PNNL

Eric Merkley is a protein/peptide mass spectrometrist with a focus on proteomics data analysis for forensics and biosecurity applications, such as analysis of protein toxins and proteomics of bacterial threat agents. Initially trained in biochemistry, his PhD research at University of Washington focused on spectroscopic, enzymatic, and molecular dynamics studies of a thermophilic enzyme and its mesophilic homologue. Postdoctoral research at Pacific Northwest National Laboratory included proteomics and the application of proteomics techniques to cross-linking mass spectrometry. Current research in the National Security Directorate emphasizes data interpretation and alternative data analysis methods (such as spectral library searching and de novo peptide identification) needed to support the unique challenges and requirements of forensic proteomics. In 2022, he became team leader of the Cheminformatic and Bioinformatics team in the Chemical and Biological Signatures group.

• Biochemistry
• Bioinformatics
• Forensics
• Proteomics
• Proteomics Data Analysis

University of Washington

Doctor of Philosophy, Biochemistry (2010)

Brigham Young University

Bachelor of Science, Biochemistry (2003)

J.-Y. Lee, H.D. Mitchell, M.C. Burnet, R. Wu, S.C. Jenson, E.D. Merkley, E.S. Nakayasu, C.D. Nicora, J.K. Jansson, K.E. Burnum-Johnson, S.H. Payne. Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics. Journal of Proteome Research, 2022, 21(8), 2023-2035.

M. Zhou, J.A. Laureanti, C. Bell, M. Kwon, Q. Meng, I.V. Novikova,  D. Thomas,  C.D. Nicora,  R. Sontag,  D. Bedgar,  I. O’Bryon, E.D. Merkley, B.Ginovska, J.R. Cort,  L.B. Davin, N.G. Lewis De novo Sequencing and Native Mass Spectrometry Reveals Hetero-Association of Dirigent Protein Homologs and Potential Interacting Proteins in Forsythia × intermedia. Analyst. 2021, 24, DOI: 10.1039/D1AN01476E.

A.D. McNaughton, E.L. Bredeweg, J. Manzer, J. Zucker, N. Munoz Munoz, M.C. Burnet, E.S. Nakayasu, K.R. Pomraning, E.D. Merkley, A. Dai, W.B. Chrisler, S.E. Baker, P.C. St. John, N. Kumar. Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling. ACS Synthetic Biology. 2021, 10(11), 2968-2981.

I. O'Bryon, S.C. Jenson, E.D. Merkley, Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification. Protein Science. 2020, 29(9), 1864-1878.

E.D. Merkley, B.L. Deatherage Kaiser, D.S. Wunschel, K.L. Wahl, Proteomics for Bioforensics. In Microbial Forensics (Third Edition), Budowle, B.; Schutzer, S.; Morse, S., Eds. Academic Press: 2020; pp 251-265.

E.D. Merkley, K.E. Burnum-Johnson, L.N. Anderson, S.C. Jenson, K.L. Wahl, Uniformly N-15-Labeled Recombinant Ricin A-Chain as an Internal Retention Time Standard for Increased Confidence in Forensic Identification of Ricin by Untargeted Nanoflow Liquid Chromatography-Tandem Mass Spectrometry. Analytical Chemistry. 2019, 91 (21), 13372-13376.

E.D. Merkley, B.L. Deatherage Kaiser, H.W. Kreuzer, A Proteomics Tutorial. In Applications in Forensic Proteomics: Protein Identification and Profiling, Merkley, E.D., Ed. American Chemical Society: 2019; Vol. 1339, pp 9-28.

E.D. Merkley, Proteomics for Microbial Forensics. In Applications in Forensic Proteomics: Protein Identification and Profiling, Merkley, E.D., Ed. American Chemical Society: 2019; Vol. 1339, pp 143-160.

K.H. Jarman, E.D. Merkley, The Statistical Defensibility of Forensic Proteomics. In Applications in Forensic Proteomics: Protein Identification and Profiling, Merkley, E.D., Ed. American Chemical Society: 2019; Vol. 1339, pp 203-228.

I. O'Bryon, A.E. Tucker, B.L. Deatherage Kaiser, K.L. Wahl, E.D. Merkley, Constructing a Tandem Mass Spectral Library for Forensic Ricin Identification. Journal of Proteome Research. 2019, 18, 11, 3926-3935.

