascal Cosette 1 Polymères Biopolymères Surfaces -Plateforme PISSARO (PBS) -Universté de Rouen, CNRS : UMR6270, CURIB -25 rue Lucien Tesnières, 76130 Mont Saint Aignan, France.
1,2, Maud Heuillet 3 , Jean-Charles Portais2,4, Guy Lippens 5 1 Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) -INSA -135 Avenue de rangueil 31077 Toulouse cedex 04, France 2 Metatoul -MetaboHUB -INRA : UMR792, CNRS : UMR5504, INSA -National Infrastructure of Metabolomics & Fluxomics (ANR-11-INBS-0010), France 3 Plateforme MetaToul Réseaux Métaboliques, LISBP -INSA Toulouse -135 avenue de Rangueil 31077 Toulouse cedex 04, France 4 Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) -INSA, CNRS : UMR5504, INRA : UMR0792 -135 Avenue de Rangueil 31077 Toulouse cedex 04, France 5 LISBP -CNRS : UMR5504, INRA : UMR792, INSA -135 Avenue de Rangueil 31077 Toulouse Cedex 4, France.
MetaToul-MetaboHUB, National Infrastructure of Metabolomics & Fluxomics (ANR-11-INBS-0010) 2 Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) -INSA, CNRS : UMR5504, INRA : UMR0792 -135 Avenue de rangueil, 31077 Toulouse cedex 04, France.
Acknowledgements This study has been financially supported by the  EU  through the  FP7  project  SOLUTIONS  ( 603437 ), and by the  Generalitat de Catalunya  (Consolidated Research Groups "2014  SGR 418-Water and Soil Quality Unit"  and  2014 SGR 291-ICRA ). Bécard, Guillaume, 411, 417 Baillet, Valentin, 174  Bailly, Karine, Ludovic ,  176 ,  182 ,  265 ,  349 ,  360   Bakhos, David, 344 Bakiri, Ali, 113 Bal dit Sollier, Claire, 351 Balabaud, Charles, 108 Balliau, Thierry, 301 Balvay, Daniel, 196 Banliat, Charles, 201, 404 Barakat, Fatima, 415 Barbier Saint Hilaire, Pierre, 229 Barcelo, Damia, 34 Bardet, Chloé, 387 Barham, Siamak, 107 Barnes, Loïc, 82 Barraud, Nicolas, 127 Barthélemy, Morgane, 418, 419 Bartolo, François, 133 Bascaules Bedin, Adeline, 305, Adeline, 417 Bassignani, Ariane, 429 Bastide, Bruno, 126 Batailler, Brigitte, 310 Batailler, Martine, 201 Bathany, Katell, 383 Batzenschlager, Morgane, 369 Baudelet, Emilie, 327, 366 Boberieth, Lise, 177 Bocca, Cinzia, 403 Boccard, Julien ,  48 ,  63 ,  153 ,  365 ,  395  Bodard, Sylvie,  355 ,  359   Bogliotti, Nicolas, 275 Bohl, Jan, 237, 326 Boireau, Wilfrid, 105 Bol, Vanesa, 203 Bolbach, Gérard, 263 Bolbach, Gerard, 215 Bomgarden, Ryan, 323 Bonnaire, Yves ,  176 ,  182 ,  265 ,  349 ,  360   Bonneau, Michel, 351 Bonnefille, Bénilde, 71, 208 Bonnefoy, Christelle, 186, 187 Bonneil, Eric, 384 Bonnel, David, 204 Bonnet, Antoine, 222 Bonnet, Muriel, 364 Bonneu, Marc, 205, 383 Bons, Joanna, 188 Bonvallot, Nathalie, 70 Bookhari, Abbes, 303 Boquien, Clair-Yves, 51 Bordes, Claire, 186, 187 Bormans, Myriam, 212 Botzanowski, Thomas, 232 Bou Nader, Charles, 234 Bou Saleh, Mohamed, 376 Boualem, Adnane, 102 Bouatrous, Yamina, 158 Boubakri, Hasna, 95 Boubred, Farid, 131 Bouchemal, Nadia, 285, 363 Bouchereau, Alain, 98 Bouchonnet, Stéphane, 72, 163, 242 Bouclon, Julien, 274 Boudah, Samia, 155 Boudra, Hamid, 87, 224 Bouffartigues, Emeline, 413 Boulanger, Pascale, 80 Boulanger, Renaud, 162 Boulay, Mylène, 423 Boulet, Jean-Claude, 296, 335 Bouloc, Philippe, 111 Boumaza, Houda, 92 Bourcier, Sophie ,  72 ,  163 , 242 Bourgain, Catherine, 33  Bourgoin-Voillard , Sandrine, 78, 173, 249, 379  Bournais, Sylvain, 96 Bousbata, Sabrina, 295 Bousset, Luc, 239 Boustie, Joël, 220 Boutinaud, Philippe, 196 Bouyssié, David, 189, 191 Bouyssiere, Brice, 116 Boychenko, Oleksandr, 257 Boyen, Catherine, 156 Brachi, Benjamin, Marion, Sophie, 77 Hériter, Lauirent, 221 Haberger, Markus, 55 Haddad, Mohamed, 415 Hadjadj Aoul, Seghir, 294 Hahm, H.
