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Aleksey Tolmachev

Aleksey Tolmachev

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


Dr. Aleksey Tolmachev's research at PNNL has focused largely on advancing mass spectrometry (MS) technologies and methods for proteomics and, more generally, for investigations of complex bio-molecular systems. He has background in chemical physics, including ion dynamics and informatics aspects pertaining to the MS technology. His research facilitated development of the ion funnel technology and led to improvements in a range of MS instrument types, such as Time of Flight, RF quadrupole, ion trap, FT-ICR, Orbitrap, and ion mobility spectrometry (IMS).

Research Interests

  • Fundamentals of ion dynamics in electric and magnetic fields in MS and IMS
  • Ion Funnel technology development
  • Radio Frequency multipoles, ion traps and ion guides
  • FT-ICR technology fundamentals
  • High resolution LC-MS platforms development, optimization and QC using custom software

Education and Credentials

  • 1984 Ph.D., Institute of Chemical Physics, Academy of Science, Moscow, Russia
  • 1979 M.S., Molecular and Chemichal Physics. Moscow Institute of Physics and Technology

Affiliations and Professional Service

  • American Society for Mass Spectrometry, member since 1998
  • Panel of Experts (one of six panel members), FT-MS Workshop, 57th ASMS Conference, 2009
  • Reviewer for Analytical Chemistry, Journal of the American Society for Mass Spectrometry, International Journal of Mass Spectrometry

Awards and Recognitions

  • EMSL highlights, May 2009
  • EMSL highlights, July 2008
  • Four U.S. patents in the fields of FT-ICR mass measurement accuracy, ion funnel technology, and MS informatics and data refining approaches

PNNL Publications


  • 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


  • 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
  • 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
  • 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


  • Huang X, C Tian, M Liu, Y Wang, AV Tolmachev, S Sharma, F Yu, K Fu, J Zheng, and SJ Ding. 2012. "Quantitative Proteomic Analysis of Mouse Embryonic Fibroblasts and Induced Pluripotent Stem Cells Using 16O /18O labeling." Journal of Proteome Research 11(4):2091-2102.  doi:10.1021/pr300155r
  • Tolmachev AV, EW Robinson, RD Smith, FE Leach, III, JH Futrell, and L Pasa-Tolic. 2012. "A Conceptual Approach for FT-ICR cell Harmonization Utilizing External Shim Electrodes ." International Journal of Mass Spectrometry 325-327:45-50.  doi:10.1016/j.ijms.2012.06.027
  • Tolmachev AV, EW Robinson, S Wu, RD Smith, JH Futrell, and L Pasa-Tolic. 2012. "Angular Averaged Profiling of the Radial Electric Field in Compensated FTICR Cells." Journal of the American Society for Mass Spectrometry 23(7):1169-1172.  doi:10.1007/s13361-012-0395-x


  • Huang X, AV Tolmachev, Y Shen, M Liu, L Huang, Z Zhang, GA Anderson, RD Smith, WC Chan, S Hinrichs, K Fu, and SJ Ding. 2011. "UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling." Journal of Proteome Research 10(3):1228-1237.  doi:10.1021/pr1010058
  • Smith DF, EW Robinson, AV Tolmachev, RM Heeren, and L Pasa-Tolic. 2011. "C60 Secondary Ion Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Analytical Chemistry 83(24):9552-9556.  doi:10.1021/ac2023348
  • Tolmachev AV, EW Robinson, S Wu, RD Smith, and L Pasa-Tolic. 2011. "Trapping radial electric field optimization in compensated FTICR Cells." Journal of the American Society for Mass Spectrometry 22(8):1334-1342.  doi:10.1007/s13361-011-0167-z


  • Marginean I, JS Page, AV Tolmachev, K Tang, and RD Smith. 2010. "Achieving 50% ionization efficiency in sub-ambient pressure ionization with nanoelectrospray." Analytical Chemistry 82(22):9344-9349. 
  • Kelly RT, AV Tolmachev, JS Page, K Tang, and RD Smith. 2010. "The Ion Funnel: Theory, Implementations and Applications." Mass Spectrometry Reviews 29(2):294-312.  doi:10.1002/mas.20232


