Joint Appointee
Joint Appointee

Biography

Dr. Ryan Kelly is an an associate professor of chemistry at Brigham Young University and PNNL joint appointee with the Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. 

As a bioanalytical chemist, Kelly focuses on developing and deploying new technological solutions to further biological research. Several technologies he’s developed or co-developed have been licensed and/or commercialized, including chemically etched nanospray emitters, multielectrospray sources, and the subambient pressure ionization with nanoelectrospray source.  

His current research efforts involve combining microfluidic nanodroplet sample preparation, nanoflow chemical separations, and ultrasensitive mass spectrometry to extend omic analyses to smaller samples, enabling spatially resolved measurements, and single cell analyses. The central component of the platform is termed nanoPOTS (Nanodroplet Processing in One-pot for Trace Samples), which has enabled in-depth proteome analyses from 1 – 100 plant or mammalian cells. 

 

Research Interest

  • Nanoscale proteomics 

  • Single cell analysis 

  • Spatially resolved omics 

  • Microfluidic sample preparation and analysis 

  • Nanoflow liquid chromatography 

  • Nano- and picoelectrospray ionization 

  • Ultrasensitive mass spectrometry 

Education

  • PhD in Chemistry, Brigham Young University, 2005 

  • BS in Biochemistry, Brigham Young University, 2001 

Publications

2021 

Liang, Y.; Truong, T.; Zhu, Y.; Kelly, R. T. In-Depth Mass Spectrometry-Based Single-Cell and Nanoscale Proteomics, in Leukemia Stem Cells: Methods and Protocols from Methods in Molecular Biology Series vol. 2125, Sanches-Garcia, I. and Cobaleda, C. Eds. SpringerNature: New York, 2021; pp. 159-179 (book chapter). 

2020 

Councill, E. E. A. W.; Axtell, N. B.; Aposhian, A. L.; Truong, T.; Liang, Y.; Zhu, Y.; Cong, Y.; Carson, R. H.; Kelly, R. T. Adapting a Low-Cost Commercial Platform for Low-Volume Liquid Handling, SLAS Tech., 2020, DOI: 10.1177/2472630320973591. 

Cong, Y., Y. Liang, K. Motamedchaboki, R. Huguet, T. Truong, R. Zhao, Y. Shen, D. Lopez-Ferrer, Y. Zhu, and R. T. Kelly. 2020. “Improved Single-Cell Proteome Coverage Using Narrow-Bore Packed NanoLC Columns and Ultrasensitive Mass Spectrometry.” Analytical Chemistry 92 (3): 2665-2671. https://doi.org/10.1021/acs.analchem.9b04631. 

Kelly, R. T. Single-cell proteomics: progress and prospects., Mol. Cell. Proteomics, 2020, 19, 1739-1748. 

Islam, M., B. Chen, J. M. Spraggins, R. T. Kelly, and K. S. Lau. 2020. “Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, from Single Cell Identities to Patient Features.” Gastroenterology 159 (2): 453-466.e1. https://doi.org/10.1053/j.gastro.2020.04.073. 

Piehowski P.D., Y. Zhu, L.M. Bramer, K.G. Stratton, R. Zhao, D.J. Orton, and R.J. Moore, et al. 2020. "Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-µm spatial resolution." Nature Communications 11, no. 1:Article No. 8.  

Williams S.M., A.V. Liyu, C. Tsai, R.J. Moore, D.J. Orton, W.B. Chrisler, and M.J. Gaffrey, et al. 2020. "Automated coupling of nanodroplet sample preparation with liquid chromatography-mass spectrometry for high-throughput single-cell proteomics." Analytical Chemistry 92, no. 15:10588-10596. PNNL-SA-152553. doi:10.1021/acs.analchem.0c01551 

Xiang P., Y. Zhu, Y. Yang, Z. Zhao, S.M. Williams, R.J. Moore, and R.T. Kelly, et al. 2020. "Picoflow Liquid Chromatography-Mass Spectrometry for Ultrasensitive Bottom-up Proteomics using 2-µm i.d. Open Tubular Columns." Analytical Chemistry 92, no. 7:4711-4715. PNNL-SA-150120. doi:10.1021/acs.analchem.9b05639 

2019 

Dou M., C. Tsai, P.D. Piehowski, Y. Wang, T.L. Fillmore, R. Zhao, and R.J. Moore, et al. 2019. "Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples." Analytical Chemistry 91, no. 15:9707-9715. PNNL-SA-141437. doi:10.1021/acs.analchem.9b01248 

