Description
Proteomics is the ‘large scale study of proteins’. Proteins represent the actual functional molecules that regulate the activity and function of cells. Proteomics enables researchers to analyse the nature and abundance of different proteins within biological samples (e.g. protein complexes, subcellular compartments, whole cells or tissues). Most state of the art proteomics methods are based on high-resolution mass spectrometry instruments with high mass accuracy.
Type of data/experiments/methods
Mass spectrometry data
- mz Markup Language
-
Open format
- various vendor formats (ABI: T2D, Agilent: MassHunter, Bruker: Compass.d, Bruker: YEP, Bruker: BAF,Bruker: FID, Bruker: TDF, Sciex: WIFF, Shimadzu: LCD, Thermo Scientific: RAW, Waters: UNIFI)
- proprietary
Metadata Standards
Standards
Ontologies
- Sample processing and separations controlled vocabulary (sepCV)
- HUPO PSI Mass Spectrometry Controlled Vocabulary (PSI-MS CV)
- NCBI Taxonomy (NCBITAXON)
- Experimental Factor Ontology (EFO)
Sources for Reusable Data
Proteomecentral - ProteomeXchange
- Search across multiple repositories (PRIDE, PeptideAtlas, MassIVE, JPOST, iProX and Panorama)
- Usage license depends on respective repository
- Identifiers:
- Digital Object Identifier (DOI)
- PX Accession number
Storage and Computing
Proteomics data collected in Norway can be analysed by the individual core facilities and stored in Nels, usegalaxy.no can be used to run proteomics analysis workflows.
Data Deposition Repository
PRIDE
- License: Creative Commons Public Domain (CC0)
- Identifiers:
- Digital Object Identifier (DOI)
- PX Accession number
- Submission guide
- Embargo for up to publication
Ethics and Regulations
Patient Data
- Pre-approval for medicinal/health-related research projects from the Regional Ethics Committee is required
- Projects handling personal data are assessed at many institutions by SIKT
- Otherwise, data must be fully anonymized - neither directly or indirectly identifiable to an individual
Services in Norway
National network of Advanced Proteomics Infrastructure (NAPI) is the research infrastructure for proteomics in Norway.
NAPI partners include proteomics core facilities in Oslo, Bergen, Trondheim, Tromsø and Ås, as well as research groups with a strong focus on proteomics technology development.
Research data is managed at individual sites and coordinated at the research infrastructure level.
RDM Services
- For help with management of proteomics data please contact your core facility
Scientific Services
- Proteomics Core Facilty at Oslo University Hospital
- Proteomics Core Facility at the Department of Biosciences, Faculty of Mathematics and Natural Sciences, UiO
- Proteomics Unit at UiB (PROBE)
- Proteomics and Modomics Experimental Core (PROMEC) at NTNU
- MS and Proteomics Core Facility, NMBU
- Tromsø University Proteomics Platform
Useful Links
- RDMkit: Your domain - Proteomics
- National network of Advanced Proteomics Infrastructure (NAPI) website
More information
