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Biological Sciences Staff information

Yehia Ibrahim

IO Prototype & Pilot
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352

PNNL Publications


  • 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
  • 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, 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
  • 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


  • 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):2766-2776.  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
  • Chen TC, TL Fillmore, SA Prost, RJ Moore, YM Ibrahim, and RD Smith. 2015. "Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadruple Mass Spectrometry." Analytical Chemistry 87(14):7326-7331.  doi:10.1021/acs.analchem.5b01482
  • Chen TC, IK Webb, SA Prost, MB Harrer, RV Norheim, K Tang, YM Ibrahim, and RD Smith. 2015. "Rectangular Ion Funnel: A New Ion Funnel Interface for Structures for Lossless Ion Manipulations." Analytical Chemistry 87(1):716-722.  doi:10.1021/ac503564c
  • Chen Y, FE Leach, III, NK Kaiser, X Dang, YM Ibrahim, RV Norheim, GA Anderson, RD Smith, and AG Marshall. 2015. "Improved ion optics for introduction of ions into a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer." Journal of Mass Spectrometry 50(1):280-284.  doi:10.1002/jms.3523
  • Gunaratne KDD, V Prabhakaran, YM Ibrahim, RV Norheim, GE Johnson, and J Laskin. 2015. "Design and Performance of a High-Flux Electrospray Ionization Source for Ion Soft-Landing." Analyst 140(9):2957-2963.  doi:10.1039/C5AN00220F
  • Hamid AM, YM Ibrahim, VBS Garimella, IK Webb, L Deng, TC Chen, GA Anderson, SA Prost, RV Norheim, AV Tolmachev, and RD Smith. 2015. "Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations." Analytical Chemistry 87(22):11301-11308.  doi:10.1021/acs.analchem.5b02481
  • 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
  • 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


  • Garimella VBS, YM Ibrahim, IK Webb, AV Tolmachev, X Zhang, SA Prost, GA Anderson, and RD Smith. 2014. "Simulation of Electric Potentials and Ion Motion in Planar Electrode Structures for Lossless Ion Manipulations (SLIM)." Journal of the American Society for Mass Spectrometry 25(11):1890-1896.  doi:10.1007/s13361-014-0976-y
  • Shvartsburg AA, YM Ibrahim, and RD Smith. 2014. "Differential Ion Mobility Separations in up to 100% Helium Using Microchips." Journal of the American Society for Mass Spectrometry 25(3):480-489.  doi:10.1007/s13361-013-0797-4
  • Webb IK, TC Chen, WF Danielson, III, YM Ibrahim, K Tang, GA Anderson, and RD Smith. 2014. "Implementation of Dipolar Resonant Excitation Collision Induced Dissociation with Ion Mobility/Time-of-Flight MS." Journal of the American Society for Mass Spectrometry 25(4):563-571.  doi:10.1007/s13361-013-0815-6
  • 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
  • Tolmachev AV, IK Webb, YM Ibrahim, VBS Garimella, X Zhang, GA Anderson, and RD Smith. 2014. "Characterization of Ion Dynamics in Structures for Lossless Ion Manipulations." Analytical Chemistry 86(18):9162-9168.  doi:10.1021/ac502054p
  • Webb IK, VBS Garimella, AV Tolmachev, TC Chen, X Zhang, JT Cox, RV Norheim, SA Prost, BL Lamarche, GA Anderson, YM Ibrahim, and RD Smith. 2014. "Mobility-Resolved Ion Selection in Uniform Drift Field Ion Mobility Spectrometry/Mass Spectrometry; Dynamic Switching in Structures for Lossless Ion Manipulations ." Analytical Chemistry 86(19):9632-9637.  doi:10.1021/ac502139e
  • Webb IK, VBS Garimella, AV Tolmachev, TC Chen, X Zhang, RV Norheim, SA Prost, BL Lamarche, GA Anderson, YM Ibrahim, and RD Smith. 2014. "Experimental Evaluation and Optimization of Structures for Lossless Ion Manipulations for Ion Mobility Spectrometry with Time-of-Flight Mass Spectrometry." Analytical Chemistry 86(18):9169-9176.  doi:10.1021/ac502055e


  • 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


  • 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
  • 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


  • 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. 
  • Belov ME, S Prasad, DC Prior, WF Danielson, III, KK Weitz, YM Ibrahim, and RD Smith. 2011. "Pulsed Multiple Reaction Monitoring Approach to Enhancing Sensitivity of a Tandem Quadrupole Mass Spectrometer." Analytical Chemistry 83(6):2162-2171.  doi:10.1021/ac103006b
  • Ibrahim YM, AA Shvartsburg, RD Smith, and ME Belov. 2011. "Ultrasensitive Identification of Localization Variants of Modified Peptides Using Ion Mobility Spectrometry ." Analytical Chemistry 83(14):5617 - 5623.  doi:10.1021/ac200719n


  • Belov ME, YM Ibrahim, and RD Smith. 2010. "Ion Accumulation Approaches for Increasing Sensitivity and Dynamic Range in the Analysis of Complex Samples." Chapter 7 in Practical Aspects of Trapped Ion Mass Spectrometry: Theory and Instrumentation , vol. IV, ed. RE March and JFJ Todd, pp. 401-432.  CRC Press, Boca Raton, FL. 
  • 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
  • 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


  • Clowers BH, ME Belov, DC Prior, WF Danielson, III, YM Ibrahim, and RD Smith. 2008. " Pseudorandom Sequence Modifications for Ion Mobility Orthogonal Time-of-Flight Mass Spectrometry." Analytical Chemistry 80(7):2464-2473.  doi:10.1021/ac7022712
  • Clowers BH, YM Ibrahim, DC Prior, WF Danielson, ME Belov, and RD Smith. 2008. "Enhanced Ion Utilization Efficiency Using an Electrodynamic Ion Funnel Trap as an Injection Mechanism for Ion Mobility Spectrometry ." Analytical Chemistry 80(3):612-623.  doi:10.1021/ac701648p
  • Ibrahim YM, ME Belov, AV Liyu, and RD Smith. 2008. "Automated Gain Control Ion Funnel Trap for Orthogonal Time-of-Flight Mass Spectrometry ." Analytical Chemistry 80(14):5367-5376.  doi:10.1021/ac8003488


  • Ibrahim YM, ME Belov, AV Tolmachev, DC Prior, and RD Smith. 2007. "Ion Funnel Trap Interface for Orthogonal Time-of-Flight Mass Spectrometry ." Analytical Chemistry 79(20):7845-7852.  doi:10.1021/ac071091m


  • Ibrahim YM, K Tang, AV Tolmachev, AA Shvartsburg, and RD Smith. 2006. "Improving Mass Spectrometer Sensitivity Using a High-Pressure Electrodynamic Ion Funnel Interface." Journal of the American Society for Mass Spectrometry 17(9):1299-1305.  doi:10.1016/j.jasms.2006.06.005

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