The complete genome of ATCC8739 was downloaded from GenBank and de novo annotated using high resolution LC-MS/MS data dependent acquisition. The 6 frame translation of the genome was used as a pseudo-protein database. Peptides were identified using MS-GF+ and ORFs were inferred by expanding the identified peptide sequences. Possible protein m/z were calculated according to gene sequences, potential posttranslational modifications and charges. Mass candidates were filtrated according to the protein production observed by LC-MS/MS and eventually matched with peaks from MALDI-TOF spectra. Evidences of few expressed genes were found by LC-MS/MS in supposedly non-coding regions, mainly for small proteins having masses lower than 10 kDa. However, the main benefit was the limitation of protein candidates.
Ainsi, l'identification de bactéries/levures pathogènes se fait de manière routinière par comparaison des empreintes spectrales MALDI-TOF de l'extrait protéique de la souche analysée avec des bases de données  (1). Depuis peu, des études s'intéressent également au développement de bases de données couvrant les champignons filamenteux mais celles-ci se focalisent sur l'analyse d'isolats cliniques (pathogènes humains ou souches environnementales opportunistes)  (2). A ce jour, très peu d'études utilisent cette technique pour l'identification de souches environnementale (phytopathogènes, micro-organismes mutualiste, endophytes. ) et aucune base de données commerciale n'est disponible pour ce type de microorganisme. Dans le cadre d'un projet portant sur l'étude d'endophytes isolés de huit spécimens de palmier de l'espèce Astrocaryum sciophilum, les spectres MALDI-TOF de 197 endophytes ont été générés selon le protocole standardisé en clinique : extraction des protéines (CH3CN/H2O/HCOOH : 50/15/35) puis analyse MALDI-TOF (matrice α-CHCA à 10 mg/ml, H2O/CH3CN/CF3COOH : 47,5/50/2,5).
Ces résultats ont été mis en parallèle avec les résultats de séquençage Sanger d'ADN sur les régions ITS, 16S et/ou 28S permettant ainsi d'identifier génétiquement les micro-organismes. Les premières analyses confirment bien la présence sur les spectres de biomarqueurs caractéristiques permettant d'identifier les souches au rang de l'espèce. Avec ce travail, une base de données MALDI TOF sur les souches environnementales est en cours de construction et facilitera les futures identifications de micro-organisme au laboratoire. (1)  Rahi, P. et al. Frontiers in Microbiology. 7, 1359 (2016). The human body is colonized by a vast number of microbes, collectively referred to as the human microbiota. The link between these microbes and our health is the focus of a growing number of research initiatives.
However, the application of gut metaproteomics has largely been limited due to the low efficiency of protein identification. PAPPSO platform works since a long time with complex samples in the Metaproteomic field with sensitive mass spectrometers. Metaproteomic samples are extremely complex which makes the mass spectrometry analysis more difficult than with others samples. In the national research agency (ANR) "ProteoCardis" 250 patients subjects, generating 250 cytosolic fractions and as many envelope-enriched fractions are analyzed with Orbitrap Fusion TM Lumos TM Tribrid TM. Proteins are identified using the specific metagenome of each patient or MetaHIT databases (3,3 or 9. 9 millions entries), using X!TandemPipeline, a software developed by the PAPPSO platform and designed to perform protein inference and manage the redundancy of peptides identifications.