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Research paper−114 Synthesiology - English edition Vol.1 No.2 (2008) Microquantity protein degraded and denatured in the test tubes, and became undetectable as they became adsorbed into the test tube wall. Although mass spectrometer was an ultra sensitive “detector,” evanescence of samples determined the real limit of analysis sensitivity and throughput. Therefore, unless this problem was solved, it was impossible to conduct microquantative protein analysis by fully employing the performance of the state of art mass spectrometer. Even if the performance of mass spectrometer increased in the future, there is concern that its advantage would not be utilized fully.2 Real problem that must be solved (liquid chromatography technology)The most important method when treat microquantity protein is to maintain the sample in micro-space at concentrated condition as much as possible. However, this is not easy since desalt and washing processes are necessary to analyze protein from organic samples by mass spectrometry. The conventional practice was the on-line reverse phase high-performance liquid chromatograph (HPLC) and the mass spectrometer. A sample was concentrated and desalted in the HPLC column, an elution fraction of liquid chromatograph was ionized, and introduced into the mass spectrometer. However, commercially available HPLC devices had low sensitivity and throughput that did not satisfy our objective of protein network analysis. Particularly, the minimum limit of the pump of conventional HPLC was a flow rate of several microliters per minute and had poor analytical reproducibility, and it was impossible to conduct large-scale, repeated and stable analyses. One of the greatest reasons was because homogenous mixing of solvents was difficult at a low flow rate of several microliters per minute.To conduct liquid chromatography (LC), proteins and 1 Background of researchHuman body consists of about 30 trillion cells, and each cell contains over 100 thousand different types of proteins to sustain life activity. These proteins do not function separately, but form groups and organizations and function as networks. The work of mapping the network of proteins in the cell is called protein network analysis.Network analysis is important not only for the clarification of biological processes, but also for the understanding of development mechanism of diseases at molecular level, and contributes to the development of new diagnosis and treatment methods and to new drug discovery targets (Figure 1). However, protein network analysis is technically not easy. There was no established methodology, because the demand in actual protein network analysis was to analyze several hundreds or several thousands of proteins at once.It was practically impossible to meet this demand with technology of the 1990s. However, the technology came to a turning point in the 21st Century, with the maturity of ionization mass spectrometry for protein invented by Koichi Tanaka of the Shimadzu Corporation. Analysis work that previously required dozens of hours to identify just one protein could be accomplished in a few minutes or even a few seconds using the new mass spectrometry method. Also in theory, the sensitivity increased several hundred times, and it seemed that the researchers were released from the limiting requirement of purifying large amount of samples. However, even after protein researchers obtained their high-tech mass spectrometers, high-sensitivity analysis did not necessarily become instantly available. That was because each of the hundred thousand types of protein possessed different form and size, varied in chemical properties, and were unstable. - Development of ultra sensitive mass spectrometry analytical platform -Shun-ichiro Iemura and Tohru Natsume*Biological Information Research Center, AIST Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan *E-mail : Inside each cell that constitutes organism, over 100 thousand different types of proteins function for vital biological processes. The proteins form groups and organizations that function as networks. We were able to achieve large-scale protein network analysis with high sensitivity, high reproducibility, and high efficiency, by newly developing liquid chromatography system with extremely low flow rate of 100 nL/min. The large scale data set obtained using this analysis contributed not only to the discovery of new cellular systems, but also to the understanding of development mechanism of diseases at molecular level. Our research developed into Full Research that led to the development of new diagnostic and treatment methods as well as new drug discovery targets.A systematic analysis of protein interaction networks leading to the drug discoveryKeywords : Proteomics, mass spectrometry, protein network, drug discovery, protein microquantative analysis[Translation from Synthesiology, Vol.1, No.2, p.123-129 (2008)](42)−

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