Dou M., C.D. Chouinard, Y. Zhu, G. Nagy, A.V. Liyu, Y.M. Ibrahim, and R.D. Smith, et al. 2019. "Nanowell-mediated multidimensional separations combining nanoLC with SLIM IM-MS for rapid, high-peak-capacity proteomic analyses." Analytical and Bioanalytical Chemistry 411, no. 21:5363-5372. PNNL-SA-146403. doi:10.1007/s00216-018-1452-5 

Kelly R.T., and Y. Zhu. 2019. "Ultrasmall sample biochemical analysis." Analytical and Bioanalytical Chemistry 411, no. 21:5349-5350. PNNL-SA-146523. doi:10.1007/s00216-019-01957-1 

Xu K., Y. Liang, P.D. Piehowski, M. Dou, K.C. Schwarz, R. Zhao, and R.L. Sontag, et al. 2019. "Benchtop-compatible sample processing workflow for proteome profiling of <100 mammalian cells." Analytical and Bioanalytical Chemistry 411, no. 19:4587-4596. PNNL-SA-146641. doi:10.1007/s00216-018-1493-9 

Yang X., R. Parashar, N. Sund, A.E. Plymale, T.D. Scheibe, D. Hu, and R.T. Kelly. 2019. "On Modeling Ensemble Transport of Metal Reducing Motile Bacteria." Scientific Reports 9. PNNL-SA-134947. doi:10.1038/s41598-019-51271-0 

Zhu Y., M. Scheibinger, D.C. Ellwanger, J.F. Krey, D. Choi, R.T. Kelly, and S. Heller, et al. 2019. "Single-cell proteomics reveals changes in expression during hair-cell development." eLife 8. PNNL-SA-144744. doi:10.7554/eLife.50777 

2018 

Liang Y., Y. Zhu, M. Dou, K. Xu, R.K. Chu, W.B. Chrisler, and R. Zhao, et al. 2018. "Spatially resolved proteomic profiling of <200 cells from tomato fruit pericarp by integrating laser-capture microdissection with nanodroplet sample preparation." Analytical Chemistry 90, no. 18:11106-11114. PNNL-SA-134717. doi:10.1021/acs.analchem.8b03005 

Moser T.H., H.S. Mehta, C. Park, R.T. Kelly, T. Shokuhfar, and J.E. Evans. 2018. "The role of electron irradiation history in liquid cell transmission electron microscopy." Science Advances 4, no. 4:eaaq1202. PNNL-SA-120688. doi:10.1126/sciadv.aaq1202 

Orton D.J., M.M. Tfaily, R.J. Moore, B.L. Lamarche, X. Zheng, T.L. Fillmore, and R.K. Chu, et al. 2018. "A Customizable Flow Injection System for Automated, High Throughput and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements." Analytical Chemistry 90, no. 1:737-744. PNNL-SA-128111. doi:10.1021/acs.analchem.7b02986 

Zhu Y., G. Clair, W.B. Chrisler, Y. Shen, R. Zhao, A.K. Shukla, and R.J. Moore, et al. 2018. "Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS." Angewandte Chemie International Edition 57, no. 38:12370-12374. PNNL-SA-132946. doi:10.1002/anie.201802843 

Zhu Y., J. Podolak, R. Zhao, A.K. Shukla, R.J. Moore, G.V. Thomas, and R.T. Kelly. 2018. "Proteome Profiling of 1 to 5 Spiked Circulating Tumor Cells Isolated from Whole Blood Using Immunodensity Enrichment, Laser Capture Microdissection, Nanodroplet Sample Processing, and Ultrasensitive nanoLC-MS." Analytical Chemistry 90, no. 20:11756-11759. PNNL-SA-140551. doi:10.1021/acs.analchem.8b03268 

Zhu Y., P.D. Piehowski, R. Zhao, J. Chen, Y. Shen, R.J. Moore, and A.K. Shukla, et al. 2018. "Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells." Nature Communications 9, no. 1:882. PNNL-SA-125235. doi:10.1038/s41467-018-03367-w 

Zhu Y., P.D. Piehowski, R.T. Kelly, and W. Qian. 2018. "Nanoproteomics Comes of Age." Expert Review of Proteomics 15, no. 11:865-871. PNNL-SA-136396. doi:10.1080/14789450.2018.1537787 

Zhu Y., R. Zhao, P.D. Piehowski, R.J. Moore, S. Lim, V.J. Orphan, and L. Pasa Tolic, et al. 2018. "Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples." International Journal of Mass Spectrometry 427. PNNL-SA-125645. doi:10.1016/j.ijms.2017.08.016 

2017 

Geng T., C.R. Smallwood, E.L. Bredeweg, K.R. Pomraning, A.E. Plymale, S.E. Baker, and J.E. Evans, et al. 2017. "Multimodal Microfluidic Platform for Controlled Culture and Analysis of Unicellular Organisms." Biomicrofluidics 11, no. 5:054104. PNNL-SA-129125. doi:10.1063/1.4986533 

