{"id":249,"date":"2022-10-21T11:54:53","date_gmt":"2022-10-21T09:54:53","guid":{"rendered":"http:\/\/proteome.u-bordeaux.fr\/?page_id=249"},"modified":"2026-01-19T08:04:06","modified_gmt":"2026-01-19T07:04:06","slug":"modalite-dacces","status":"publish","type":"page","link":"https:\/\/proteome.u-bordeaux.fr\/en\/modalite-dacces\/","title":{"rendered":"Modalit\u00e9 de prestation"},"content":{"rendered":"<h1 class=\"wp-block-heading justification_texte has-medium-font-size\"><\/h1>\n\n\n\n<h1 class=\"wp-block-heading justification_texte has-small-font-size\" style=\"font-style:normal;font-weight:300\"><a href=\"#Processus-analyse\">Analysis pipeline<\/a><\/h1>\n\n\n\n<h1 class=\"wp-block-heading justification_texte has-small-font-size\" style=\"font-style:normal;font-weight:300\"><a data-type=\"URL\" data-id=\"ancre\" href=\"#ancre-Prise-de-contact\">Contact<\/a><\/h1>\n\n\n\n<h1 class=\"wp-block-heading has-small-font-size\" style=\"font-style:normal;font-weight:300\"><a href=\"#Modalites\" data-type=\"internal\" data-id=\"#Modalites\">Prestation<\/a><\/h1>\n\n\n\n<h1 class=\"wp-block-heading has-small-font-size\" style=\"font-style:normal;font-weight:300\"><a href=\"#Reception\" data-type=\"internal\" data-id=\"#Reception\">Receipt of samples<\/a><\/h1>\n\n\n\n<h1 class=\"wp-block-heading has-small-font-size\" style=\"font-style:normal;font-weight:300\"><a href=\"#Realisation\" data-type=\"internal\" data-id=\"#Realisation\">Realization of the service<\/a><\/h1>\n\n\n\n<h1 class=\"wp-block-heading has-small-font-size\" style=\"font-style:normal;font-weight:300\"><a href=\"#Rendu\" data-type=\"internal\" data-id=\"#Rendu\">Return of results<\/a><\/h1>\n\n\n\n<h1 class=\"wp-block-heading has-small-font-size\" style=\"font-style:normal;font-weight:300\"><a href=\"#Service\" data-type=\"internal\" data-id=\"#Service\">Service after delivery<\/a><\/h1>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<h2 class=\"wp-block-heading has-accent-color has-text-color has-medium-font-size\" id=\"Processus-analyse\">Analysis pipeline<\/h2>\n\n\n\n<figure class=\"wp-block-image size-large justification_texte\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" width=\"750\" height=\"404\" src=\"https:\/\/i0.wp.com\/proteome.u-bordeaux.fr\/wp-content\/uploads\/2023\/10\/pipeline_EN-1.jpg?resize=750%2C404&#038;ssl=1\" alt=\"\" class=\"wp-image-1441\" srcset=\"https:\/\/i0.wp.com\/proteome.u-bordeaux.fr\/wp-content\/uploads\/2023\/10\/pipeline_EN-1.jpg?resize=1024%2C551&amp;ssl=1 1024w, https:\/\/i0.wp.com\/proteome.u-bordeaux.fr\/wp-content\/uploads\/2023\/10\/pipeline_EN-1.jpg?resize=300%2C161&amp;ssl=1 300w, https:\/\/i0.wp.com\/proteome.u-bordeaux.fr\/wp-content\/uploads\/2023\/10\/pipeline_EN-1.jpg?resize=768%2C413&amp;ssl=1 768w, https:\/\/i0.wp.com\/proteome.u-bordeaux.fr\/wp-content\/uploads\/2023\/10\/pipeline_EN-1.jpg?resize=1536%2C826&amp;ssl=1 1536w, https:\/\/i0.wp.com\/proteome.u-bordeaux.fr\/wp-content\/uploads\/2023\/10\/pipeline_EN-1.jpg?resize=2048%2C1102&amp;ssl=1 2048w, https:\/\/i0.wp.com\/proteome.u-bordeaux.fr\/wp-content\/uploads\/2023\/10\/pipeline_EN-1.jpg?resize=18%2C10&amp;ssl=1 18w\" sizes=\"auto, (max-width: 750px) 100vw, 750px\" \/><figcaption class=\"wp-element-caption\">Bordeaux Proteome supports you in all stages of the project, from its design and, in the context of collaborative projects, to their development. The results are directly interpretable or may require the use of bioinformatics analysis tools, which, in this specific case, are not managed by the Platform.<\/figcaption><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<h2 class=\"wp-block-heading has-accent-color has-text-color has-medium-font-size\" id=\"Prise-de-contact\">Contact<\/h2>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">Before submitting samples, it is advisable to contact the Bordeaux Prot\u00e9ome Platform in order to establish an analysis strategy adapted to the context and to develop the experimental conditions (preparation and analysis).<\/p>\n\n\n\n<p class=\"has-text-align-justify justification_texte translation-block\">New projects must be submitted to Caroline Tokarski. Other requests can be made directly to your usual contacts. An analysis request form is available and must be completed in order to study the feasibility of the project. A preparatory meeting may be organized between the partners if necessary. The person in charge of the platform designates a \u201ccontact\u201d who will become the privileged interlocutor of the user. The user validates the analysis request (specifications, type of service, schedule, estimate, personnel involved).<\/p>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<h1 class=\"wp-block-heading justification_texte has-accent-color has-text-color has-medium-font-size\" id=\"Modalites\">Prestation<\/h1>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">The services are rendered either in the form of collaboration, or in the form of a research service:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li class=\"justification_texte\">In the case of a collaboration, the laboratory carrying out the scientific project assumes the operating costs. In this case, the platform personnel involved are co-owners of the results and co-author of any scientific publications resulting from the collaboration.