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Staff information


Erin Baker

Integrative Omics
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352


Dr. Erin Baker is a bioanalytical chemist with more than 16 years’ experience utilizing ion mobility spectrometry in conjunction with mass spectrometry (IMS-MS) to study environmental and biological systems. In the last 10 years she has worked primarily on IMS-MS applications in the field of proteomics and more recently she has worked to optimize IMS-MS metabolomic, glycomic and lipidomic separations. Her research involves the development and evaluation of high-throughput IMS-MS, SPE-IMS-MS and LC-IMS-MS analyses to quickly study numerous samples in a short time period without losing valuable biological information, as well as assessing the number and quality of features detected with IMS-MS for comparison with existing MS platforms. Dr. Baker is also presently working with the PNNL Informatics team to design and implement software tools that automatically analyze the complex multidimensional SPE-IMS-MS and LC-IMS-MS data.

Research Interests

  • Separation and dynamic range enhancement of peptides from complex plasma mixtures
  • Development of HPLC methods and mass spectrometry instrumentation
  • Structural variations between biological molecules in the solution, solid and gas phases

Education and Credentials

  • Ph.D., Chemistry (specializing in Physical Chemistry), University of California, Santa Barbara, 2001-2005.
  • B.S., Chemistry (minor in Mathematics), Montana State University, Bozeman, 1997-2001.

PNNL Publications


  • Cong Y, S Katipamula, CD Trader, DJ Orton, T Geng, ES Baker, and RT Kelly. 2016. "Mass Spectrometry-Based Monitoring of Millisecond Protein-Ligand Binding Dynamics Using an Automated Microfluidic Platform." Lab on a Chip 16(9):1544-1548.  doi:10.1039/c6lc00183a
  • Kyle JE, X Zhang, KK Weitz, ME Monroe, YM Ibrahim, RJ Moore, J Cha, X Sun, ES Lovelace, J Wagoner, S Polyak, TO Metz, SK Dey, RD Smith, KE Burnum-Johnson, and ES Baker. 2016. "Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Analyst 141(5):1649-1659.  doi:10.1039/C5AN02062J
  • Chen TC, YM Ibrahim, IK Webb, VBS Garimella, X Zhang, AM Hamid, L Deng, WE Karnesky, SA Prost, JA Sandoval, RV Norheim, GA Anderson, AV Tolmachev, ES Baker, and RD Smith. 2016. "Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations." Analytical Chemistry 88(3):1728-1733.  doi:10.1021/acs.analchem.5b03910
  • Liu R, S Cheng, ES Baker, RD Smith, XC Zeng, and B Gong. 2016. "Surprising Impact of Remote Groups on the Folding-Unfolding and Dimer-Chain Equilibria of Bifunctionl H-Bonding Unimers." Chemical Communications 52(19):3773-3776.  doi:10.1039/C6CC00224B


  • Baker ES, KE Burnum-Johnson, YM Ibrahim, DJ Orton, ME Monroe, RT Kelly, RJ Moore, X Zhang, R Theberge, CE Costello, and RD Smith. 2015. "Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations." Proteomics 15(16):27662776.  doi:10.1002/pmic.201500048
  • Garimella VBS, YM Ibrahim, IK Webb, AB Ipsen, TC Chen, AV Tolmachev, ES Baker, GA Anderson, and RD Smith. 2015. "ION MANIPULATIONS IN STRUCTURES FOR LOSSLESS ION MANIPULATIONS (SLIM): COMPUTATIONAL EVALUATION OF A 90o TURN AND A SWITCH." Analyst 140(20):6845-6852.  doi:10.1039/c5an00844a
  • Cha J, KE Burnum-Johnson, A Bartos, Y Li, ES Baker, SC Tilton, BJM Webb-Robertson, PD Piehowski, ME Monroe, A Jegga, S Murata, Y Hirota, and SK Dey. 2015. "Muscle segment homeobox genes direct embryonic diapause by limiting inflammation in the uterus." Journal of Biological Chemistry 290(24):15337-15349.  doi:10.1074/jbc.M115.655001
  • Ibrahim YM, ES Baker, WF Danielson, RV Norheim, DC Prior, GA Anderson, ME Belov, and RD Smith. 2015. "Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer." International Journal of Mass Spectrometry 377:655-662.  doi:10.1016/j.ijms.2014.07.034
  • Wu C, T Liu, ES Baker, KD Rodland, and RD Smith. 2015. "Mass spectrometry for biomarker development." In General Methods in Biomarker Research and their Applications. Biomarkers in Disease: Methods, Discoveries and Applications, ed. V Preedy and V Patel, pp. 17-48.  Springer, Heidelberg , Germany. 
  • Zhang X, VBS Garimella, SA Prost, IK Webb, TC Chen, K Tang, AV Tolmachev, RV Norheim, ES Baker, GA Anderson, YM Ibrahim, and RD Smith. 2015. "Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations ." Analytical Chemistry 87(12):6010-6016.  doi:10.1021/acs.analchem.5b00214
  • Zhang X, YM Ibrahim, TC Chen, JE Kyle, RV Norheim, ME Monroe, RD Smith, and ES Baker. 2015. "Enhancing Biological Analyses with Three Dimensional Field Asymmetric Ion Mobility, Low Field Drift Time Ion Mobility and Mass Spectrometry (µFAIMS/IMS-MS) Separations." Analyst doi:10.1039/c5an00897b


