Protein chips proteome

Protein interaction databases Affinity selection Protein pathways/protein chips Proteome, MDS-Proteomics (Blainville, QC, Canada), Celera Neogenesis (Cambridge, MA), MDS-Proteomics Zyomyx (Hayward, CA), Combimatrix (Seattle, WA), Ciphergen (Palo Alto, CA), Sense Proteomics (Cambridge, UK)... 

Stress specific mRNAs or proteins Real-time RT-PCR DNA- or protein-chips, proteome analysis... 

Protein microchips have a significant impact on the development of safer drugs through the comprehensive profiling of drugs or lead compounds for effects. Zhu et al. [35] used a microarray of an entire eukaryotic proteome to screen different biochemical activities. First, protein chips can screen potential lead compounds at high throughput... 

Proteomics includes a variety of technologies that include differential protein display on gels, protein chips, quantitation of protein amoimts, analysis of post-translational modifications, characterization of protein complexes and networks and bioinformatics. All this information in combination with genome and phenotype studies will ultimately yield a comprehensive picture of a cellular or tissue proteome (Wasinger and Corthals 2002). 

Schlessinger 1990). These phosphorylation events stand at the beginning of specific signaling cascades that ultimately lead to transcription initiation and cell mitosis or differentiation. Because of the complexity of the proteome, it is at this stage most reasonable to think about protein chips that have a defined number of antibodies against known disease markers. 

In a more modified approach, differential display proteomics can also be done with no separation of proteins. This is called the protein chip approach. In this method, a variety of bait proteins such as antibodies, peptides, or protein fragments may be immobilized in an array format on specially treated surfaces. The surface is then probed with the samples of interest. Proteins that bind to the relevant target can then be analyzed by direct MALDI readout of the bound material (Nelson, 1997 Davies et ah, 1999). Lor example, well-characterized antibodies can be used as bait. Protein samples from two different cell states are then labeled by different fluorophores, mixed together, and used as probe. In such a case, the fluorescent color acts as an indicator for any change in the abundance of the protein that remains bound to the chip (Lueking et ah, 1999). A number of technical problems would still need to be overcome before applying this technique for large-scale analysis of proteins. 

Mian S, Ball G, Hornbuckle J, et al. A prototype methodology combining surface-enhanced laser desorption/ionization protein chip technology and artificial neural network algorithms to predict the chemoresponsiveness of breast cancer cell lines exposed to Paclitaxel and Doxorubicin under in vitro conditions. Proteomics 2003 3(9) 1725-1737. 

Weissenstein U, Schneider MJ, Pawlak M, Cicenas J, Eppenberger-Castori S, Oroszlan P, Ehret S, Geurts-Moespot A, Sweep FCGJ, Eppenberger U (2006) Protein chip based miniaturized assay for simultaneous quantitative monitoring of cancer biomarkers in tissue extracts. Proteomics 6 1427-1436... 

Perhaps the area in proteomics that is generating most excitement at the moment is applications focusing on biomarker discovery. The development of protein chips, high-throughput mass spectrometry, and sensitive quantitation (ICAT, DICE, etc.) has provided a... 

Another method using protein "chips has also been developed (Haab et al., 2001 Zhao et al., 2001 Zhu et al., 2001). These chips contain ordered arrays of protein-binding molecules with the proteins then bound or enriched on a segment of the chip to be analyzed via various technologies. Antibodies recognizing specific protein sequences or modifications can be used, for example, to separate proteins with a specific activity from a complex mixture. A different version of a protein chip has been created by Zhu et al. (2001) and by Martzen et al. (1999). In these cases, the proteins are arrayed on the chip and the proteome can then be screened for interaction with particular substrates and ligands, and for certain classes of biochemical properties and activities. 

Two hundred and forty-eight serum samples provided from the National Ovarian Cancer Early Detection Program clinic at Northwestern University Hospital (Chicago, IlUnios) were analyzed on the same ProteinChip arrays using both a PBS-II and a Qq-TOF MS fitted with a SELDI interface. The proteomic patterns of the serum samples were acquired on the PBS-II TOF MS, immediately followed by their acquisition on the Qq-TOF MS. The key to this study is that the identical set of serum samples was analyzed on the exact same protein-chip surface, eliminating all experimental variability other than the use of two different instruments. 

Ruetschi, U., Rosen, A., Karlsson, G., Zetterberg, H., Rymo, L., Hagberg, H., and Jacobsson, B. Proteomic analysis using protein chips to detect biomarkers in cervical and amniotic fluid in women with intra-amniotic inflammation. J Proteome Res, 4 2236-2242, 2005. 

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