<\/li>\n\n\n\n<li class=\"justification_texte\">In the case of a research service, the laboratory carrying out the scientific project assumes not only the operating costs but also the costs of expertise. In this case, the laboratory carrying out the project remains the exclusive owner of the results.<\/li>\n<\/ul>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">A definition of the strict framework of the service as well as an estimate will be established for each request made to Bordeaux Proteome.<\/p>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<h1 class=\"wp-block-heading has-accent-color has-text-color has-medium-font-size\" id=\"Reception\">Receipt of samples<\/h1>\n\n\n\n<p class=\"has-text-align-justify justification_texte translation-block\"><a href=\"https:\/\/proteome.u-bordeaux.fr\/en\/conseils\/\" target=\"_self\">Advices<\/a> and precautions around the preparation of samples are given for information on our site web. We strongly advise users to follow these few rules in order to place themselves in the optimal conditions for obtaining a relevant result.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li class=\"justification_texte\">Receipt of samples (solution, gel, strip\/spot) on site (during working hours) or by post (-20\u00b0C or dry ice for samples in solution, sending a piece of gel at room temperature in 1% acetic acid) .&nbsp;<\/li>\n\n\n\n<li class=\"justification_texte\">Immediate storage of samples at the appropriate temperature: -20\u00b0C or -80\u00b0C on request for samples in solution, 4\u00b0C for gels and spots\/strips).&nbsp;<\/li>\n\n\n\n<li class=\"justification_texte\">Monitoring of samples and records according to a precise nomenclature.<\/li>\n<\/ul>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">Bordeaux Proteome accepts to treat pieces of gels stained with silver nitrate. In this case, the PP cannot be held responsible in the event of failure of the analysis.<\/p>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">In the case of samples in solution, the user will avoid the presence in his samples of salts, glycerol, detergents or even polymers. Failing this, the user will indicate to Bordeaux Proteome the presence and concentration of these contaminants.<\/p>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">For mass spectrometry, the only containers accepted are tubes or microplates in uncoloured and untreated polypropylene. The user will ensure the tightness of his tubes or his plate.<\/p>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<h2 class=\"wp-block-heading has-accent-color has-text-color has-medium-font-size\" id=\"Realisation\">Description<\/h2>\n\n\n\n<figure id=\"justification_texte\" class=\"wp-block-table\"><table><thead><tr><th scope=\"col\">Prestations<\/th><th scope=\"col\">Details<\/th><\/tr><\/thead><tbody><tr><td>Sample Preparation<\/td><td>Carried out in line with the technological strategies chosen and in consultation with the project leader.<\/td><\/tr><tr><td>Protein Assay<\/td><td>Bradford test. A standard curve is established at each assay.<\/td><\/tr><tr><td>Electrophor\u00e8se<\/td><td>1D-PAGE with molecular weight markers.<\/td><\/tr><tr><td>Image analysis<\/td><td>Digitization of gels and analysis by densitometry. Gel images are sent in .jpeg format by default. Raw data is stored and sent on request.<\/td><\/tr><tr><td>Liquid vein electrophoresis<\/td><td>Rotofor, Offgel (pI) ; gel Free (MW)<\/td><\/tr><tr><td>Sample Preparation<\/td><td>Trypsin or endoprotease of your choice depending on the imperative or specificity of the project.<\/td><\/tr><tr><td>LC-MS\/MS analysis<\/td><td>L\u2019analyse repose sur un couplage nanoLC-ESI-MS\/MS utilisant un spectrom\u00e8tre de masse de type Orbitrap. La dur\u00e9e du gradient chromatographique est ajust\u00e9e en fonction de la complexit\u00e9 de l\u2019\u00e9chantillon. L\u2019acquisition des donn\u00e9es est r\u00e9alis\u00e9e en mode DDA (Data Dependent Acquisition) ou DIA (Data Independent Acquisition), conform\u00e9ment au cahier des charges initial. Les fichiers bruts sont trait\u00e9s avec le logiciel Proteome Discoverer, en interrogeant la banque de donn\u00e9es la plus appropri\u00e9e, d\u00e9finie en concertation avec le porteur de projet. L\u2019algorithme Sequest HT est utilis\u00e9 par d\u00e9faut pour l\u2019identification des peptides et des prot\u00e9ines. Sur demande, la plateforme peut \u00e9galement effectuer le traitement des donn\u00e9es \u00e0 l\u2019aide de l\u2019algorithme Chimerys.