Lab Fellow, Lead Scientist for Visual Proteomics
Environmental Molecular Sciences Division
Lab Fellow, Lead Scientist for Visual Proteomics
Environmental Molecular Sciences Division


Dr. Ljiljana (Lili) Paša-Tolić is a PNNL Lab Fellow and lead scientist for visual proteomics with the Functional and Systems Biology group in PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. Paša-Tolić brings world-leading expertise in native-state and top-down proteomics, as well as mass spectrometry and the Biomolecular Pathways Integrated Research Platform (IRP), and combines them with the Functional Bioimaging and Cell Signaling and Communications IRPs. These efforts provide a first-of-a-kind, and transformational capability, that enables dynamic spatio-temporarily resolved proteomic imaging in cells for connecting proteins with biological function.

Research Interest

  • Developing sophisticated analytical methods with emphasis on Fourier transform (FT) mass spectrometry (MS) and micro-separations, as well as the application of these techniques to accurately quantify spatiotemporal changes in protein (metabolite) abundance, identity, and activity. 

  • Mass spectrometry  

  • Proteomics  

  • Metabolomics 

  • Mass spectrometry imaging 

  • Complex mixture analysis


  • Shipley Capturing Federal Business Course, 2013 

  • Emerging Leader Program, 2012 

  • Management Skills Development Program, 2003 

  • Postdoc, National High Magnetic Field Laboratory, 1995 – 1997   

  • Postdoc, PNNL, 1993 – 1995  

  • PhD in Chemistry, University of Zagreb, 1992 

  • MS in Theoretical and Physical-Organic Chemistry, University of Zagreb, 1989 

  • BS in Chemistry, University of Zagreb, 1986 

Affiliations and Professional Service

  • American Chemical Society 

  • American Society for Mass Spectrometry  

  • Treasurer, ASMS (2020 – 2022) 

  • Advisory Committee Member, Berkeley Synchrotron Infrared Structural Biology Program, Biological and Environmental Research program (BER), U.S. Department of Energy (DOE) (2020) 

  • Editorial Board Member, Journal of the American Society for Mass Spectrometry (2017 – Present) 

  • Member at Large, Board of Directors, Consortium for Top-Down Proteomics (2012 – Present) 

  • Member, External Advisory Committee, MIT Superfund Research Program (2018 – Present) 

  • Officer and Investigator, Consortium for Top-down Proteomics (2012 – Present) 

  • Organizer and Lecturer, “Mass Spectrometry in Biology and Medicine” summer school, Dubrovnik, Croatia (2007 – Present) 

  • Reviewer, Small Business Innovation Research Proposals, BER, DOE (2019 – 2020)  

  • Reviewer, Horizon 2020 EU Funded Project, European Proteomics Infrastructure Consortium (2019 – Present)  

  • Review Committee, Genome Canada Technology Platform Interim Review (2019) 

  • Editorial Advisory Board Member, Journal of Proteome Research, (2017 – 2019) 

  • Member, User Executive Committee, National High Magnetic Field Laboratory, (2017 – 2019) 

  • Member, Nominating Committee, ASMS (2016 – 2017) 

  • Participant, National Science Foundation sponsored workshops “Mass Spectrometry: Data to Knowledge” (2015, 2016) 

  • Participant, “Microbiome Innovation: ‘Roadmap to the Future’ Forum,” White House Office of Science and Technology Policy (2015) 

  • Participant, Kavli Futures Symposium “Microbiome Discussion: Decoding Microbial Networks,” National Academy of Sciences (2015) 

  • Member, Scientific Committee, European FT-MS Workshop (2014) 

  • PhD Thesis Committee, Erasmus University Rotterdam and Utrecht University, Netherlands (2008, 2012, 2013) 

  • Program Co-Chair, Sanibel Conference on Top-Down Mass Spectrometry Conference, ASMS (2013) 

  • Guest Editor, Special Issue of PROTEOMICS on “Top-Down Proteomics” (2013) 

  • Reviewer, Innovative Molecular Analysis Technologies Program, National Institutes of Health (NIH) (2006 – 2013) 

  • Reviewer, S10 Instrumentation Programs, NIH (2004 – 2012)  

  • Reviewer, SBIR Program, NCI (2004 – 2011) 

  • Editor, Mass Spectrometry of Proteins and Peptides: Methods and Protocols, Second Ed. “Methods in Molecular Biology” (2009) 

  • Member, Sanibel Committee, ASMS (2006 – 2008) 

  • Reviewer, Innovations in Cancer Sample Preparation Program, NIH (2006, 2007) 

  • Reviewer, Bioanalytical Engineering and Chemistry Study Section, NIH (2004) 

Awards and Recognitions

  • The Analytical Scientist Power List (2019) 

  • Spectrometry Global Impact Award (2015) 

  • Director’s Award, EMSL (2010) 

  • Systems Biology Fellows Mentor Award (2007) 

  • Outstanding Merit Award, International Immunology (2007) 

  • Key Contributor Award, PNNL (2002, 2003) 