Geng T., C.R. Smallwood, Y. Zhu, E.L. Bredeweg, S.E. Baker, J.E. Evans, and R.T. Kelly. 2017. "Multimodal Microchannel and Nanowell-Based Microfluidic Platforms for Bioimaging." In Proceedings of the 10th IEEE International Conference on Nano/Molecular Medicine and Engineering (NANOMED 2016), October 30- November 2, 2016, Macau, China, 155-158. Piscataway, New Jersey:IEEE. PNNL-SA-124699. doi:10.1109/NANOMED.2016.7883480 

Huang C., Y. Zhu, D. Jin, R.T. Kelly, and Q. Fang. 2017. "Direct Surface and Droplet Microsampling for Electrospray Ionization Mass Spectrometry Analysis with an Integrated Dual-Probe Microfluidic Chip." Analytical Chemistry 89, no. 17:9009-9016. PNNL-SA-128967. doi:10.1021/acs.analchem.7b01679 

2016 

Cong Y., S. Katipamula, C.D. Trader, D.J. Orton, T. Geng, E.S. Baker, and R.T. Kelly. 2016. "Mass Spectrometry-Based Monitoring of Millisecond Protein-Ligand Binding Dynamics Using an Automated Microfluidic Platform." Lab on a Chip 16, no. 9:1544-1548. PNNL-SA-115886. doi:10.1039/c6lc00183a 

Cong Y., S. Katipamula, T. Geng, S.A. Prost, K. Tang, and R.T. Kelly. 2016. "Electrokinetic Sample Preconcentration and Hydrodynamic Sample Injection for Microchip Electrophoresis Using a Pneumatic Microvalve." Electrophoresis 37, no. 3:455-462. PNNL-SA-109445. doi:10.1002/elps.201500286 

Jambovane S.R., S.K. Nune, R.T. Kelly, B.P. McGrail, Z. Wang, M.I. Nandasiri, and S. Katipamula, et al. 2016. "Continuous, One-pot Synthesis and Post-Synthetic Modification of NanoMOFs Using Droplet Nanoreactors." Scientific Reports. PNNL-SA-119000. doi:10.1038/srep36657 

Mahoney C.M., R.T. Kelly, M.L. Alexander, M.K. Newburn, S.P. Bader, R.G. Ewing, and A.J. Fahey, et al. 2016. "Bayesian Integration and Characterization of Composition C-4 Plastic Explosives Based on Time-of-Flight Secondary Ion Mass Spectrometry and Laser Ablation-Inductively Coupled Plasma Mass Spectrometry." Analytical Chemistry 88, no. 7:3598-3607. PNNL-SA-113646. doi:10.1021/acs.analchem.5b04151 

2015 

Baker E.S., K.E. Burnum-Johnson, Y.M. Ibrahim, D.J. Orton, M.E. Monroe, R.T. Kelly, and R.J. Moore, et al. 2015. "Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations." Proteomics 15, no. 16:2766-2776. PNNL-SA-107785. doi:10.1002/pmic.201500048 

Geng T., E.L. Bredeweg, C.J. Szymanski, B. Liu, S.E. Baker, G. Orr, and J.E. Evans, et al. 2015. "Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics." Scientific Reports 5. PNNL-SA-109268. doi:10.1038/srep16111 

Grate J.W., K. Mo, Y. Shin, A. Vasdekis, M.G. Warner, R.T. Kelly, and G. Orr, et al. 2015. "Alexa Fluor-labeled Fluorescent Cellulose Nanocrystals for Bioimaging Solid Cellulose in Spatially Structured Microenvironments." Bioconjugate Chemistry 26, no. 3:593-601. PNNL-SA-88815. doi:10.1021/acs.bioconjchem.5b00048 

Hutchison J.R., R.L. Erikson, A.M. Sheen, R.M. Ozanich, and R.T. Kelly. 2015. "Reagent-free and portable detection of Bacillus anthracis spores using a microfluidic incubator and smartphone microscope." Analyst 140, no. 18:6269-6276. PNNL-SA-109030. doi:10.1039/C5AN01304F 

Karim A.M., N.M. Al Hasan, S.A. Ivanov, S. Siefert, R.T. Kelly, N.G. Hallfors, and A.D. Benavidez, et al. 2015. "Synthesis of 1 nm Pd Nanoparticles in a Microfluidic Reactor: Insights from in Situ X ray Absorption Fine Structure Spectroscopy and Small-Angle X ray Scattering." Journal of Physical Chemistry C 119, no. 23:13257-13267. PNNL-SA-100863. doi:10.1021/acs.jpcc.5b01681