<\/td><\/tr><tr><td>Differential expression analysis<\/td><td>Quantitative analyzes conducted on an orbitrap-type mass spectrometer allowing optimal sensitivity and scan rates for the analysis of very complex samples. Data processing via Proteome Discoverer software for the identification and integration of quantitative data. Calculations of ratios and statistical tests established in agreement with the project leader. Raw data available. Reports submitted in excel format.<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<h1 class=\"wp-block-heading has-accent-color has-text-color has-medium-font-size\" id=\"Rendu\">Return of results<\/h1>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">Results will be sent electronically via email or ftp server. On request, the results can be communicated to the user on the medium of his choice. The files will be in *.zip, *.docx, *.xlsx or *.pptx format. The protein balance sheets are present in .xlsx format. The reports specifying the complete processing of the samples and the conclusions formulated by the personnel of the platform are sent in .docx format.<\/p>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">The platform staff remains at the entire disposal of the users to answer all the questions raised and to assist them in the stages of valorization of the results.<\/p>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">Bordeaux Proteome considers that, without a response within 10 days from the client, the file as accepted and closed.<\/p>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">Bordeaux Proteome undertakes not to disclose any information relating to the project other than the name of the user and the title of the project. On request, the title of the project can also be confidential.<\/p>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">Bordeaux Proteome only ensures the storage of samples for the duration of the performance of the service. The sample storage conditions are specified by the customer in the analysis request. Otherwise, the biological samples are stored at -20\u00b0C. The gels are systematically stored at 4\u00b0C. The customer can also specify if he wishes to collect the remaining samples. Otherwise, the samples will be disposed of through the biological waste disposal process.<\/p>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">Bordeaux Proteome only ensures the retention of raw data for the duration of the performance of the service. The customer, if he wishes to have the raw data, must specify it in the analysis request.<\/p>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<h1 class=\"wp-block-heading has-accent-color has-text-color has-medium-font-size\" id=\"Service\">Service after delivery<\/h1>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">Bordeaux Proteome offers project leaders the opportunity to organize a closing meeting to discuss results and project's prospects. The project leader can request this closing meeting from his contact and\/or the Platform manager.<\/p>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">Provided that the raw data is still available, Bordeaux Proteome may re-interrogate the raw data. Requests for re-questioning must be substantiated and addressed to the head of the structure directly.<\/p>\n\n\n\n<p class=\"has-text-align-justify justification_texte\">As part of the promotion of the results from Bordeaux Proteome, its staff undertakes to write the corresponding material and method and to help project leaders in the exploitation of the results.<\/p>\n\n\n\n<p>The plateform affilation must appear as:<\/p>\n\n\n\n<p><em>Univ. Bordeaux, CNRS, Bordeaux Proteome, UAR 2046, F-33076 Bordeaux, France<\/em><\/p>","protected":false},"excerpt":{"rendered":"<p>Processus d&rsquo;analyse Prise de contact Modalit\u00e9s de la prestation R\u00e9ception des \u00e9chantillons R\u00e9alisation de la prestation Rendu des r\u00e9sultats Service apr\u00e8s livraison Processus d&rsquo;analyse Prise de contact Avant de soumettre des \u00e9chantillons, il est souhaitable de prendre contact avec la plateforme Bordeaux Prot\u00e9ome afin d\u2019\u00e9tablir une strat\u00e9gie d\u2019analyse adapt\u00e9e et [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-249","page","type-page","status-publish","hentry"],"aioseo_notices":[],"jetpack-related-posts":[],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/proteome.u-bordeaux.fr\/en\/wp-json\/wp\/v2\/pages\/249","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/proteome.u-bordeaux.fr\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/proteome.u-bordeaux.fr\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/proteome.u-bordeaux.fr\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/proteome.u-bordeaux.fr\/en\/wp-json\/wp\/v2\/comments?post=249"}],"version-history":[{"count":48,"href":"https:\/\/proteome.u-bordeaux.fr\/en\/wp-json\/wp\/v2\/pages\/249\/revisions"}],"predecessor-version":[{"id":2208,"href":"https:\/\/proteome.u-bordeaux.fr\/en\/wp-json\/wp\/v2\/pages\/249\/revisions\/2208"}],"wp:attachment":[{"href":"https:\/\/proteome.u-bordeaux.fr\/en\/wp-json\/wp\/v2\/media?parent=249"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}