  • Heibeck TH, SJ Ding, LK Opresko, R Zhao, AA Schepmoes, F Yang, AV Tolmachev, ME Monroe, DG Camp, II, RD Smith, HS Wiley, and W Qian. 2009. "An Extensive Survey of Tyrosine Phosphorylation Revealing New Sites in Human Mammary Epithelial Cells." Journal of Proteome Research 8(8):3852-3861. 
  • Tolmachev AV, EW Robinson, S Wu, L Pasa-Tolic, and RD Smith. 2009. "FT-ICR MS optimization for the analysis of intact proteins." International Journal of Mass Spectrometry 287(1-3 SP ISS):32-38.  doi:10.1016/j.ijms.2008.10.010
  • Tolmachev AV, BH Clowers, ME Belov, and RD Smith. 2009. "Coulombic Effects on Ion Mobility Spectrometry ." Analytical Chemistry 81(12):4778-4787. 
  • Wu S, NM Lourette, N Tolic, R Zhao, R Robinson, AV Tolmachev, RD Smith, and L Pasa-Tolic. 2009. "An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications." Journal of Proteome Research 8(3):1347-1357. 


  • Ding SJ, Y Wang, JM Jacobs, W Qian, F Yang, AV Tolmachev, X Du, W Wang, RJ Moore, ME Monroe, SO Purvine, KM Waters, TH Heibeck, JN Adkins, DG Camp, II, RL Klemke, and RD Smith. 2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step 8O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7(10):4215-24.  doi:10.1021/pr7007785
  • Petyuk VA, N Jaitly, RJ Moore, J Ding, TO Metz, K Tang, ME Monroe, AV Tolmachev, JN Adkins, ME Belov, AR Dabney, W Qian, DG Camp, II, and RD Smith. 2008. "Elimination of Systematic Mass Measurement Errors in Liquid Chromatography-Mass Spectrometry Based Proteomics using Regression Models and a priori Partial Knowledge of the Sample Content ." Analytical Chemistry 80(3):693-706.  doi:10.1021/ac701863d
  • Tolmachev AV, ME Monroe, SO Purvine, RJ Moore, N Jaitly, JN Adkins, GA Anderson, and RD Smith. 2008. "Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS instruments ." Analytical Chemistry 80(22):8514-8525.  doi:10.1021/ac801376g
  • Tolmachev AV, EW Robinson, S Wu, H Kang, NM Lourette, L Pasa-Tolic, and RD Smith. 2008. " Trapped-ion cell with improved DC potential harmonicity for FT-ICR MS." Journal of the American Society for Mass Spectrometry 19(4):586 - 597.  doi:10.1016/j.jasms.2008.01.006


  • 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
  • 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


  • Page JS, AV Tolmachev, K Tang, and RD Smith. 2006. "Theoretical and experimental evaluation of the low m/z transmission of an electrodynamic ion funnel." Journal of the American Society for Mass Spectrometry 17(4):586-592. 
  • 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
  • Tolmachev AV, ME Monroe, N Jaitly, VA Petyuk, JN Adkins, and RD Smith. 2006. "Mass Measurement Accuracy In Analyses Of Highly Complex Mixtures Based Upon Multidimensional Recalibration." Analytical Chemistry 78(24):8374-8385.  doi:10.1021/ac0606251


  • Page JS, AV Tolmachev, K Tang, and RD Smith. 2005. "Variable low-mass filtering using an electrodynamic ion funnel." Journal of Mass Spectrometry 40(9):1215-1222.  doi:10.1002/jms.900
  • Tang K, AA Shvartsburg, HN Lee, DC Prior, MA Buschbach, F Li, AV Tolmachev, GA Anderson, and RD Smith. 2005. "High-Sensitivity Ion Mobility Spectrometry/Mass Spectrometry Using Electrodynamic Ion Funnel Interfaces ." Analytical Chemistry 77(10):3330-3339.  doi:10.1021/ac048315a


