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Fundamental and Computational Sciences Directorate

Staff information


Erin Baker

Instrument Dev & Deploy
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352


Dr. Erin Baker is a bioanalytical chemist with more than 18 years’ experience and 100 publications utilizing ion mobility spectrometry in conjunction with mass spectrometry (IMS-MS) to study environmental and biological systems. In the last 12 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

  • Developing rapid omic separations for complex biological and environmental samples
  • Increasing the current dynamic range in mass spectrometry instrumentation for omic analyses
  • Uncovering statistically significant molecular changes due to biological conditions and environmental perturbations
  • Understanding 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


  • Barran P., and E.M. Baker. 2018. "Editorial Overview: Omics." Current Opinion in Chemical Biology 42. PNNL-SA-134047. doi:10.1016/j.cbpa.2018.02.007
  • Bilbao Pena A., B.C. Gibbons, G.W. Slysz, K.L. Crowell, M.E. Monroe, Y.M. Ibrahim, and R.D. Smith, et al. 2018. "An Algorithm to Correct Saturated Mass Spectrometry Ion Abundances for Enhanced Quantitation and Mass Accuracy in Omic Studies." International Journal of Mass Spectrometry 427. PNNL-SA-126312. doi:10.1016/j.ijms.2017.11.003
  • Garabedian A., P. Benigni, C. Ramirez, E.M. Baker, T. Liu, R.D. Smith, and F. Fernandez-Lima. 2018. "Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS." Journal of the American Society for Mass Spectrometry 29, no. 5:817-826. PNNL-SA-129610. doi:10.1007/s13361-017-1787-8
  • Horney J.A., G.A. Casillas, E.M. Baker, K.W. Stone, K.R. Kirsch, K. Camargo, and T. Wade, et al. 2018. "Comparing Residential Contamination in a Houston Environmental Justice Neighborhood before and after Hurricane Harvey." PLoS One 13, no. 2:Article No. e0192660. PNNL-SA-134072. doi:10.1371/journal.pone.0192660
  • Kyle J.E., N.A. Aly, X. Zheng, K.E. Burnum-Johnson, R.D. Smith, and E.M. Baker. 2018. "Evaluating Lipid Mediator Structural Complexity Using Ion Mobility Spectrometry." Bioanalysis 10, no. 5:279-289. PNNL-SA-130733. doi:10.4155/bio-2017-0245
  • Nicora C.D., K.E. Burnum-Johnson, E.S. Nakayasu, C.P. Casey, R.A. White, T. Roy Chowdhury, and J.E. Kyle, et al. 2018. "The MPLEx Protocol for Multi-Omic Analyses of Soil Samples." Journal of Visualized Experiments e57343, no. 135. PNNL-SA-129344. doi:10.3791/57343
  • 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
  • Poad B.L., X. Zheng, T.A. Mitchell, R.D. Smith, E.M. Baker, and S.J. Blanksby. 2018. "Online ozonolysis combined with ion mobility-mass spectrometry provides a new platform for lipid isomer analyses." Analytical Chemistry 90, no. 2:1292-1300. PNNL-SA-129778. doi:10.1021/acs.analchem.7b04091
  • Zheng X., R.D. Smith, and E.M. Baker. 2018. "Recent Advances in Lipid Separations and Structural Elucidation Using Mass Spectrometry Combined with Ion Mobility Spectrometry, Ion-Molecule Reactions and Fragmentation Approaches." Current Opinion in Chemical Biology 42. PNNL-SA-131398. doi:10.1016/j.cbpa.2017.11.009


