Skip to Main Content U.S. Department of Energy

Biological Sciences 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 EM Baker. 2018. "Editorial Overview: Omics." Current Opinion in Chemical Biology 42:A1-A2.  doi:10.1016/j.cbpa.2018.02.007
  • Bilbao Pena A, BC Gibbons, GW Slysz, KL Crowell, ME Monroe, YM Ibrahim, RD Smith, SH Payne, and EM Baker. 2018. "An Algorithm to Correct Saturated Mass Spectrometry Ion Abundances for Enhanced Quantitation and Mass Accuracy in Omic Studies." International Journal of Mass Spectrometry 427:91-99.  doi:10.1016/j.ijms.2017.11.003
  • Garabedian A, P Benigni, C Ramirez, EM Baker, T Liu, RD 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(5):817-826.  doi:10.1007/s13361-017-1787-8
  • Horney JA, GA Casillas, EM Baker, KW Stone, KR Kirsch, K Camargo, T Wade, and TJ Mcdonald. 2018. "Comparing Residential Contamination in a Houston Environmental Justice Neighborhood before and after Hurricane Harvey." PLoS One 13(2):Article No. e0192660.  doi:10.1371/journal.pone.0192660
  • Nicora CD, KE Burnum-Johnson, ES Nakayasu, CP Casey, RA White, III, T Roy Chowdhury, JE Kyle, YM Kim, RD Smith, TO Metz, JK Jansson, and EM Baker. 2018. "The MPLEx Protocol for Multi-Omic Analyses of Soil Samples." Journal of Visualized Experiments e57343(135):, doi:10.3791/57343
  • Orton DJ, MM Tfaily, RJ Moore, BL Lamarche, X Zheng, TL Fillmore, RK Chu, KK Weitz, ME Monroe, RT Kelly, RD Smith, and EM Baker. 2018. "A Customizable Flow Injection System for Automated, High Throughput and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements." Analytical Chemistry 90(1):737-744.  doi:10.1021/acs.analchem.7b02986
  • Poad BL, X Zheng, TA Mitchell, RD Smith, EM Baker, and SJ Blanksby. 2018. "Online ozonolysis combined with ion mobility-mass spectrometry provides a new platform for lipid isomer analyses." Analytical Chemistry 90(2):1292-1300.  doi:10.1021/acs.analchem.7b04091
  • Zheng X, RD Smith, and EM 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 42:111-118.  doi:10.1016/j.cbpa.2017.11.009


