Standardization and Quality Control in Proteomics Juan-Pablo Albar 1 , Francesc Canals CNB-CSIC, Darwin 3, E-28049 Madrid, Spain Mass spectrometry (MS) based proteomics has evolved substantially over the past decade. Major improvements in instrumentation, and continuous methodological develop- ment, have lead to an ever increasing proteome coverage. Thousands of proteins can be identified and quantified in proteomic experiments within the reach of many laboratories. Increasingly complex experimental designs can be undertaken, whereby researchers can start to tackle the biological complex- ity, and help answering biologically relevant questions or contribute to the development of tools for personalized medicine applications. However, for Proteomics to reach its technological maturity and being able to successfully deliver all its potential to the scientific community, there is an unavoid- able need for quality control procedures that cover all the steps involved in proteomic analysis. It is crucial that the huge amount of data that is being gathered faster and faster is of demonstrable reliability, and that can be shared among the scientific community in readily exchangeable formats. More and more candidate biomarkers are published every year (>5.000 Medline entries during the last 5 years using proteomics approaches out of >40.000 entries per year related to biomarkers in general). However, only very few of these candidate biomarkers or bio-signatures are followed up and even less are approved for clinical use. The problems and drawbacks of these studies, may be due to different causes such us poor study design, insufficient power and/or the lack of appropriate validation. So far, the majority of proteome-centric studies on human serum and plasma have been hampered by poor reproducibility, inadequate significance and a lack of robustness, which is all needed for clinical translation of results. The introduction of quantitative proteomic technologies, the advancement in bioinformatics and computational biolo- gy and the existence of large sample collections (biobanks) may enable us now to translate proteomics to clinical chemistry and thereby advancing disease diagnosis and prevention. Large patient cohorts as well as high quality biobanks with standardized and quality-controlled human material are needed and currently being established. Prob- lems in proteomics that made this technique not applicable in the clinical field can now be tackled as a consequence of new quantitative technologies and assays, such as selected/ multiple reaction monitoring (SRM/MRM) and standardized validation strategies. Therefore these bio-repositories could have an enormous impact beyond the level of genetic variation. Several efforts to develop test standards and QC proce- dures have been undertaken by different organizations (ABRF, HUPO, NCI, ProteoRed), underscoring the importance of standardization and QC to improve the quality and evaluate the robustness and reproducibility of defined proteomics workflows. On line with this, EuPA as organization has promoted an initiative on the field of Standardization and Quality Control by creating a devoted working group to standardization within the new EuPA committee on New Developments. Standardization in how to report proteomic experiments is being defined through several Minimal Infor- mation About a Proteomic Experiment (MIAPE) guidelines established by the community over the recent years. The definition of standard exchangeable data formats has been the object of a sustained effort by the HUPO Proteomics Standard Initiative (PSI). The introduction of QC metrics along the whole analytical process has become increasingly relevant in the field. QC metrics provide the necessary confidence in each step of a typical proteomics workflow, including sample preparation, separation, mass spectrometric analysis, data processing, data analysis and storage. Furthermore, publishers in the field are currently tightening their guidelines and are keen on requiring QC metrics along with manuscripts, as is already standard practice in most analytical disciplines. Finally, robust QC approaches will clearly be an indispensable prerequisite for the ongoing HUPO Human Proteome Project initiative. Several issues are still unresolved or unsatisfactorily resolved regarding standardization and harmonization in JOURNAL OF PROTEOMICS 95 (2013) 1 – 2 E-mail address: jpalbar@cnb.csic.es (J.-P. Albar). 1 Tel.: +34 91 5854696; fax: +34 91 5854506. Available online at www.sciencedirect.com ScienceDirect www.elsevier.com/locate/jprot 1874-3919/$ – see front matter © 2013 Published by Elsevier B.V. http://dx.doi.org/10.1016/j.jprot.2013.11.002