  • Baker E.M., R. Wojcik, I.K. Webb, V. Garimella, S.A. Prost, Y.M. Ibrahim, and R.D. Smith. 2017. "Lipid and Glycolipid Isomer Analyses Using Ultra-high Resolution Ion Mobility Spectrometry Separations." International Journal of Molecular Sciences 18, no. 1:183. PNNL-SA-122274. doi:10.3390/ijms18010183
  • Burnum-Johnson K.E., E.M. Baker, and T.O. Metz. 2017. "Characterizing the Lipid and Metabolite Changes Associated with Placental Function and Pregnancy Complications Using Ion Mobility Spectrometry-Mass Spectrometry and Mass Spectrometry Imaging." Placenta 60, no. Supplement 1:S67-S72. PNNL-SA-123563. doi:10.1016/j.placenta.2017.03.016
  • Deng L., I.K. Webb, V. Garimella, A.M. Hamid, X. Zheng, R.V. Norheim, and S.A. Prost, et al. 2017. "Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations." Analytical Chemistry 89, no. 8:4628-4634. PNNL-SA-123438. doi:10.1021/acs.analchem.7b00185
  • Deng L., V. Garimella, A.M. Hamid, I.K. Webb, I.K. Attah, R.V. Norheim, and S.A. Prost, et al. 2017. "Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM)." Analytical Chemistry 89, no. 12:6432-6439. PNNL-SA-123357. doi:10.1021/acs.analchem.7b00189
  • Ibrahim Y.M., A.M. Hamid, L. Deng, V. Garimella, I.K. Webb, E.M. Baker, and R.D. Smith. 2017. "New Frontiers for Mass Spectrometry based upon Structures for Lossless Ion Manipulations." Analyst 142, no. 7:1010-1021. PNNL-SA-123137. doi:10.1039/C7AN00031F
  • 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
  • Ligare M.R., E.M. Baker, J. Laskin, and G.E. Johnson. 2017. "Ligand Induced Structural Isomerism in Phosphine Coordinated Gold Clusters Revealed by Ion Mobility-Mass Spectrometry." Chemical Communications 53, no. 53:7389-7392. PNNL-SA-124840. doi:10.1039/C7CC02251D
  • Ma J., C.P. Casey, X. Zheng, Y.M. Ibrahim, C.S. Wilkins, R.S. Renslow, and D.G. Thomas, et al. 2017. "PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association." Bioinformatics 33, no. 17:2715-2722. PNNL-SA-122828. doi:10.1093/bioinformatics/btx305
  • Metz T.O., E.M. Baker, E.L. Schymanski, R.S. Renslow, D.G. Thomas, T.J. Causon, and I.K. Webb, et al. 2017. "Integrating Ion Mobility Spectrometry into Mass Spectrometry-based Exposome Measurements: What Can It Add and How Far Can It Go?." Bioanalysis 9, no. 1:81-98. PNNL-SA-121158. doi:10.4155/bio-2016-0244
  • Nielson C., J. Wiedrick, J. Shen, J.M. Jacobs, E.M. Baker, A. Baraff, and P.D. Piehowski, et al. 2017. "Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics." Journal of Bone and Mineral Research 32, no. 7:1559-1567. PNNL-SA-111322. doi:10.1002/jbmr.3125
  • Rosnow J.J., L.N. Anderson, R.N. Nair, E.S. Baker, and A.T. Wright. 2017. "Emerging Multi-Omic Technologies for Improved Functional Characterization of Lignocellulose Degrading Enzymes." Critical Reviews in Biotechnology 37, no. 5:626-640. PNNL-SA-116817. doi:10.1080/07388551.2016.1209158
  • Stow S., T.J. Causon, X. Zheng, R.T. Kurulugama Lekamlage, T. Mairinger, J.C. May, and E.E. Rennie, et al. 2017. "An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass." Analytical Chemistry 89, no. 17:9048-9055. PNNL-SA-129678. doi:10.1021/acs.analchem.7b01729
  • Zheng X., L. Deng, E.M. Baker, Y.M. Ibrahim, V.A. Petyuk, and R.D. Smith. 2017. "Distinguishing D- and L-Aspartic and Isoaspartic Acids in Amyloid ß Peptides with Ultrahigh Resolution Ion Mobility Spectrometry." Chemical Communications 53, no. 56:7913-7916. PNNL-SA-124064. doi:10.1039/C7CC03321D
  • 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., R.S. Renslow, M.M. Makola, I.K. Webb, L. Deng, D.G. Thomas, and N. Govind, et al. 2017. "Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry." The Journal of Physical Chemistry Letters 8, no. 7:1381-1388. PNNL-SA-123119. doi:10.1021/acs.jpclett.6b03015
  • 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
  • Chen T., Y.M. Ibrahim, I.K. Webb, V. Garimella, X. Zhang, A.M. Hamid, and L. Deng, et al. 2016. "Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations." Analytical Chemistry 88, no. 3:1728-1733. PNNL-SA-113681. doi:10.1021/acs.analchem.5b03910
  • 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
  • Deng L., Y.M. Ibrahim, A.M. Hamid, V. Garimella, I.K. Webb, X. Zheng, and S.A. Prost, et al. 2016. "Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13-m Serpentine Path Length Structures for Lossless Ion Manipulations Module." Analytical Chemistry 88, no. 18:8957-8964. PNNL-SA-118270. doi:10.1021/acs.analchem.6b01915
  • Deng L., Y.M. Ibrahim, E.S. Baker, N.A. Aly, A.M. Hamid, X. Zhang, and X. Zheng, et al. 2016. "Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry." ChemistrySelect 1, no. 10:2396-2399. PNNL-SA-116187. doi:10.1002/slct.201600460
  • Deng L., Y.M. Ibrahim, V. Garimella, I.K. Webb, A.M. Hamid, R.V. Norheim, and S.A. Prost, et al. 2016. "Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations." Analytical Chemistry 88, no. 20:10143-10150. PNNL-SA-119618. doi:10.1021/acs.analchem.6b02678
  • Garimella V., A.M. Hamid, L. Deng, Y.M. Ibrahim, I.K. Webb, E.M. Baker, and S.A. Prost, et al. 2016. "Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations using Compression Ratio Ion Mobility Programming." Analytical Chemistry 88, no. 23:11877-11885. PNNL-SA-121131. doi:10.1021/acs.analchem.6b03660
  • Garimella V., Y.M. Ibrahim, K. Tang, I.K. Webb, E.M. Baker, A.V. Tolmachev, and T. Chen, et al. 2016. "Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry." Journal of the American Society for Mass Spectrometry 27, no. 6:1128-1135. PNNL-SA-114168. doi:10.1007/s13361-016-1371-7
  • Hamid A.M., V. Garimella, Y.M. Ibrahim, L. Deng, X. Zheng, I.K. Webb, and G.A. Anderson, et al. 2016. "Achieving high resolution ion mobility separations using traveling waves in compact multi-turn Structures for Lossless Ion Manipulations modules." Analytical Chemistry 88, no. 18:8949-8956. PNNL-SA-118269. doi:10.1021/acs.analchem.6b01914
  • Heyman H.M., X. Zhang, K. Tang, E.S. Baker, and T.O. Metz. 2016. "Conventional and Advanced Separations in Mass Spectrometry-Based Metabolomics: Methodologies and Applications." In Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, edited by Reedijk, J. Amsterdam, :Elsevier. PNNL-SA-111253. doi:10.1016/B978-0-12-409547-2.12132-8
  • Ibrahim Y.M., V. Garimella, S.A. Prost, R. Wojcik, R.V. Norheim, E.M. Baker, and I. Rusyn, et al. 2016. "Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform." Analytical Chemistry 88, no. 24:12152-12160. PNNL-SA-123568. doi:10.1021/acs.analchem.6b03027
  • Jansson J.K., and E.S. Baker. 2016. "A multi-omic future for microbiome studies." Nature Microbiology 1, no. 5:Article No. 16049. PNNL-SA-116189. doi:10.1038/NMICROBIOL.2016.49
  • Khadempour L., K.E. Burnum-Johnson, E.S. Baker, C.D. Nicora, B.M. Webb-Robertson, R.A. White, and M.E. Monroe, et al. 2016. "The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates." Molecular Ecology 25, no. 22:5795-5805. PNNL-SA-113016. doi:10.1111/mec.13872
  • Kyle J.E., X. Zhang, K.K. Weitz, M.E. Monroe, Y.M. Ibrahim, R.J. Moore, and J. Cha, et al. 2016. "Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Analyst 141, no. 5:1649-1659. PNNL-SA-111991. doi:10.1039/C5AN02062J
  • Liu R., S. Cheng, E.S. Baker, R.D. Smith, X. 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, no. 19:3773-3776. PNNL-SA-115916. doi:10.1039/C6CC00224B
  • Webb I.K., V. Garimella, R.V. Norheim, E.S. Baker, Y.M. Ibrahim, and R.D. Smith. 2016. "A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation." Journal of the American Society for Mass Spectrometry 27, no. 7:1285-1288. PNNL-SA-115654. doi:10.1007/s13361-016-1397-x
  • White R.A., S.J. Callister, R.J. Moore, E.M. Baker, and J.K. Jansson. 2016. "The Past, Present and Future of Microbiome Analyses." Nature Protocols 11, no. 11:2049-2053. PNNL-SA-119986. doi:10.1038/nprot.2016.148
  • 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


