Chemist, Biological Sciences
Chemist, Biological Sciences


Danny Orton’s research expertise is in laboratory automation, with a focus on methods to deliver biological samples to mass spectrometers. He has experience designing hardware and architecting software to meet high throughput demands by bridging the gap between the one-off sample and complete statistically significant datasets. Danny is cognizant of the importance of quality (and quantity) of data, to create data sets that will allow decisions to be made correctly. Currently, he is focusing on ever smaller sample sizes to overcome barriers to high throughput analysis.

Disciplines and Skills

  • Instrument Development and Deployment


  • BS, Chemistry/Biology, Weber State University



  • 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. PNNL-SA-138884. doi:10.1038/s41467-019-13858-z


  • Wakasaki R., K. Matsushita, K. Golgotiu, S. Anderson, M.B. Eiwaz, D.J. Orton, and S. Han, et al. 2019. "Glomerular filtrate proteins in acute cardiorenal syndrome." JCI Insight 4, no. 4:Article No. e122130. PNNL-SA-129539. doi:10.1172/jci.insight.122130


  • 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
  • Stanfill B.A., E.S. Nakayasu, L.M. Bramer, A.M. Thompson, C.K. Ansong, T. Clauss, and M.A. Gritsenko, et al. 2018. "Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data." Molecular and Cellular Proteomics 17, no. 9:1824-1836. PNNL-SA-129934. doi:10.1074/mcp.RA118.000648


  • Kyle J.E., C.P. Casey, K.G. Stratton, E.M. Zink, Y. Kim, X. Zheng, and M.E. Monroe, et al. 2017. "Comparing Identified and Statistically Significant Lipids and Metabolites in 15-Year Old Serum and Dried Blood Spot Samples for Longitudinal Studies." Rapid Communications in Mass Spectrometry 31, no. 5:447-456. PNNL-SA-121197. doi:10.1002/rcm.7808
  • Zheng X., N.A. Aly, Y. Zhou, K.T. Dupuis, A. Bilbao Pena, V.L. Paurus, and D.J. Orton, et al. 2017. "A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry." Chemical Science 8, no. 11:7724-7736. PNNL-SA-126802. doi:10.1039/C7SC03464D
  • Zheng X., R. Wojcik, X. Zhang, Y.M. Ibrahim, K.E. Burnum-Johnson, D.J. Orton, and M.E. Monroe, et al. 2017. "Coupling Front-end Separations, Ion Mobility Spectrometry, and Mass Spectrometry for Enhanced Multidimensional Biological and Environmental Analyses." Annual Review of Analytical Chemistry 10. PNNL-SA-121198. doi:10.1146/annurev-anchem-061516-045212
  • Zheng X., X. Zhang, N. Schocker, R.S. Renslow, D.J. Orton, J. Khamsi, and R.A. Ashmus, et al. 2017. "Enhancing Glycan Isomer Separations with Metal Ions and Positive and Negative Polarity Ion Mobility Spectrometry-Mass Spectrometry Analyses." Analytical and Bioanalytical Chemistry 409. PNNL-SA-118977. doi:10.1007/s00216-016-9866-4


  • Burnum-Johnson K.E., S. Nie, C.P. Casey, M.E. Monroe, D.J. Orton, Y.M. Ibrahim, and M.A. Gritsenko, et al. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Molecular and Cellular Proteomics 15, no. 12:3694-3705. PNNL-SA-118308. doi:10.1074/mcp.M116.061143
  • Clair G., P.D. Piehowski, T. Nicola, J. Kitzmiller, E.L. Huang, E.M. Zink, and R.L. Sontag, et al. 2016. "Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples." Scientific Reports 6. PNNL-SA-119185. doi:10.1038/srep39223
  • 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
  • Huang E.L., P.D. Piehowski, D.J. Orton, R.J. Moore, W. Qian, C.P. Casey, and X. Sun, et al. 2016. "SNaPP: Simplified Nano-Proteomics Platform for reproducible global proteomic analysis of nanogram protein quantities." Endocrinology 157, no. 3:1307-14. PNNL-SA-111854. doi:10.1210/en.2015-1821
  • Zhang X., M.V. Romm, X. Zheng, E.M. Zink, Y. Kim, K.E. Burnum-Johnson, and D.J. Orton, et al. 2016. "SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in bio?uids." Clinical Mass Spectrometry 2. PNNL-SA-117436. doi:10.1016/j.clinms.2016.11.002


  • Aylward F.O., L. Khadempour, D. Tremmel, B.R. McDonald, C.D. Nicora, S. Wu, and R.J. Moore, et al. 2015. "Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants." PLoS One 10, no. 8:e0134752. PNNL-SA-108498. doi:10.1371/journal.pone.0134752
  • 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