  • Baker ES, DC Muddiman, and J Loo. 2014. "Focus on Advancing High Performance Mass Spectrometry, Honoring Dr. Richard D. Smith, Recipient of the 2013 Award for a Distinguished Contribution in Mass Spectrometry." Journal of the American Society for Mass Spectrometry 25(12):1997-1999.  doi:10.1007/s13361-014-1007-8
  • Baker ES, KE Burnum-Johnson, JM Jacobs, DL Diamond, RN Brown, YM Ibrahim, DJ Orton, PD Piehowski, DE Purdy, RJ Moore, WF Danielson, III, ME Monroe, KL Crowell, GW Slysz, MA Gritsenko, JD Sandoval, BL Lamarche, MM Matzke, BJM Webb-Robertson, BC Simons, BJ McMahon, R Bhattacharya, JD Perkins, RL Carithers, S Strom, S Self, MG Katze, GA Anderson, and RD Smith. 2014. "Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry." Molecular and Cellular Proteomics 13(4):1119-1127.  doi:10.1074/mcp.M113.034595
  • Ibrahim YM, VBS Garimella, AV Tolmachev, ES Baker, and RD Smith. 2014. "Improving Ion Mobility Measurement Sensitivity by Utilizing Helium in an Ion Funnel-Trap." Analytical Chemistry 86(11):5295-5299.  doi:10.1021/ac404250z
  • Prost SA, KL Crowell, ES Baker, YM Ibrahim, BH Clowers, ME Monroe, GA Anderson, RD Smith, and SH Payne. 2014. "Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements." Journal of the American Society for Mass Spectrometry 25(12):2020-2027.  doi:10.1007/s13361-014-0895-y


  • Crowell KL, ES Baker, SH Payne, YM Ibrahim, ME Monroe, GW Slysz, BL Lamarche, VA Petyuk, PD Piehowski, WF Danielson, III, GA Anderson, and RD Smith. 2013. "Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry." International Journal of Mass Spectrometry 354-355:312-317.  doi:10.1016/j.ijms.2013.06.028
  • Crowell KL, GW Slysz, ES Baker, BL Lamarche, ME Monroe, YM Ibrahim, SH Payne, GA Anderson, and RD Smith. 2013. "LC-IMS-MS Feature Finder: Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets." Bioinformatics 29(21):2804-2805 .  doi:10.1093/bioinformatics/btt465
  • Merkley ED, ES Baker, KL Crowell, DJ Orton, T Taverner, C Ansong, YM Ibrahim, MC Burnet, JR Cort, GA Anderson, RD Smith, and JN Adkins. 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(3):444-449.  doi:10.1007/s13361-012-0565-x
  • Venceslau SS, JR Cort, ES Baker, RK Chu, EW Robinson, C Dahl, LM Saraiva, and IA Pereira. 2013. "Redox states of Desulfovibrio vulgaris DsrC, a key protein in dissimilatory sulfite reduction." Biochemical and Biophysical Research Communications 441(4):731-736.  doi:10.1016/j.bbrc.2013.10.116