  • 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
  • Cha J., K.E. Burnum-Johnson, A. Bartos, Y. Li, E.S. Baker, S.C. Tilton, and B.M. Webb-Robertson, et al. 2015. "Muscle segment homeobox genes direct embryonic diapause by limiting inflammation in the uterus." Journal of Biological Chemistry 290, no. 24:15337-15349. PNNL-SA-107786. doi:10.1074/jbc.M115.655001
  • Garimella V., Y.M. Ibrahim, I.K. Webb, A.B. Ipsen, T. Chen, A.V. Tolmachev, and E.S. Baker, et al. 2015. "ION MANIPULATIONS IN STRUCTURES FOR LOSSLESS ION MANIPULATIONS (SLIM): COMPUTATIONAL EVALUATION OF A 90o TURN AND A SWITCH." Analyst 140, no. 20:6845-6852. PNNL-SA-107773. doi:10.1039/c5an00844a
  • Ibrahim Y.M., E.M. Baker, W.F. Danielson, R.V. Norheim, D.C. Prior, G.A. Anderson, and M.E. Belov, et al. 2015. "Development of a New Ion Mobility Time-of-Flight Mass Spectrometer." International Journal of Mass Spectrometry 377. PNNL-SA-119651. doi:10.1016/j.ijms.2014.07.034
  • Ibrahim Y.M., E.S. Baker, W.F. Danielson, R.V. Norheim, D.C. Prior, G.A. Anderson, and M.E. Belov, et al. 2015. "Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer." International Journal of Mass Spectrometry 377. PNNL-SA-102133. doi:10.1016/j.ijms.2014.07.034
  • Wu C., T. Liu, E.S. Baker, K.D. Rodland, and R.D. Smith. 2015. "Mass spectrometry for biomarker development." In General Methods in Biomarker Research and their Applications. Biomarkers in Disease: Methods, Discoveries and Applications, edited by V Preedy and V Patel. 17-48. Heidelberg:Springer. PNNL-SA-97608.
  • Zhang X., V. Garimella, S.A. Prost, I.K. Webb, T. Chen, K. Tang, and A.V. Tolmachev, et al. 2015. "Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations." Analytical Chemistry 87, no. 12:6010-6016. PNNL-SA-107651. doi:10.1021/acs.analchem.5b00214
  • Zhang X., Y.M. Ibrahim, T. Chen, J.E. Kyle, R.V. Norheim, M.E. Monroe, and R.D. Smith, et al. 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 140. PNNL-SA-110080. doi:10.1039/c5an00897b


