All researchers from within Erasmus MC, other academic institutions or (biotechnology) companies can make use of the expertise and services provided by the Proteomics Center if projects are considered feasible by the Center. The feasibility of a project is first discussed in a consultation meeting with the Proteomics Center’s Director. Final approval of a project can be only granted after this meeting, when the scope of the project order has been clarified. Users with approved projects can file sample analysis requests via the sample submission form. The decision to initiate a project is based on its feasibility in context of the service types offered by the Proteomics Center, the available instrument time in relation to the number of the planned sample number and expected scientific outcome. In unclear situations, the Proteomics Center will seek advice from its Expert Panel.
Collaborators are responsible for ensuring that the submitted samples are prepared as agreed upon. Samples which do not adhere to the Proteomics Center standards will not be measured. If, during the analysis, contaminants that can interfere with the lifespan of the LC column or mass spectrometer performance appear in a sample, an analysis might be stopped and samples may be returned to the collaborator. The Proteomics Center has the authority to reject requests, or samples, which do not fulfil the requirements as agreed upon during the intake meeting.
The Proteomics Center will primarily use their own established instrument methods and workflows for measurements. Adaptions of methods will only be done in exceptional cases (e.g., when a data set needs to match another one from a specific publication, etc.). Once analyzed, the remaining sample material will be kept at the Proteomics Center for no more than two years from completion of the analysis and can be collected upon arrangement. The Proteomics Center is not responsible for lost or missing samples during transportation.
2. Publication policy
All services and projects undertaken are on a collaborative basis and are expected to result in co-authorship for the staff members involved. The costs that the Proteomics Center has to charge include reagent costs only – the Center realizes no profit. Consultation regarding study design, data interpretation, publication and public access of raw data are provided at no cost. Contact the Proteomics Center’s Director for further information.
Please include the following affiliation in publications:
[Proteomics Center staff member #1]*, [Proteomics Center staff member #2]*, …
* Proteomics Center
Erasmus University Medical Center
3015 CN Rotterdam
3. Technical Details
The performance of all nLC-MS/MS instrumentation is continuously monitored by QC runs (e.g., Hela digest, BSA digests, purified (labeled) peptides, etc.), at least once per week. The Proteomics Center cannot be hold responsible for sample loss by technical breakdowns or any other means of machine failure. MS data typically strongly depends on the quality of samples. In case the samples were prepared by the collaborators themselves, the Proteomics Center will regard requests as completed regardless of the outcome.
4. Data storage and processing of personal data
All raw and processed data is stored on servers hosted on the ResearchSuite platform at Erasmus MC. Raw data files are stored for a guaranteed period of five years. The Proteomics Center is not responsible for any loss of data from the backup servers. Processing of personal data (e.g., clinical parameters of human study subjects, or genomic sequencing data) is subject to the General Data Protection Regulation (GDPR). The Proteomics Center is following the internal guidelines set by Erasmus MC to comply with the GDPR. Clinical project orders require a valid ethical approval (METC), which is effective for at least six more months from the sample submission date. The Proteomics Center does not hold responsibility for the collaborator’s ethical approval documentation; the collaborator holds ultimate responsibility in ensuring the adequate ethical approval documentations are in place, up-to-date and legitimate throughout the project duration.
When proteomic data produced by the Proteomics Center is used in a publication, the dataset must be made publicly available by depositing it to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository. The Proteomics Center will take care of the complete process. Collaborators are requested to inform the Proteomics Center when a manuscript is submitted that includes data acquired by the Proteomics Center.
5. Prices and invoicing
The current fee schedule can be downloaded here. Service costs are continuously reviewed. If prices change during the processing of a request, prices from the submission date are applied. All clients are requested to enter internal financial information (‘kostenplaats‘ for Erasmus MC clients) upon sample submission. The financial department of the Proteomics Center will send invoices with a breakdown of the services provided and costs to the budget responsible contact person (usually the the group leader / PI).