  • Outstanding Performance Award, PNNL (1998, 1999, 2000) 

  • International Institute of Quantum Chemistry and Solid-State Theory Award (1988) 


  • “Method for Calibrating Mass Spectrometers.” 2002. US Pat. 6,498,340 



Agtuca, B. J., S. A. Stopka, S. Evans, L. Samarah, Y. Liu, D. Xu, M. G. Stacey, D. W. Koppenaal, L. Paša-Tolić, C. R. Anderton, A. Vertes, and G. Stacey. 2020. “Metabolomic Profiling of Wild-Type and Mutant Soybean Root Nodules Using Laser-Ablation Electrospray Ionization Mass Spectrometry Reveals Altered Metabolism.” Plant Journal 103 (5): 1937-1958.  

Agtuca, B. J., S. A. Stopka, T. R. Tuleski, F. P. Do Amaral, S. Evans, Y. Liu, D. Xu, R. A. Monteiro, D. W. Koppenaal, L. Paša-Tolić, C. R. Anderton, A. Vertes, and G. Stacey. 2020. “In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria.” Molecular Plant-Microbe Interactions 33 (2): 272-283.  

Hagen, L. H., C. G. Brooke, C. A. Shaw, A. D. Norbeck, H. Piao, M. Ø. Arntzen, H. M. Olson, A. Copeland, N. Isern, A. Shukla, S. Roux, V. Lombard, B. Henrissat, M. A. O’Malley, I. V. Grigoriev, S. G. Tringe, R. I. Mackie, L. Pasa-Tolic, P. B. Pope, and M. Hess. 2020. “Proteome Specialization of Anaerobic Fungi During Ruminal Degradation of Recalcitrant Plant Fiber.” ISME Journal.  

Samarah, L. Z., R. Khattar, T. H. Tran, S. A. Stopka, C. A. Brantner, P. Parlanti, D. Veličković, J. B. Shaw, B. J. Agtuca, G. Stacey, L. Paša-Tolić, N. Tolić, C. R. Anderton, and A. Vertes. 2020. “Single-Cell Metabolic Profiling: Metabolite Formulas from Isotopic Fine Structures in Heterogeneous Plant Cell Populations.” Analytical Chemistry 92 (10): 7289-7298.  

Srzentić, K., L. Fornelli, Y. O. Tsybin, J. A. Loo, H. Seckler, J. N. Agar, L. C. Anderson, D. L. Bai, A. Beck, J. S. Brodbelt, Y. E. M. van der Burgt, J. Chamot-Rooke, S. Chatterjee, Y. Chen, D. J. Clarke, P. O. Danis, J. K. Diedrich, R. A. D'Ippolito, M. Dupré, N. Gasilova, Y. Ge, Y. A. Goo, D. R. Goodlett, S. Greer, K. F. Haselmann, L. He, C. L. Hendrickson, J. D. Hinkle, M. V. Holt, S. Hughes, D. F. Hunt, N. L. Kelleher, A. N. Kozhinov, Z. Lin, C. Malosse, A. G. Marshall, L. Menin, R. J. Millikin, K. O. Nagornov, S. Nicolardi, L. Paša-Tolić, S. Pengelley, N. R. Quebbemann, A. Resemann, W. Sandoval, R. Sarin, N. D. Schmitt, J. Shabanowitz, J. B. Shaw, M. R. Shortreed, L. M. Smith, F. Sobott, D. Suckau, T. Toby, C. R. Weisbrod, N. C. Wildburger, J. R. Yates, 3rd, S. H. Yoon, N. L. Young, and M. Zhou. 2020. “Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry.” Journal of the American Society for Mass Spectrometry 31 (9): 1783-1802.  

Tsai, C. F., R. Zhao, S. M. Williams, R. J. Moore, K. Schultz, W. B. Chrisler, L. Pasa-Tolic, K. D. Rodland, R. D. Smith, T. Shi, Y. Zhu, and T. Liu. 2020. “An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-Cell Proteomics.” Molecular and Cellular Proteomics 19 (5): 828-838.  

Veličković, D., G. Zhang, D. Bezbradica, A. Bhattacharjee, L. Paša-Tolić, K. Sharma, T. Alexandrov, C. R. Anderton, and K. Consortium. 2020. “Response Surface Methodology as a New Approach for Finding Optimal MALDI Matrix Spraying Parameters for Mass Spectrometry Imaging.” Journal of the American Society for Mass Spectrometry 31 (3): 508-516.  

Williams, S. M., A. V. Liyu, C. F. Tsai, R. J. Moore, D. J. Orton, W. B. Chrisler, M. J. Gaffrey, T. Liu, R. D. Smith, R. T. Kelly, L. Pasa-Tolic, and Y. Zhu. 2020. “Automated Coupling of Nanodroplet Sample Preparation with Liquid Chromatography-Mass Spectrometry for High-Throughput Single-Cell Proteomics.” Analytical Chemistry 92 (15): 10588-10596.  