  • Baker E.S., D.C. 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, no. 12:1997-1999. PNNL-SA-106985. doi:10.1007/s13361-014-1007-8
  • 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
  • Ibrahim Y.M., V. Garimella, A.V. Tolmachev, E.S. Baker, and R.D. Smith. 2014. "Improving Ion Mobility Measurement Sensitivity by Utilizing Helium in an Ion Funnel-Trap." Analytical Chemistry 86, no. 11:5295-5299. PNNL-SA-100190. doi:10.1021/ac404250z
  • Prost S.A., K.L. Crowell, E.S. Baker, Y.M. Ibrahim, B.H. Clowers, M.E. Monroe, and G.A. Anderson, et al. 2014. "Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements." Journal of the American Society for Mass Spectrometry 25, no. 12:2020-2027. PNNL-SA-100086. doi:10.1007/s13361-014-0895-y


  • Crowell K.L., E.S. Baker, S.H. Payne, Y.M. Ibrahim, M.E. Monroe, G.W. Slysz, and B.L. Lamarche, et al. 2013. "Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry." International Journal of Mass Spectrometry 354-355. PNNL-SA-95461. doi:10.1016/j.ijms.2013.06.028
  • Crowell K.L., G.W. Slysz, E.S. Baker, B.L. Lamarche, M.E. Monroe, Y.M. Ibrahim, and S.H. Payne, et al. 2013. "LC-IMS-MS Feature Finder: Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets." Bioinformatics 29, no. 21:2804-2805. PNNL-SA-95214. doi:10.1093/bioinformatics/btt465
  • 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
  • Venceslau S.S., J.R. Cort, E.S. Baker, R.K. Chu, E.W. Robinson, C. Dahl, and L.M. Saraiva, et al. 2013. "Redox states of Desulfovibrio vulgaris DsrC, a key protein in dissimilatory sulfite reduction." Biochemical and Biophysical Research Communications 441, no. 4:731-736. PNNL-SA-98016. doi:10.1016/j.bbrc.2013.10.116