  • Baker EM, R Wojcik, IK Webb, VBS Garimella, SA Prost, YM Ibrahim, and RD Smith. 2017. "Lipid and Glycolipid Isomer Analyses Using Ultra-high Resolution Ion Mobility Spectrometry Separations." International Journal of Molecular Sciences 18(1):183.  doi:10.3390/ijms18010183
  • Burnum-Johnson KE, EM Baker, and TO 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(Supplement 1):S67-S72.  doi:10.1016/j.placenta.2017.03.016
  • Deng L, IK Webb, VBS Garimella, AM Hamid, X Zheng, RV Norheim, SA Prost, GA Anderson, JA Sandoval, EM Baker, YM Ibrahim, and RD Smith. 2017. "Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations." Analytical Chemistry 89(8):46284634.  doi:10.1021/acs.analchem.7b00185
  • Deng L, VBS Garimella, AM Hamid, IK Webb, IK Attah, RV Norheim, SA Prost, X Zheng, JA Sandoval, EM Baker, YM Ibrahim, and RD Smith. 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(12):6432-6439.  doi:10.1021/acs.analchem.7b00189
  • Ibrahim YM, AM Hamid, L Deng, VBS Garimella, IK Webb, EM Baker, and RD Smith. 2017. "New Frontiers for Mass Spectrometry based upon Structures for Lossless Ion Manipulations." Analyst 142(7):1010-1021.  doi:10.1039/C7AN00031F
  • Kyle JE, CP Casey, KG Stratton, EM Zink, YM Kim, X Zheng, ME Monroe, KK Weitz, KJ Bloodsworth, DJ Orton, YM Ibrahim, RJ Moore, C Lee, C Pedersen, ES Orwoll, RD Smith, KE Burnum-Johnson, and EM Baker. 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(5):447-456.  doi:10.1002/rcm.7808
  • Ligare MR, EM Baker, J Laskin, and GE Johnson. 2017. "Ligand Induced Structural Isomerism in Phosphine Coordinated Gold Clusters Revealed by Ion Mobility-Mass Spectrometry." Chemical Communications 53(53):7389-7392.  doi:10.1039/C7CC02251D
  • Ma J, CP Casey, X Zheng, YM Ibrahim, CS Wilkins, RS Renslow, DG Thomas, SH Payne, ME Monroe, RD Smith, JG Teeguarden, EM Baker, and TO Metz. 2017. "PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association." Bioinformatics 33(17):27152722.  doi:10.1093/bioinformatics/btx305
  • Metz TO, EM Baker, EL Schymanski, RS Renslow, DG Thomas, TJ Causon, IK Webb, S Hann, RD Smith, and JG Teeguarden. 2017. "Integrating Ion Mobility Spectrometry into Mass Spectrometry-based Exposome Measurements: What Can It Add and How Far Can It Go?" Bioanalysis 9(1):81-98.  doi:10.4155/bio-2016-0244
  • Nielson C, J Wiedrick, J Shen, JM Jacobs, EM Baker, A Baraff, PD Piehowski, C Lee, A Baratt, VA Petyuk, SK Mcweeney, JY Lim, DC Bauer, NE Lane, PM Cawthon, RD Smith, J Lapidus, and ES Orwoll. 2017. "Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics." Journal of Bone and Mineral Research 32(7):1559-1567.  doi:10.1002/jbmr.3125
  • Rosnow JJ, LN Anderson, RN Nair, ES Baker, and AT Wright. 2017. "Emerging Multi-Omic Technologies for Improved Functional Characterization of Lignocellulose Degrading Enzymes." Critical Reviews in Biotechnology 37(5):626-640.  doi:10.1080/07388551.2016.1209158
  • Stow S, TJ Causon, X Zheng, RT Kurulugama Lekamlage, T Mairinger, JC May, EE Rennie, EM Baker, RD Smith, J McLean, S Hann, and JC Fjeldsted. 2017. "An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass." Analytical Chemistry 89(17):90489055.  doi:10.1021/acs.analchem.7b01729
  • Zheng X, NA Aly, Y Zhou, KT Dupuis, A Bilbao Pena, VL Paurus, DJ Orton, RE Wilson, SH Payne, RD Smith, and EM Baker. 2017. "A Structural Examination and Collision Cross Section Database for Over 500 Metabolites and Xenobiotics Using Drift Tube Ion Mobility Spectrometry." Chemical Science 8(11):7724-7736.  doi:10.1039/C7SC03464D
  • Zheng X, RS Renslow, MM Makola, IK Webb, L Deng, DG Thomas, N Govind, YM Ibrahim, MM Kabanda, IA Dubery, HM Heyman, RD Smith, NE Madala, and EM Baker. 2017. "Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry." The Journal of Physical Chemistry Letters 8(7):1381-1388.  doi:10.1021/acs.jpclett.6b03015
  • Zheng X, L Deng, EM Baker, YM Ibrahim, VA Petyuk, and RD Smith. 2017. "Distinguishing D- and L-Aspartic and Isoaspartic Acids in Amyloid ß Peptides with Ultrahigh Resolution Ion Mobility Spectrometry." Chemical Communications 53(56):7913-7916.  doi:10.1039/C7CC03321D
  • Zheng X, R Wojcik, X Zhang, YM Ibrahim, KE Burnum-Johnson, DJ Orton, ME Monroe, RJ Moore, RD Smith, and EM Baker. 2017. "Coupling Front-end Separations, Ion Mobility Spectrometry, and Mass Spectrometry for Enhanced Multidimensional Biological and Environmental Analyses." Annual Review of Analytical Chemistry 10:71-92.  doi:10.1146/annurev-anchem-061516-045212
  • Zheng X, X Zhang, N Schocker, RS Renslow, DJ Orton, J Khamsi, RA Ashmus, IC Almeida, K Tang, CE Costello, RD Smith, K Michael, and EM Baker. 2017. "Enhancing Glycan Isomer Separations with Metal Ions and Positive and Negative Polarity Ion Mobility Spectrometry-Mass Spectrometry Analyses." Analytical and Bioanalytical Chemistry 409:467-476.  doi:10.1007/s00216-016-9866-4


