HUPO initiation

Hanash, S. (2004b). HUPO initiatives relevant to clinical proteomics. 

Enriched subcellular compartments can be analyzed by MS/MS to determine their constituent proteins. One advantage of analysis of different cellular fractions is pre-analytical simplification that offers rewarding yields in dealing with the proteins identified in large-scale MS experiments. One of the major initiatives of the Human Proteome Organization (HUPO) is the comprehensive characterization of the complete subproteome of each cell type. 

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. 

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 Human Proteome Project (HUPO, www.hupo.org) initiated the Plasma Proteome Project (PPP) in 2002, and numerous laboratories have contributed to this ambitious project of deciphering all proteins contained in the human plasma. Plasma, the soluble component of the human blood, is believed to harbor thousands of distinct proteins that originate from a variety of cells and tissues through either active secretion or leakage from blood cells or tissues. For the reasons described above, HUPO recommends use of plasma instead of serum, with EDTA (or citrate) for anticoagulation and standardized sample preparation. HUPO proposes combinations of serum depletion, fractionation procedures, and MS/MS technologies, with explicit... 

Several languages are focusing on more specialized areas of physical measurements. MatML (http //www.matml.org/) has been developed for the exchange of materials information. The HUPO proteomics standards initiative (http //www.psidev.info/) is developing several standards including mzML (http //www.psidev.info/index.php q=node/257), a standard for encoding raw data from mass spectrometers that builds on the previous formats DataML (http //www.psidev.info/index.php q=node/80) and mzML (Pedrioli et al. 2004). Another HUPO standard, PSI MI XML, provides syntax for the description of molecular interactions (http //www.psidev.info/index.php q=node/31). 

At an initial HUPO-PSI-sponsored meeting of this group it was decided that the approach to designing such a format should be multilayered, with Level 1 designed to fulfil basic requirements and be suitable for rapid implementahon. Subsequent levels will supply further complexity and flexibility, for example the ability to deal with other interactors such as nucleic acids. Wherever possible, the potential values of attributes in the data model are defined by controlled vocabularies researchers may also ascribe confidence levels to the data at various points throughout the data entry process and add free comments in appropriate places. 

S, et al. Comparison of the methods for profiling glycoprotein glycans-HUPO Hnman Disease Glycomics/Proteome Initiative multi-instimtional stndy. Glycobiology 2007 17 411-422. 

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