  • Angel T.E., U.K. Aryal, S.M. Hengel, E.S. Baker, R.T. Kelly, E.W. Robinson, and R.D. Smith. 2012. "Mass spectrometry-based proteomics: existing capabilities and future directions." Chemical Society Reviews 41, no. 10:3912-3928. PNNL-SA-84530. doi:10.1039/C2CS15331A
  • Baker E.S., T. Liu, V.A. Petyuk, K.E. Burnum-Johnson, Y.M. Ibrahim, G.A. Anderson, and R.D. Smith. 2012. "Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications." Genome Medicine 4. PNNL-SA-86783. doi:10.1186/gm364
  • Burnum K.E., Y. Hirota, E.S. Baker, M. Yoshie, Y.M. Ibrahim, M.E. Monroe, and G.A. Anderson, et al. 2012. "Uterine deletion of Trp53 compromises antioxidant responses in mouse decidua." Endocrinology 153, no. 9:4568-4579. PNNL-SA-87211. doi:10.1210/en.2012-1335
  • Hengel S.M., E.A. Floyd, E.S. 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, no. 21:3138-3142. PNNL-SA-87924. doi:10.1002/pmic.201200168


  • Belov M.E., R.T. Kurulugama, D. Lopez-Ferrer, Y.M. Ibrahim, and E.S. Baker. 2011. "New Developments in LC-MS and Other Hyphenated Techniques." In Sample Preparation in Biological Mass Spectrometry, edited by AR Ivanov & AV Lazarev. 981-1030. New York, New York:Springer. PNNL-SA-74555.


  • 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
  • Buchko G.W., G. Niemann, E.S. Baker, M.E. Belov, R.D. Smith, F. Heffron, and J.N. Adkins, et al. 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, no. 12:2448-2458. PNNL-SA-73691. doi:10.1039/c0mb00097c
  • Ibrahim Y.M., D.C. Prior, E.S. Baker, R.D. Smith, and M.E. Belov. 2010. "Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation- Tandem Time-of-Flight Mass Spectrometry Approach." International Journal of Mass Spectrometry 293, no. 1-3:34-44. PNNL-SA-68112.
  • Shah A.R., K. Agarwal, E.S. Baker, M. Singhal, A.M. Mayampurath, Y.M. Ibrahim, and L.J. Kangas, et al. 2010. "Machine learning based prediction for peptide drift times in ion mobility spectrometry." Bioinformatics 26, no. 13:1601-1607. PNWD-SA-8802. doi:10.1093/bioinformatics/btq245


  • Page J.S., I. Marginean, E.S. Baker, R.T. Kelly, K. Tang, and R.D. Smith. 2009. "Biases in Ion Transmission Through an Electrospray Ionization-Mass Spectrometry Capillary Inlet." Journal of the American Society for Mass Spectrometry 20, no. 12:2265-2272. PNNL-SA-66725. doi:10.1016/j.jasms.2009.08.018


  • Baker E.S., K. Tang, W.F. Danielson, D.C. Prior, and R.D. Smith. 2008. "Simultaneous Fragmentation of Multiple Ions Using IMS Drift Time Dependent Collision Energies." Journal of the American Society for Mass Spectrometry 19, no. 3:411-419. PNWD-SA-7952. doi:10.1016/j.jasms.2007.11.018
  • Metz T.O., J.S. Page, E.S. Baker, K. Tang, J. Ding, Y. Shen, and R.D. Smith. 2008. "High Resolution Separations and Improved Ion Production and Transmission in Metabolomics." Trends in Analytical Chemistry. TrAC 27, no. 3:205-214. PNNL-SA-56841. doi:10.1016/j.trac.2007.11.003


  • Baker E.S., B.H. Clowers, F. Li, K. Tang, A.V. Tolmachev, D.C. Prior, and M.E. Belov, et al. 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, no. 7:1176-1187. PNNL-SA-52620. doi:doi:10.1016/j.jasms.2007.03.031
  • Shvartsburg A.A., S.V. Mashkevich, E.S. Baker, and R.D. Smith. 2007. "Optimization of Algorithms for Ion Mobility Calculations." Journal of Physical Chemistry A 111, no. 10:2002-2010. PNNL-SA-52282. doi:10.1021/jp066953m

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