Proteomic data

Waters KM, Shankaran H, Wiley HS, Resat H, Thrall BD. Integration of microarray and proteomics data for biological pathway analysis and network modeling of epidermal growth factor signaling in human mammary epithelial cells. Keystone Symposia, 2005. 

Nesvizhskii, A.I., Aebersold, R. (2005). Interpretation of shotgun proteomics data the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440. 

The use of mass tagging reagents to analyze proteomic data has greatly improved the ability to compare samples for protein expression differences. However, a major limitation of the ICAT procedure (Section 1, this chapter) is that it can only compare two samples simultaneously, usually a test and a control. Even with the ECAT design (Section 2) using multiple lanthanide metals to make a series of different mass tag signatures, it is difficult to extend the... 

W. Liebermeister and E. Klipp, Bringing metabolic networks to life Integration of kinetic, metabolic, and proteomic data. Theor. Biol. Med Modeling 3(42), (2006). 

Zeeberg BRet al (2003) GoMtner a resource for biological interpretation of genomic and proteomic data. Genome Biol 4 R28... 

Human Protein Reference Database as a Centralized Repository for Proteomic Data Annotation... 

Proteomic data annotation by HPRD team and scientific community... 

Fig. 4. Application of bioinformatics tools to 2D-DIGE data analysis. Proteome data consisting of the normalized spot intensity values are exported from the image analysis software and their correlation with clinicopathological data examined. Using informatics tools including clustering algorithms and machine-learning methods, a novel cancer classification based on proteome data is established, and key proteomic features and proteins corresponding to biomarker candidates are identified.

The x,y,z coordinates of all atoms in published, refined three-dimensional structures have been deposited in the Protein Data Bank (Table 3-4).568 571 Many other related databases are available,572 e.g., covering molecular modeling,573 gene sequences, proteome data,574 and much, much more. A good way to keep up to date is to read the "computer comer" in Trends in Biochemical Sciences (TIBS). Most databases can be reached on the World Wide Web.572 A selected list is... 

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. 

Zimmer, J. S., Monroe, M. E., Qian, W. J., and Smith, R. D. (2006). Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom. Rev. 25 450-482. 

Functional Profiling and Data Visualization Using Proteomic Data 182... 

---