N.C. Heller, A.M. Garrett, E.D. Merkley, S.R. Cendrowski, A.M. Melville, J.S. Arce, S.C. Jenson, K.L. Wahl, K.H. Jarman, Probabilistic Limit of Detection for Ricin Identification Using a Shotgun Proteomics Assay. Analytical Chemistry. 2019, 91, 19, 12399-12406.

J. Caswell, J.D. Gans, N. Generous, C.M. Hudson, E.D. Merkley, C. Johnson, C. Oehmen, K. Omberg, E. Purvine, K. Taylor, C.L. Ting, M. Wolinsky, G. Xie, Defending Our Public Biological Databases as a Global Critical Infrastructure. Frontiers in Bioengineering and Biotechnology. 2019, 7, 58.

E.D. Merkley, D. Wunschel, K.L. Wahl, K.H. Jarman, Applications and Challenges of Forensic Proteomics. Forensic Science International. 2019, 297, 350-363.

J. Dunbar, S. Pillai, D.S. Wunschel, M. Dickens, S.A. Morse, D. Franz, A. Bartko, J. Challacombe, T. Persons, M.A. Hughes, S.R. Blanke, R. Holland, J. Hutchison, E.D. Merkley, K. Campbell, C.S. Branda, S. Sharma, L. Lindler, K. Anderson, D. Hodge, Perspective on Improving Environmental Monitoring of Biothreats. Frontiers in Bioengineering and Biotechnology. 2018, 6.

K.H. Jarman, N.C. Heller, S.C. Jenson, J.R. Hutchison, B.L. Deatherage Kaiser, S.H. Payne, D.S. Wunschel, E.D. Merkley. Proteomics Goes to Court: A Statistical Foundation for Forensic Toxin/Organism Identification Using Bottom-Up Proteomics. Journal of Proteome Research. 2018, 17, 9, 3075-3085.

D.S. Wunschel, J.R. Hutchison, B.L. Deatherage Kaiser, E.D. Merkley, B.M. Hess, A. Lin, M.G. Warner. Proteomic signatures differentiating Bacillus anthracis Sterne sporulation on soil relative to laboratory media. Analyst. 2018, 143,1,123-132.

E.D. Merkley, S.C.Jenson, J.S. Arce, A.M. Melville, O.P. Leiser, D.S. Wunschel, K.L. Wahl. Ricin-Like Proteins from the Castor Plant Do Not Influence Liquid Chromatography-Mass Spectrometry Detection of Ricin in Forensically Relevant Samples. Toxicon. 2017, 140, 18-31.

E.D. Merkley, L.H. Sego, A. Lin, O.P. Leiser, B.L. Deatherage Kaiser, J.N. Adkins, P.A. Keim, D.M. Wagner, H.W. Kreuzer. Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague. PloS ONE. 2017, 12, 8, e0183478.

O.P. Leiser, E.D. Merkley, B.H. Clowers, B.L. Deatherage Kaiser, A. Lin, J.R. Hutchison, A.M. Melville, D.M. Wagner, P.S Keim, J.T. Foster, H.W Kreuzer. Investigation of Yersinia pestis laboratory adaptation through a combined genomics and proteomics approach. PloS ONE. 2015, 10, 11, e0142997.

E.D. Merkley, A. Lin, B.H. Clowers, J.R. Hutchison, H.W. Kreuzer. Effects of bacterial inactivation methods on downstream analysis. Journal of Microbiological Methods. 2015, 112, 3-10.

E.D. Merkley, K.C. Wrighton, C.J. Castelle, B.J. Anderson, M.J. Wilkins, V. Shah, T. Arbour, J.N. Brown, S.W. Singer, R.D. Smith, M.S. Lipton. Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis. Journal of Proteome Research. 2015, 14(3), 1361-1375.

G. Saxer, M.D. Krepps, E.D. Merkley, C. Ansong, B.L. Deatherage Kaiser, M.-T. Valovska, N.Ristic, P.T. Yeh, V.P. Prakash, O.P. Leiser, L. Nakhleh, H.S. Gibbons, H.W. Kreuzer, Y. Shamoo. Mutations in global regulators lead to metabolic selection during adaptation to complex environments. PloS Genetics. 2014, 10(12), e1004872.

E.D. Merkley, S. Rysavy, R.P. Hafen, V. Daggett, J.N. Adkins. Distance Restraints from Cross-Linking Mass Spectrometry: Mining a Molecular Dynamics Simulation Database to Evaluate Lysine-Lysine Distances. Protein Science. 2014, 23(6). 747-759.

