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Erin

Erin Baker

Omic, Inst, Infra & Inform
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352

Biography

Dr. Erin Baker is a bioanalytical chemist with 12 years experience utilizing ion mobility spectrometry in conjunction with mass spectrometry (IMS-MS) to study biological systems. Her research involves the development and evaluation of high-throughput LC-IMS-MS analyses to quickly study numerous samples in a short time period without losing valuable biological information. Dr. Baker's technical background includes evaluating short LC gradients for use with IMS-MS in proteomic analyses, as well as studying the number and quality of features detected with LC-IMS-MS and comparing them to existing LC-MS and LC-MS/MS instruments such as the LTQ-Orbitrap and LTQ Orbitrap Velos.

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

2014

  • 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

2013

  • 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

2012

  • 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

2011

  • 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. 

2010

  • 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

2009

  • 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

2008

  • 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

2007

  • 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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