  • 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
  • Garimella VBS, AM Hamid, L Deng, YM Ibrahim, IK Webb, EM Baker, SA Prost, RV Norheim, GA Anderson, and RD Smith. 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(23):11877-11885.  doi:10.1021/acs.analchem.6b03660
  • Garimella VBS, YM Ibrahim, K Tang, IK Webb, EM Baker, AV Tolmachev, TC Chen, GA Anderson, and RD Smith. 2016. "Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry." Journal of the American Society for Mass Spectrometry 27(6):1128-1135.  doi:10.1007/s13361-016-1371-7
  • 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
  • Burnum-Johnson KE, S Nie, CP Casey, ME Monroe, DJ Orton, YM Ibrahim, MA Gritsenko, TRW Clauss, AK Shukla, RJ Moore, SO Purvine, T Shi, W Qian, T Liu, ES Baker, and RD Smith. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Molecular and Cellular Proteomics 15(12):3694-3705.  doi:10.1074/mcp.M116.061143
  • 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
  • Deng L, YM Ibrahim, VBS Garimella, IK Webb, AM Hamid, RV Norheim, SA Prost, JA Sandoval, EM Baker, and RD Smith. 2016. "Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations." Analytical Chemistry 88(20):1014310150.  doi:10.1021/acs.analchem.6b02678
  • Deng L, YM Ibrahim, AM Hamid, VBS Garimella, IK Webb, X Zheng, SA Prost, JA Sandoval, RV Norheim, GA Anderson, AV Tolmachev, ES Baker, and RD Smith. 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(18):8957-8964.  doi:10.1021/acs.analchem.6b01915
  • Deng L, YM Ibrahim, ES Baker, NA Aly, AM Hamid, X Zhang, X Zheng, VBS Garimella, IK Webb, SA Prost, JA Sandoval, RV Norheim, GA Anderson, AV Tolmachev, and RD Smith. 2016. "Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry." ChemistrySelect 1(10):2396-2399.  doi:10.1002/slct.201600460
  • Hamid AM, VBS Garimella, YM Ibrahim, L Deng, X Zheng, IK Webb, GA Anderson, SA Prost, RV Norheim, AV Tolmachev, ES Baker, and RD Smith. 2016. "Achieving high resolution ion mobility separations using traveling waves in compact multi-turn Structures for Lossless Ion Manipulations modules." Analytical Chemistry 88(18):8949-8956.  doi:10.1021/acs.analchem.6b01914
  • Heyman HM, X Zhang, K Tang, ES Baker, and TO Metz. 2016. "Conventional and Advanced Separations in Mass Spectrometry-Based Metabolomics: Methodologies and Applications." In Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, ed. Reedijk, J.  Elsevier, Amsterdam, , Netherlands.  doi:10.1016/B978-0-12-409547-2.12132-8
  • Ibrahim YM, VBS Garimella, SA Prost, R Wojcik, RV Norheim, EM Baker, I Rusyn, and RD Smith. 2016. "Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform." Analytical Chemistry 88(24):12152-12160.  doi:10.1021/acs.analchem.6b03027
  • Jansson JK, and ES Baker. 2016. "A multi-omic future for microbiome studies." Nature Microbiology 1(5):Article No. 16049.  doi:10.1038/NMICROBIOL.2016.49
  • Khadempour L, KE Burnum-Johnson, ES Baker, CD Nicora, BJM Webb-Robertson, RA White, III, ME Monroe, EL Huang, RD Smith, and CR Currie. 2016. "The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates." Molecular Ecology 25(22):5795-5805.  doi:10.1111/mec.13872
  • 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
  • Webb IK, VBS Garimella, RV Norheim, ES Baker, YM Ibrahim, and RD Smith. 2016. "A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation." Journal of the American Society for Mass Spectrometry 27(7):1285-1288.  doi:10.1007/s13361-016-1397-x
  • White RA, III, SJ Callister, RJ Moore, EM Baker, and JK Jansson. 2016. "The Past, Present and Future of Microbiome Analyses." Nature Protocols 11(11):2049-2053.  doi:10.1038/nprot.2016.148
  • Zhang X, MV Romm, X Zheng, EM Zink, YM Kim, KE Burnum-Johnson, DJ Orton, A Apffel, YM Ibrahim, ME Monroe, RJ Moore, JN Smith, J Ma, RS Renslow, DG Thomas, A Blackwell, G Swinford, J Sausen, RT Kurulugama Lekamlage, N Eno, E Darland, G Stafford, JC Fjeldsted, TO Metz, JG Teeguarden, RD Smith, and ES Baker. 2016. "SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in bio?uids." Clinical Mass Spectrometry 2:1-10.  doi:10.1016/j.clinms.2016.11.002


  • 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, EM Baker, WF Danielson, RV Norheim, DC Prior, GA Anderson, ME Belov, and RD Smith. 2015. "Development of a New Ion Mobility Time-of-Flight Mass Spectrometer." International Journal of Mass Spectrometry 377:655-662.  doi:10.1016/j.ijms.2014.07.034
  • 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 140:6955-6963.  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

Biological Sciences

Science at PNNL

Research Highlights

View All BSD Highlights