Proteomics Research for Integrative Biology

Proteomics Research for Integrative Biology

Research Emphasis

This resource focuses on assisting biomedical researchers through the development and application of advanced proteomics technologies designed for the characterization of biomedically important systems, including pathogenic microbes, viruses, animal models, human tissues, biofluids, cultured cell lines, and clinically obtained samples. Unique capabilities include nanoscale sample handling combined with high-throughput, high-pressure, high-resolution capillary liquid chromatography (LC) coupled to electrospray ionization interfaced high-sensitivity, wide-dynamic-range Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS).

Current Research

Development and application of new MS instrumentation and online and offline LC separation methods for the characterization of highly complex proteomic systems, including peptide and protein identification, and quantitation methods; characterization methods implement bottom-up and top-down approaches to facilitate identification of protein posttranslational modifications. Development of new informatics software tools to facilitate the quantitation, validation, and interpretation of proteomic data.

Resource Capabilities

Methods

Information is available on the Proteomics Research Resource for Integrative Biology Web site under Training & Protocols.

Instruments

Five FT-ICR mass spectrometers have been developed or modified, including an instrument with the world's highest magnetic field (based around an 11.5 tesla superconducting magnet), a high-performance FT-ICR, and 7, 9.4, and 12 tesla FT-ICR instruments. A Micromass Ultima quadrupole time-of-flight, a QSTAR Hybrid LC/MS/MS system, a ThermoFinnigan MAT TSQ 7000, a PE SCIEX API 3000, and six ThermoElectron Finnigan ion trap mass spectrometers complete the instrumentation suite. These instruments are equipped with automated high-pressure capillary LC systems and in-house electrospray or nanospray ionization interfaces for ultrahigh sensitivity. Further information is available on the Proteomics Research Resource for Integrative Biology Web site under Instrumentation.

Software

In-house developed ICR-2LS and VIPER are publicly accessible on the Proteomics Research Resource for Integrative Biology Web site under Software & Tools.

Special Features

Automated, high-throughput, ultrasensitive, wide-dynamic-range proteome characterization of microbial, mammalian, and viral systems is afforded by the instrumentation suite at the Pacific Northwest National Laboratory.

Available Resources

Information is available on the Proteomics Research Resource for Integrative Biology Web site under Software & Tools and Training & Protocols.

Training Opportunities and Workshops

Information is available on the Proteomics Research Resource for Integrative Biology Web site under Training & Protocols

Publications

Shen, Y., Zhang, R., Moore, R. J., Kim, J., Metz, T. O., Hixson, K. K., Zhao, R., Livesay, E. A., Udseth, H. R., and Smith, R. D., Automated 20 Kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1,000-1,500 for proteomics and metabolomics. Analytical Chemistry 70:3090–3100, 2005.

1. Shvartsburg, A. A., Tang, K., and Smith, R. D., FAIMS operation for realistic gas flow profile and asymmetric waveforms including electronic noise and ripple. Journal of the American Society for Mass Spectrometry 16:1447–1455, 2005.
2. Liu, T., Oian, W.-J., Chen, W.-N. U., Jacobs, J. M., Moore, R. J., Anderson, D. J., Gritsenko, M. A., Monroe, M. E., Thrall, B. D., Camp, D. G. II, and Smith, R. D., Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: The human mammary epithelial cell proteome. Proteomics 5:1263–1273, 2005.
3. Oian, W.-J., Jacobs, J. M., Camp, D. G. II, Monroe, M. E., Moore, R. J., Gritsenko, M. A., Calvano, S. E., Lowry, S. F., Xiao, W., Moldawer, L. L., Davis, R.W., Tompkins, R. G., and Smith, R. D., Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry. Proteomics 5:572-584, 2005.