Before submitting samples, it is advisable to contact the Bordeaux Protéome Platform in order to establish an analysis strategy adapted to the context and to develop the experimental conditions (preparation and analysis).
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 “contact” who will become the privileged interlocutor of the user. The user validates the analysis request (specifications, type of service, schedule, estimate, personnel involved).
The services are rendered either in the form of collaboration, or in the form of a research service:
- 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.
- 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.
A definition of the strict framework of the service as well as an estimate will be established for each request made to Bordeaux Proteome.
Receipt of samples
Advices 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.
- Receipt of samples (solution, gel, strip/spot) on site (during working hours) or by post (-20°C or dry ice for samples in solution, sending a piece of gel at room temperature in 1% acetic acid) .
- Immediate storage of samples at the appropriate temperature: -20°C or -80°C on request for samples in solution, 4°C for gels and spots/strips).
- Monitoring of samples and records according to a precise nomenclature.
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.
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.
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.
|Sample Preparation||Carried out in line with the technological strategies chosen and in consultation with the project leader.|
|Protein Assay||Bradford test. A standard curve is established at each assay.|
|Electrophorèse||1D-PAGE with molecular weight markers.|
|Image analysis||Digitization of gels and analysis by densitometry. Gel images are sent in .jpeg format by default. Raw data is stored and sent on request.|
|Liquid vein electrophoresis||Rotofor, Offgel (pI) ; gel Free (MW)|
|Sample Preparation||Trypsin or endoprotease of your choice depending on the imperative or specificity of the project.|
|LC-MS/MS analysis||Protein identification by nanoLC-ESI-MS/MS Orbitrap coupling. Variable chromatographic gradient duration. Data queried via Proteome Discoverer against the most suitable database (defined in agreement with the project leader).|
|Differential expression analysis||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.|
Return of results
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.
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.
Bordeaux Proteome considers that, without a response within 10 days from the client, the file as accepted and closed.
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.
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°C. The gels are systematically stored at 4°C. 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.
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.
Service after delivery
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.
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.
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.
The plateform affilation must appear as:
Univ. Bordeaux, Bordeaux Proteome, Bordeaux, France.