Proteome Standards Initiative

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. 

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). 

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... 

Fi/Fo ATPase or other highly abundant mitochondrial proteins, in addition to other unexpected proteins from other subcellular locations. Of course, it is likely that no one actually looked for such proteins in rafts before and with the unbiased nature of proteomics one expects (or even hopes ) to find components that had not been previously described. However, any analysis of a biochemical fraction can only be as good as the initial preparation of that fraction and in previous lipid raft studies the minimum standard one has to meet to claim a protein is in rafts is to demonstrate sensitivity to cholesterol disruption. 

In standard MS proteomics, well-established and efficient protocols allow for the en masse identification of proteins from tissue extracts. A key step within this process is the initial separation and purification of the molecules before submitting them to the mass spectrometer. However, in MSI studies, a general identification strategy for proteins, peptides, and metabolites is still missing due to several reasons. First, in comparison to LC-MS-based... 

The Human Proteome Organization has initiated an effort to establish standards for the interchange of information between the various interaction databases. The... 

An unusual approach to chemical tagging for purposes of identification and quantitation of proteins has been described (Ornatsky 2006) in proof-of-principle experiments. Very briefly, this approach uses chemical tags that contain one of a series of metal atoms (gold, europium, samarium or terbium) that are then detected and quantitated using inductively-coupled-plasma (ICP)-MS, a standard analytical technique for elemental metal analysis (Nelms 2005) that can provide very high sensitivity and precision. At present this approach is very much in its initial stages of development, but the sensitivity is such that single cell proteomics may not be out of reach. 

The orbitrap mass analyzer is an ion trap device that provides high accuracy and resolution mass measurement without the need of a magnetic field, (Hu et al. 2005 Zubarev and Makarov 2013) and thus it is more accessible in terms of lab requirements, and initial and operating costs. Some consider it to be the gold standard mass spectrometer for proteomic-based measurements (Mitchell 2010). The orbitrap mass analyzer is usually found in a hybrid configuration interfaced with a linear ion trap mass analyzer and transfer octopoles and C-trap (Fig. 2.5) (Senko et al. 2013). 

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