  • Baker ES, T Liu, VA Petyuk, KE Burnum-Johnson, YM Ibrahim, GA Anderson, and RD Smith. 2012. "Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications." Genome Medicine 4:Article No. 63.  doi:10.1186/gm364
  • Angel TE, UK Aryal, SM Hengel, ES Baker, RT Kelly, EW Robinson, and RD Smith. 2012. "Mass spectrometry-based proteomics: existing capabilities and future directions." Chemical Society Reviews 41(10):3912-3928.  doi:10.1039/C2CS15331A
  • Burnum KE, Y Hirota, ES Baker, M Yoshie, YM Ibrahim, ME Monroe, GA Anderson, RD Smith, T Daikoku, and SK Dey. 2012. "Uterine deletion of Trp53 compromises antioxidant responses in mouse decidua." Endocrinology 153(9):4568-4579.  doi:10.1210/en.2012-1335
  • Hengel SM, EA Floyd, ES Baker, R Zhao, S Wu, and L Pasa-Tolic. 2012. "Evaluation of SDS depletion using an affinity spin column and IMS-MS detection." Proteomics 12(21):3138-3142.  doi:10.1002/pmic.201200168


  • Belov ME, RT Kurulugama, D Lopez-Ferrer, YM Ibrahim, and ES Baker. 2011. "New Developments in LC-MS and Other Hyphenated Techniques." Chapter 47 in Sample Preparation in Biological Mass Spectrometry, ed. AR Ivanov & AV Lazarev, pp. 981-1030.  Springer, New York, NY. 


  • Baker ES, EA Livesay, DJ Orton, RJ Moore, WF Danielson, DC Prior, YM Ibrahim, BL Lamarche, AM Mayampurath, AA Schepmoes, DF Hopkins, K Tang, RD Smith, and ME Belov. 2010. "An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies." Journal of Proteome Research 9(2):997-1006.  doi:10.1021/pr900888b
  • Buchko GW, G Niemann, ES Baker, ME Belov, RD Smith, F Heffron, JN Adkins, and JE McDermott. 2010. "A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins." Molecular Biosystems 6(12):2448-2458.  doi:10.1039/c0mb00097c
  • Ibrahim YM, DC Prior, ES Baker, RD Smith, and ME Belov. 2010. "Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation- Tandem Time-of-Flight Mass Spectrometry Approach." International Journal of Mass Spectrometry 293(1-3):34-44. 
  • Shah AR, K Agarwal, ES Baker, M Singhal, AM Mayampurath, YM Ibrahim, LJ Kangas, ME Monroe, R Zhao, ME Belov, GA Anderson, and RD Smith. 2010. "Machine learning based prediction for peptide drift times in ion mobility spectrometry ." Bioinformatics 26(13):1601-1607.  doi:10.1093/bioinformatics/btq245


  • Page JS, I Marginean, ES Baker, RT Kelly, K Tang, and RD Smith. 2009. "Biases in Ion Transmission Through an Electrospray Ionization-Mass Spectrometry Capillary Inlet." Journal of the American Society for Mass Spectrometry 20(12):2265-2272.  doi:10.1016/j.jasms.2009.08.018


  • Baker ES, K Tang, WF Danielson, III, DC Prior, and RD Smith. 2008. "Simultaneous Fragmentation of Multiple Ions Using IMS Drift Time Dependent Collision Energies." Journal of the American Society for Mass Spectrometry 19(3):411-419.  doi:10.1016/j.jasms.2007.11.018
  • Metz TO, JS Page, ES Baker, K Tang, J Ding, Y Shen, and RD Smith. 2008. "High Resolution Separations and Improved Ion Production and Transmission in Metabolomics." Trends in Analytical Chemistry. TrAC 27(3):205-214.  doi:10.1016/j.trac.2007.11.003


  • Baker ES, BH Clowers, F Li, K Tang, AV Tolmachev, DC Prior, ME Belov, and RD Smith. 2007. "Ion Mobility Spectrometry Mass Spectrometry Performance Using Electrodynamic Ion Funnels and Elevated Drift Gas Pressures." Journal of the American Society for Mass Spectrometry 18(7):1176-1187.  doi:doi:10.1016/j.jasms.2007.03.031
  • Shvartsburg AA, SV Mashkevich, ES Baker, and RD Smith. 2007. "Optimization of Algorithms for Ion Mobility Calculations." Journal of Physical Chemistry A 111(10):2002-2010.  doi:10.1021/jp066953m

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