Terms

General User Terms for internal users of the Proteomics Research Infrastructure (PRI)

1.  General

  • To initiate a project, users are asked to submit some background information via the submission form on the PRI website. The decision to initiate a project is based on its feasibility in context of the service types offered by PRI, the available instrument time in relation to the number of the planned sample number and expected scientific outcome. In unclear situation, PRI will seek advice from its User Advisory Board, who takes the final decision.
  • Upon acceptance, a project will be discussed in a ‘consultation’ meeting. 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 service requests from their bookitlab account page.
  • Samples are quality controlled (QC) by peptide concentration measurement (OD280) prior to loading on the LC-MS/MS. For desalted peptide samples, the sample volume needs to allow retrieval of 2.2μL for QC.
  • The user is obliged to read and follow UCPH’s protocols on how to handle or prepare the material for the request. UCPH’s protocols can be accessed here. PRI has the authority to reject requests, or samples, which do not fulfil these requirements.
  • PRI will primarily use their own established instrument methods for measurements. Adaptions of methods will be only done in exceptional cases (e.g., if a dataset needs to match another one from a paper).
  • Once analysed, any remaining sample material will be kept at PRI for no more than three months from completion of the analysis and can be collected upon arrangement. PRI is not responsible for lost or missing samples.
  • PRI will primarily use their own established instrument methods for measurements. Adaptions of methods will be only done in exceptional cases (e.g., dataset needs to match another one from a paper)
  • Once analysed, the remaining sample material will be kept at the PRI for no more than three months from completion of the analysis and can be collected upon arrangement. The PRI is not responsible for lost or missing samples.

2.  Publication policy

  • For PRI services without involvement in experimental planning or data interpretation intellectual contributions to user projects are generally limited. Hence, PRI will usually not require co-authorship of publications entailing data generated by the unit.
  • In case of extensive consultancy in the design and analysis of proteomic experiments, co-authorships will be agreed on in accordance to academic tradition and the rules laid down in the Danish Code of Conduct for Research Integrity. This policy is under strict supervision of the PRI User Advisory Board, to ensure fair practice.
  • Any communication (publication, oral presentation, poster or similar) using data generated at the PRI must include a statement in the acknowledgement section describing the analytical support provided by PRI, and acknowledge the associated funding agency:

“Mass spectrometry-based proteomics analyses were performed by the Proteomics Research Infrastructure (PRI) at the University of Copenhagen (UCPH), supported by the Novo Nordisk Foundation (NNF) (grant agreement number NNF19SA0059305)”

  • When proteomic data acquired at PRI is used in a publication, the dataset must be made publicly available by depositing it to the ProteomeXchange Consortium via the PRIDE partner repository. PRI will assist users to upload their data to PRIDE if needed. Users are required to inform PRI, when a manuscript is submitted including data acquired at PRI.
  • Manuscripts including data generated at PRI must be made available to PRI at least seven (7) days prior to submission for the opportunity to verify that the material and methods as well as acknowledgement sections are correctly formulated, and that proteomics data is used in a scientifically correct way. In case of disagreement, PRI will forward the case to its User and Advisory Board (UAB), to provide further input. Users are bound by the decision of the UAB.
  • Users must notify PRI as soon as an article incorporating data generated at PRI gets published.

 3. Technical Details

  • The performance of the LC-MS/MS instrumentation is continuously monitored by QC runs (e.g., Hela digest), at least once per week.
  • PRI cannot be hold responsible for sample loss by technical breakdowns, or any other means of machine failure.
  • MS data strongly depends on the quality of samples. If samples are prepared by the user themselves, PRI will regard requests as completed regardless of the outcome.

4.  Data storage and processing of personal data

  • Data is stored on servers hosted and housed by UCPH-IT, as well as a cloud-based data solution (Box.com)
  • Data is stored for a guaranteed period of three months for direct download. A data backup is stored for five years on UCPH-IT servers, however, access to this backup cannot be guaranteed in a timely manner, and PRI is not responsible for any loss of data from the backup.
  • 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 PRI is following the internal guidelines set by UCPH to comply with the GDPR.
  • Clinical project requests require a valid ethical approval, which is effective for at least six more months from the sample submission date. The start and end date of the ethical approval needs to be sent to PRIadmin@sund.ku.dk, together with a copy of the ethical approval document. PRI does not hold responsibility for the user’s ethical approval documentation; the user holds ultimate responsibility in ensuring the adequate ethical approval documentations are in place, up-to-date and legitimate throughout the project duration. 

5.  Prices and invoicing

  • Service costs are continuously reviewed. If prices change during the processing of a request, prices from the submission date are applied.
  • UCPH users are requested to enter internal financial information (Stedkode, Alias Number and KU Specification) upon project registration. Service fees are automatically deducted from the user projects account when services have been completed. Users can review the services they will be billed for in their BookitLab account profile. Further to this, PRI will send pro-forma invoices with a breakdown of the services used and cost to the budget responsible contact person (ordinarily the Group Leader/PI).