Standardization, proteomic data

However, it is clear that the ease of collecting proteome data currently exceeds the capacity to analyse it. Therefore, international standards are being sought for proteomic experiments, such as the proteomics standards initiative (PSI, http //psidev.source forge.net/), and the proteomics experiment data repository (PEDRo, http //pedro.man.ac.uk). The aim is to provide proteomic researchers with the opportunity to query and reproduce protocols, analyse raw or metadata from other laboratories, and to link the proteome with the respective transcriptome and the metabolome. The Human Proteome Organization (HUPO) is establishing a defined infrastructure for human data submission, and annotation for the numerous proteomic data platforms. This will also be required to effectively develop parasitic flatworm proteomics. 

The MAGE has built within it a controlled vocabulary that is used to standardize communication between data providers. However, MAGE can also be extended to encode other types of omic data beyond genomics, such as proteomic data, so long as a reference to the ontology or controlled vocabulary is provided. Although a description of the extension mechanism is beyond scope of this book, practitioners must become familiar with it in order to ensure their software products and applications will be able to accept any and all annotation data that may be submitted with the genomic data. 

Sherman, D., Woicik, J., Zhu, W., Apweiler, R. (2004). Common interchange standards for proteomics data Public availability of tools and schema. Proteomics 4, 490-491. 

The need for standardization, most notably in bioinformatics, e.g., data formats and exchange, is stressed in the chapter Proteomic Data Standardization,... 

Protein interaction format [248] httpJ/www.nature.com/cgi-taf/DynaPage.taf file=/ nbt/journal/v22/n2/abs/nbt926.html PEDRo prescribes standards for proteomic data for databases [249] http //psidev.sourceforge.net/... 

Orchard, S. and Hermjakob, H. (2008) The HUPO Proteomics Standards Initiative - Easing Communication and Minimizing Data Loss in a Changing World. Brief Bioinform, 9, 166-173. 

Due to the lack of suitable standard reference material for quantification purposes in phospho-proteomics and metallomics, reliable calibration strategies were developed for the direct microlocal analysis of phosphorus and metals in protein spots and in thin sections of brain tissue using LA-ICP-MS.16,17,116 For quantification of analytical data, the application of a solution based calibration strategy was proposed with LA-ICP-MS6 and the simultaneous determination of P, S, Si, Al, Cu and Zn concentrations in human brain proteins (Alzheimer s disease) or for imaging thin... 

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