  • Tolmachev AV, AN Vilkov, B Bogdanov, L Pasa-Tolic, CD Masselon, and RD Smith. 2004. "Collisional Activation of Ions in RF Ion Traps and Ion Guides: The Effective Ion Temperature Treatment." Journal of the American Society for Mass Spectrometry 15(11):1616-1628. 


  • Tolmachev AV, AN Vilkov, L Pasa-Tolic, HR Udseth, and RD Smith. 2003. "Suppression of the Lower Charge State Ions in the External Accumulation RF Multipole with a Reduced Trapping DC Potential." Journal of the American Society for Mass Spectrometry 14(11):1229-1235. 
  • Tolmachev AV, HR Udseth, and RD Smith. 2003. "Modeling the ion density distribution in collisional cooling RF multipole ion guides." International Journal of Mass Spectrometry 222(1-3):155-174. 


  • Tolmachev AV, CD Masselon, GA Anderson, HR Udseth, and RD Smith. 2002. "Frequency Shifts Due to the Interference of Resolved Peaks in Magnitude-Mode Fourier-Transform Ion Cyclotron Resonance Mass Spectra." Journal of the American Society for Mass Spectrometry 13(4):387-401. 
  • Masselon CD, AV Tolmachev, GA Anderson, R Harkewicz, and RD Smith. 2002. "Mass Measurement Errors Caused by "Local" Frequency Perturbations in FTICR Mass Spectrometry"." Journal of the American Society for Mass Spectrometry 13:99-106. 
  • Tang K, AV Tolmachev, EN Nikolaev, R Zhang, ME Belov, HR Udseth, and RD Smith. 2002. "Independent Control of Ion Transmission in a Jet Disrupter Dual-Channel Ion Funnel Electrospray Ionization MS Interface." Analytical Chemistry 74(20):5431-5437. 


  • Tolmachev AV, HR Udseth, and RD Smith. 2000. "Charge Capacity Limitations of Radio Frequency Ion Guides in Their Use for Improved Ion Accumulation and Trapping in Mass Spectrometry." Analytical Chemistry 72(5):970-978. 
  • Belov ME, MV Gorshkov, HR Udseth, GA Anderson, AV Tolmachev, DC Prior, R Harkewicz, and RD Smith. 2000. "Initial Implementation of an Electrodynamic Ion Funnel with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Journal of the American Society for Mass Spectrometry 11(1):19-23. 
  • Tolmachev AV, HR Udseth, and RD Smith. 2000. "Radial Stratification of Ions as a Function of Mass to Charge Ratio in Collisional Cooling Radio Frequency Multipoles Used as Ion Guides or Ion Traps." Rapid Communications in Mass Spectrometry 14(20):1907-1913. 
  • Tolmachev AV, TM Kim, HR Udseth, RD Smith, TH Bailey, and JH Futrell. 2000. "Simulation-Based Optimization of the Electrodynamic Ion Funnel for High Sensitivity Electrospray Ionization-Mass Spectrometry." International Journal of Mass Spectrometry 203(1-3):31-47. 
  • Kim TM, AV Tolmachev, R Harkewicz, DC Prior, GA Anderson, HR Udseth, RD Smith, TH Bailey, VS Rakov, and JH Futrell. 2000. "Design and Implementation of a New Electrodynamic Ion Funnel." Analytical Chemistry 72:2247-2255. 


  • Shaffer SA, AV Tolmachev, DC Prior, GA Anderson, HR Udseth, and RD Smith. 1999. "Characterization of an Improved Electrodynamic Ion Funnel Interface for Electrospray Ionization Mass Spectrometry." Analytical Chemistry 71(15):2957-2964. 

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