Molecular interactions, proteomic data

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). 

Recent proteomic analysis indicated that the cilia of mammalian photoreceptor cells are significantly more complex than other eukaryotic cilium (Liu et al. 2006). Over 1200 different polypeptides have been identified by the quantitative analysis of the proteome of photoreceptor outer segment compared with the proteome of the axoneme/ciliary fraction of mouse photoreceptor cells. This data set contains all previously identified protein components of the photoreceptor cilium (e.g. Schmitt and Wolfrum 2001). An understanding how the identified proteins function in their native environment of the diverse compartments of the photoreceptor cilia will require increased knowledge of their molecular interaction and networking. Insights into the organization and composition of diverse protein complexes may also provide novel information on how functional modules of the cell, recently proposed by Hofmann et al. 2006, are connected. 

Modeling is getting progressively harder as we transcend from single molecules or molecular interactions to networks of interactions. As data on proteomics and metabolomics mount, we can expect this question to move into the center of attention. Some over-optimistic scientists predicted that the first simulation of a bacterial cell could be working in the year 2005. I think, we will take much longer to have the first executable cell model that stands up to the scrutiny of scientific standards. 

We see two major appearing frontiers for new kinds of molecular data. The first is proteomics (See Chapter 4 of volume 2) and metabolomics. With a combination of 2D gel, mass spectrometry, protein microarray and yeast-two-hybrid methods, a large amount of protein sequence, expression, and interaction data will be produced on a cell-wide level. On the one hand, bioinformatics has to address the challenge of interpreting these data. On the other hand, especially the protein interaction data will provide an interesting basis for probing deeper into the details of regulatory networks. Such data are collected in special protein interaction databases such as DIP [9,10] and BIND [11],... 

---