E.D. Merkley, T.O. Metz, Richard D. Smith, John W. Baynes, Norma Frizzell. The Succinated Proteome. Mass Spectrometry Reviews. 2013, 33(2). 98-109.

N.C. Sadler, M.R. Melnicki, M.H. Serres, E.D. Merkley, W.B. Chrisler, E.A. Hill, M.F. Romine, S. Kim, E.M. Zink, S. Datta, A.T. Wright. Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium. ACS Chemical Biology. 2013, 9(1). 291-300.

E.D. Merkley, J.R. Cort, J.N. Adkins. Cross-linking and Mass Spectrometry Methodologies to Facilitate Structural Biology: Finding a Path Through the Maze. Journal of Structural and Functional Genomics. 2013, 13(3). 77-90.  

E.D. Merkley, E.S. Baker, C. K.L., D. J. Orton, T. Taverner, C. Ansong, Y. M. Ibrahim, M.C. Burnet, J. R. Cort, G. A. Anderson, R. D. Smith, J. N. Adkins, Journal of the American Society of Mass Spectrometry. 2013, 24(3). 444-449.

E.D. Merkley, B.J. Anderson, J.H. Park, S. M. Belchik, L. Shi, M E. Monroe, R.D. Smith, M.S. Lipton, Detection and Identification of Heme c-Modified Peptides by Histidine Affinity Chromatography, High-Performance Liquid Chromatography-Mass Spectrometry, and Database Searching. Journal of Proteomics Research. 2012, 11(3). 6147-6158.

J. Liu, Z. Wang, S.M. Belchik, M.J. Edwards, C. Liu, D.W. Kennedy, E.D. Merkley, M.S. Lipton, J.N. Butt, D.J. Richardson, J.M. Zachara, J.K. Fredrickson, K.M. Rosso, L. Shi, Identification and Characterization of MtoA: a Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-oxidizing Bacterium Sideroxydans lithotrophicus ES-1. Frontiers in Microbiology 2012, 3. 1-11.

E.D. Merkley, V. Daggett, W.W. Parson, A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8. Proteins: Structure, Function, and Bioinformatics 2011, 80. 546-555.

M.W. van der Kamp, R.D. Schaeffer, A.L. Jonsson, A.D. Scouras, A.M. Simms, R.D. Toofanny, N.C. Benson, P.C. Anderson, E.D. Merkley, S. Rysavy, D. Bromley, D.A.C. Beck, V. Daggett, Dynameomics: A Comprehensive Database of Protein Dynamics. Structure 2010, 18. 423-435.

E.D. Merkley, W.W. Parson, V. Daggett, Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold. Protein Engineering Design & Selection 2010, 23. 327-336.

E.D. Merkley, B. Bernard, V. Daggett, Conformational changes below the T_m: Molecular dynamics studies of the thermal pretransition of ribonuclease A. Biochemistry 2008, 47. 880-892.

S.P. Ziemer, T.L. Niederhauser, E.D. Merkley, J.L. Price, E.C. Sorenson, B. McRae, B.A. Patterson, M.L. Origlia-Luster, E.M. Woolley, Thermodynamics of proton dissociations from aqueous glycine at temperatures from 278.15 to 393.15 K, molalities from 0 to 1.0 mol · kg^-1, and at the pressure 0.35 MPa: Apparent molar heat capacities and apparent molar volumes of glycine, glycinium chloride, and sodium glycinate. J. Chem. Thermodyn. 2006, 38. 467-483.

B.R. Brown, E.D. Merkley, B.R. McRae, M.L. Origlia-Luster, E.M. Woolley, Apparent molar volumes and apparent molar heat capacities of aqueous nickel(II) nitrate, copper(II) nitrate, and zinc(II) nitrate at temperatures from (278.15 to 393.15) K at the pressure 0.35 MPa. J. Chem. Thermodyn. 2004, 36. 437-446.

J.L. Price, E.C. Sorenson, E.D. Merkley, B.R. McRae, E.M. Woolley, Thermodynamics of proton dissociations from aqueous L-valine and L-2-amino-n-butanoic acid: apparent molar volumes and apparent molar heat capacities of the protonated cationic, neutral zwitterionic, and deprotonated anionic species at temperatures from 278.15 <= T/K <= 393.15, at molalities 0.015 <= m/mol·kg^-1<= 0.67, and pressure p=0.35 MPa. J. Chem. Thermodyn. 2003, 35. 1425-1467.