Proteomics Standards
Here at Fixing Proteomics, we believe that running standard samples is key for any laboratory involved in proteomics. It's the first step in our 4-steps to Fixing Proteomics towards running reproducible proteomics experiments. Validating results within-lab then sharing them with experimental details so they can be reproduced across-labs are also part of the 4-steps.
Samples you can use
If you can reproducibly run a reference standard within set limits, then your confidence is much higher when you come to run your experimental sample.
Universal Proteomics Standard for Protein Mass Spectrometry (Sigma Aldrich)
The HUPO Gold MS Protein Standards (Invitrogen)
2DE protocols and a HeLa cell sample from the Reproducibility Study - Phase 2 (available soon)
Do you have any standard samples that can help? Contact us and we'll add it
Standardise and share your data
There are important initiatives designed to help share data and allow you to build on results from other labs
MIAPE are reporting guidelines from whole proteomics experiments; making explicit both where samples came from, and how analyses of them were performed.
PRIDE (PRoteomics IDEntifications database) is a centralized, standards compliant, public data repository for proteomics data
ProteomeCommons.org is a public proteomics database for annotations and other information linked to the Tranche data repository
Proteomics Journal instructions to authors encourages providing information recommended for MIAPE and says "only one biological/analytical replicate will not be acceptable", which we like!
Proteomics - Clinical Applications instructions to authors are similar to the above but include additional information specific for reporting large scale/clinical proteomics studies
Journal of Proteome Research proteomics guidelines state data and methods are "considered sufficient when it is possible to reproduce the reported results or critically reanalyze the data"
Molecular and Cellular Proteomics checklist is useful to see what they require to publish quantitative protein information, which includes things like how you addressed reproducibility with your experimental design
Organisations providing standards
These organisations are taking practical steps to help make proteomics reproducible
HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification.
ABRF Proteomics Standards Research Group (sPRG) promote and support the development and use of standards in proteomics for the benefit of all research laboratories, resource facilities and individual scientists including ABRF members and member laboratories.
The National Institute for Biological Standards and Control (NIBSC) in the UK has committed to fund the development of biological reference materials to the proteomics community in an effort called the Biological Reference Material Initiative.
US National Institute of Standards and Technology (NIST) is developing methods for the quantification of clinically-relevant protein biomarkers by mass spectrometry. NIST is also working to demonstrate the reproducibility of quantitative mass spectrometry methods through participation in inter-laboratory studies.