  • Amidan B.G., D.J. Orton, B.L. Lamarche, M.E. Monroe, R.J. Moore, A.M. Venzin, and R.D. Smith, et al. 2014. "Signatures for Mass Spectrometry Data Quality." Journal of Proteome Research 13, no. 4:2215-2222. PNNL-SA-97216. doi:10.1021/pr401143e
  • Baker E.S., K.E. Burnum-Johnson, J.M. Jacobs, D.L. Diamond, R.N. Brown, Y.M. Ibrahim, and D.J. Orton, et al. 2014. "Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry." Molecular and Cellular Proteomics 13, no. 4:1119-1127. PNNL-SA-90826. doi:10.1074/mcp.M113.034595
  • Hyung S., P.D. Piehowski, R.J. Moore, D.J. Orton, A.A. Schepmoes, T.R. Clauss, and R.K. Chu, et al. 2014. "Microscale Depletion of High Abundance Proteins in Human Biofluids using IgY14 Immunoaffinity Resin: Analysis of Human Plasma and Cerebrospinal Fluid." Analytical and Bioanalytical Chemistry 406, no. 28:7117-7125. PNNL-SA-92758. doi:10.1007/s00216-014-8058-3
  • Sigdel T.K., N. Salomonis, C.D. Nicora, S. Ryu, J. He, V. Dinh, and D.J. Orton, et al. 2014. "The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics." Molecular & Cellular Proteomics. MCP 13, no. 2:621-631. PNWD-SA-10124. doi:10.1074/mcp.M113.030577
  • Smith J.S., T.E. Angel, C. Chavkin, D.J. Orton, R.J. Moore, and R.D. Smith. 2014. "Characterization of individual mouse cerebrospinal fluid proteomes." Proteomics 14, no. 9:1102-1106. PNNL-SA-93378. doi:10.1002/pmic.201300241


  • Merkley E.D., E.S. Baker, K.L. Crowell, D.J. Orton, T. Taverner, C. Ansong, and Y.M. Ibrahim, et al. 2013. "Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking." Journal of the American Society for Mass Spectrometry 24, no. 3:444-449. PNNL-SA-88464. doi:10.1007/s13361-012-0565-x
  • Piehowski P.D., V.A. Petyuk, D.J. Orton, F. Xie, R.J. Moore, M. Ramirez Restrepo, and A. Engel, et al. 2013. "Sources of Technical Variability in Quantitative LC-MS Proteomics: Human Brain Tissue Sample Analysis." Journal of Proteome Research 12, no. 5:2128-2137. PNNL-SA-92104. doi:10.1021/pr301146m
  • Qu Y., S. Wu, R. Zhao, E.M. Zink, D.J. Orton, R.J. Moore, and D. Meng, et al. 2013. "Automated Immobilized Metal Affinity Chromatography System for Enrichment of Escherichia coli Phosphoproteome." Electrophoresis 34, no. 11:1619-1626. PNNL-SA-92228. doi:10.1002/elps.201200628
  • Wang D., S. Dasari, M.C. Chambers, J.D. Holman, K. Chen, D. Liebler, and D.J. Orton, et al. 2013. "Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates." Genomics, Proteomics & Bioinformatics 11, no. 2:86-95. PNNL-SA-98549. doi:10.1016/j.gpb.2012.11.004


  • Shukla A.K., R. Zhang, D.J. Orton, R. Zhao, T.R. Clauss, R.J. Moore, and R.D. Smith. 2011. "Formation of iron complexs from trifluoroacetic acid based liquid chromatography mobile phases as interference ions in liquid chromatography/electrospray ionization mass spectrometric analysis." Rapid Communications in Mass Spectrometry 25, no. 10:1452-1456. PNNL-SA-68066. doi:10.1002/rcm.5017
  • Wang Y., F. Yang, Y. Fu, X. Huang, W. Wang, X. Jiang, and M.A. Gritsenko, et al. 2011. "Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction." Journal of Biological Chemistry 286, no. 20:18190-18201. PNNL-SA-79165.


  • Baker E.S., E.A. Livesay, D.J. Orton, R.J. Moore, W.F. Danielson, D.C. Prior, and Y.M. Ibrahim, et al. 2010. "An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies." Journal of Proteome Research 9, no. 2:997-1006. PNNL-SA-67461. doi:10.1021/pr900888b


  • Yang F., S. Wu, D.L. Stenoien, R. Zhao, M.E. Monroe, M.A. Gritsenko, and S.O. Purvine, et al. 2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ-labeled phosphopeptides." Analytical Chemistry 81, no. 10:4137-4143. PNNL-SA-63701. doi:10.1021/ac802605m



  • Kelly R.T., J.S. Page, Q. Luo, R.J. Moore, D.J. Orton, K. Tang, and R.D. Smith. 2006. "Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry." Analytical Chemistry 78, no. 22:7796-7801. PNNL-SA-50640.