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June 2005

Ultra-high performance separations and mass spectrometry work featured in IJMS

The article "Ultra-sensitive, high throughput and quantitative proteomics measurements" was published in the February 1, 2005, issue of the International Journal of Mass Spectrometry. The article describes the basis and application of an approach developed at Pacific Northwest National Laboratory (PNNL) for very high-throughput, ultra-sensitive, and quantitative proteomic measurements based upon the use of ultra-high performance separations and mass spectrometry (MS). These developments are illustrated in the context of studies of complex biological systems.

The article gives an overview of the accurate mass and time (AMT) tag approach developed by PNNL scientists and describes the incorporated data analysis pipeline necessary for efficient proteomic studies. The AMT tag approach is based on advanced separations combined with very accurate MS measurements; in particular, ultra-high pressure capillary liquid chromatography (LC) combined with Fourier transform ion cyclotron resonance (FTICR) MS, and a supporting data analysis and management infrastructure. Advantages include greater sensitivity and increased throughput. The greater sensitivity provides improved identification of lower abundance proteins, and thus better proteome coverage. Figure 1 is a schematic of the AMT tag approach.

The described analysis pipeline comprises a large component of the analytical procedures performed at PNNL for application in solving biological problems using proteomic MS analysis. Specifically, the advantages of high sensitivity and increased throughput have direct implications to work being performed with clinical human tissue and fluid samples at the Laboratory. The challenges presented in analyzing large numbers of these highly complex and large dynamic range samples are beginning to be addressed by using these technologies developed at PNNL.

The authors are Jon M. Jacobs, Matthew E. Monroe, Weijun Qian, Yufeng Shen, Gordon A. Anderson, and Richard D. Smith, all scientists at the Environmental Molecular Sciences Laboratory at PNNL. The work was supported by the U.S. Department of Energy's (DOE) Office of Biological and Environmental Research and the National Institutes of Health National Center for Research Resources.

Figure 1. Basic schematic of the accurate mass and time (AMT) tag approach. The AMT approach consists of two main components: 1) Creation of a mass and time (MT) tag database using a LC-MS/MS peptide identification strategy and (2) use of LC-FTICR-MS for high-throughput accurate mass measurements which will be compared against the MT tag database for the identification of peptides and creation of an accurate mass and time (AMT) tag. Full Image


Jacobs JM, ME Monroe, W-J Qian, Y Shen, GA Anderson, and RD Smith. 2005. "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements." International Journal of Mass Spectrometry 240(3):195-212. DOI:10.1016/j.ijms.2004.09.024.

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