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Development of a Universal Multiplex Assay System fot High-Throughput Biological Applications


EMSL Project ID
40991

Abstract

Recent advances in genomics, proteomics, and metabolomics make the 'omics' technologies powerful discovery-based tools for identifying candidate biomarkers for human diseases; however, it has not been successful so far to establish new biomarkers for clinical practice by utilizing these technologies. The main bottleneck lies in the lack of effective tools for high-throughput validation. To overcome this bottleneck I propose to develop a novel 'reagent-free' mass spectrometry-based universal multiplex assay system that will provide high throughput quantitative measurements for hundreds of low-abundance protein and metabolite analytes, independent of antibody-based reagents. The goal for this technology platform is to achieve a profound advance over current MS-platforms by providing >1000-fold enhancement in analyte signal intensities, sufficient for detecting low-abundance species, and >5000-fold improvement in resolving power for extremely high specificity detection. These advances will be achieved by developing and integrating 1) a novel subambient pressure ionization source with nanoelectrospray array, 2) advanced ion-funnel interfaces, 3) novel multi-stage gas-phase ion mobility technology (differential mobility analyzer coupled to field asymmetric ion mobility spectrometry) for separating and selecting analytes of interest, and (4) a new triple-stage pentaquardrupole (QqQqQ) mass spectrometer for further isolating as well as detecting ions.

Project Details

Start Date
2010-11-02
End Date
2013-11-17
Status
Closed

Team

Principal Investigator

Weijun Qian
Institution
Pacific Northwest National Laboratory

Team Members

Tujin Shi
Institution
Pacific Northwest National Laboratory

Related Publications

Aryal UK, CT Lin, JS Kim, TH Heibeck, J Wang, W Qian, and Y Lin. 2012. "Identification of phosphorylated butyrylcholinesterase in human plasma using immunoaffinity purification and mass spectrometry." Analytica Chimica Acta 723:68-75.
Duan J, VK Kodali, MJ Gaffrey, J Guo, RK Chu, DG Camp, II, RD Smith, BD Thrall, and W Qian. 2015. "Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function During Nanoparticle-Induced Oxidative Stress." ACS Nano Epub ahead of print:, doi:10.1021/acsnano.5b05524
Kim JS, ME Monroe, DG Camp, II, RD Smith, and W Qian. 2013. "In-Source Fragmentation and the Sources of Partially Tryptic Peptides in Shotgun Proteomics ." Journal of Proteome Research 12(2):910-916. doi:10.1021/pr300955f.Epub 2013 January 16.
Shi T, and W Qian. 2013. "Antibody-free PRISM-SRM for multiplexed protein quantification: Is this the new competition for immunoassays in bioanalysis?" Bioanalysis 5(3):267-269. doi:10.4155/bio.12.336
Shi T, D Su, T Liu, K Tang, DG Camp, II, W Qian, and RD Smith. 2012. "Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics." Proteomics 12(8):1074-1092. doi:10.1002/pmic.201100436
Shi T, J Zhou, MA Gritsenko, M Hossain, DG Camp, II, RD Smith, and W Qian. 2012. "IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomic biomarker discovery." Methods 56(2):246–253. doi:10.1016/j.ymeth.2011.09.001
Shi T, TL Fillmore, X Sun, R Zhao, AA Schepmoes, M Hossain, S Wu, JS Kim, NJ Jones, RJ Moore, L Pasa-Tolic, J Kagan, KD Rodland, T Liu, K Tang, DG Camp, II, RD Smith, and W Qian. 2012. "An antibody-free, targeted mass spectrometry approach for quantification of proteins at low picogram/milliliter levels in human plasma/serum." Proceedings of the National Academy of Sciences of the United States of America. doi:10.1073/pnas.1204366109 [In Press]
Shi T, TL Fillmore, Y Gao, R Zhao, J He, AA Schepmoes, CD Nicora, C Wu, JL Chambers, RJ Moore, J Kagan, S Srivastava, KD Rodland, T Liu, DG Camp, II, RD Smith, and W Qian. 2013. "Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis." Analytical Chemistry 85(19):9196-9203. doi:10.1021/ac402105s
Shi T, X Sun, Y Gao, TL Fillmore, AA Schepmoes, R Zhao, J He, RJ Moore, J Kagan, KD Rodland, T Liu, AY Liu, RD Smith, K Tang, DG Camp, II, and W Qian. 2013. "Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion." Journal of Proteome Research 12(7):3353-3361. doi:10.1021/pr400178v
Sigdel TK, Y Gao, J He, A Wang, CD Nicora, TL Fillmore, T Shi, BJM Webb-Robertson, RD Smith, W Qian, O Salvatierra, DG Camp, II, and M Sarwal. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury ." Kidney International 89(6):1244-1252. doi:10. 1016/j. kint. 2015. 12. 049
Su D, AK Shukla, B Chen, JS Kim, ES Nakayasu, Y Qu, UK Aryal, KK Weitz, TRW Clauss, ME Monroe, DG Camp, II, DJ Bigelow, RD Smith, RN Kulkarni, and W Qian. 2013. "Quantitative Site-specific Reactivity Profiling of S-Nitrosylation in Mouse Skeletal Muscle Using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry." Free Radical Biology & Medicine 57:68-78. doi:10.1016/j.freeradbiomed.2012.12.010
Su D, MJ Gaffrey, J Guo, KE Hatchell, RK Chu, TRW Clauss, JT Aldrich, S Wu, SO Purvine, DG Camp, II, RD Smith, BD Thrall, and W Qian. 2013. "Proteomic Identification and Quantification of S-glutathionylation in Mouse Macrophages Using Resin-Assisted Thiol-affinity Enrichment and Isobaric Labeling." Free Radical Biology & Medicine. doi:10.1016/j.freeradbiomed.2013.12.004
Wu C, J Duan, T Liu, RD Smith, and W Qian. 2016. "Contributions of Immunoaffinity Chromatography to Deep Proteome Profiling of Human Biofluids." Journal of Chromatography B. doi:10.1016/j.jchromb.2016.01.015