Zhou, M., N. Uwugiaren, S. M. Williams, R. J. Moore, R. Zhao, D. Goodlett, D. Goodlett, I. Dapic, L. Paša-Tolić, and Y. Zhu. 2020. “Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform.” Analytical Chemistry 92 (10): 7087-7095.


Adair E., C. Afonso, N.A. Bell, A.N. Davies, M. Delsuc, R. Godfrey, and R. Goodacre, et al. 2019. "High resolution techniques: general discussion." Faraday Discussions 218. PNNL-SA-147038. doi:10.1039/C9FD90045D 

Afonso C., M. Barrow, A.N. Davies, M. Delsuc, T. Ebbels, F.A. Fernandez-Lima, and C. Gauchotte-Lindsay, et al. 2019. "Data mining and visualisation: general discussion." Faraday Discussions 218. PNNL-SA-147037. doi:10.1039/C9FD90044F 

Afonso C., M. Barrow, N.A. Bell, A.N. Davies, D. Duca, C. Focsa, and C. Gauchotte-Lindsay, et al. 2019. "Dealing with complexity: general discussion." Faraday Discussions 218. PNNL-SA-147036. doi:10.1039/C9FD90055A 

Boiteau R.M., S.J. Fansler, Y. Farris, J.B. Shaw, D.W. Koppenaal, L. Pasa Tolic, and J.K. Jansson. 2019. "Siderophore Profiling of Co-Habitating Soil Bacteria by Ultra-High Resolution Mass Spectrometry." Metallomics 11, no. 1:166-175. PNNL-SA-139283. doi:10.1039/c8mt00252e 

Donnelly D.P., C.M. Rawlins, C.J. Dehart, L. Fornelli, L.F. Schachner, Z. Lin, and J. Lippens, et al. 2019. "Best practices and benchmarks for intact protein analysis for top-down mass spectrometry." Nature Methods 16, no. 7:587-594. PNNL-SA-141748. doi:10.1038/s41592-019-0457-0 

Rivas-Ubach A., J. Penuelas, J.A. Hodar, M. Oravec, L. Pasa Tolic, O. Urban, and J. Sardans. 2019. "We are what we eat: a stoichiometric and ecometabolomic study of caterpillars feeding on two pine subspecies of Pinus sylvestris." International Journal of Molecular Sciences 20, no. 1:59. PNNL-SA-140210. doi:10.3390/ijms20010059 

Rivas-Ubach A., Y. Liu, A.L. Steiner, J. Sardans, M.M. Tfaily, G.R. Kulkarni, and Y. Kim, et al. 2019. "Atmo-ecometabolomics: a novel atmospheric particle chemical characterization methodology for ecological research." Environmental Monitoring and Assessment 191, no. 2:Article No. 78. PNNL-SA-118888. doi:10.1007/s10661-019-7205-x 

Shen Y., R. Zhao, N. Tolic, M. Tfaily, E.W. Robinson, R.M. Boiteau, and L. Pasa Tolic, et al. 2019. "Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter." Faraday Discussions 218. PNNL-SA-141115. doi:10.1039/C9FD00011A 

Smith L.M., P.M. Thomas, M.R. Shortreed, L.V. Schaffer, R.T. Fellers, R.D. Leduc, and T.M. Tucholski, et al. 2019. "A five-level classification system for proteoform identifications." Nature Methods 16, no. 10:939-940. PNNL-SA-147035. doi:10.1038/s41592-019-0573-x 

Stopka S.A., L.Z. Samarah, J.B. Shaw, A.V. Liyu, D. Velickovic, B.J. Agtuca, and C. Kukolj, et al. 2019. "Ambient Metabolic Profiling and Imaging of Biological Samples with Ultrahigh Molecular Resolution using Laser Ablation Electrospray Ionization 21 Tesla FTICR Mass Spectrometry." Analytical Chemistry 91, no. 8:5028-5035. PNNL-SA-137600. doi:10.1021/acs.analchem.8b05084 


Boiteau R.M., J.B. Shaw, L. Pasa Tolic, D.W. Koppenaal, and J.K. Jansson. 2018. "Micronutrient metal speciation is controlled by competitive organic chelation in grassland soils." Soil Biology and Biochemistry 120. PNNL-SA-128577. doi:10.1016/j.soilbio.2018.02.018 

Callister S.J., T.L. Fillmore, C.D. Nicora, J.B. Shaw, S.O. Purvine, D.J. Orton, and R.A. White, et al. 2018. "Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage Through two-dimensional liquid chromatography." Soil Biology and Biochemistry 125. PNNL-SA-131999. doi:10.1016/j.soilbio.2018.07.018 

Gargano A., J.B. Shaw, M. Zhou, C.S. Wilkins, T.L. Fillmore, R.J. Moore, and G.W. Somsen, et al. 2018. "Increasing the Separation Capacity of Intact Histone Proteoforms Chromatography Coupling Online Weak Cation Exchange-HILIC to Reversed Phase LC UVPD-HRMS." Journal of Proteome Research 17, no. 11:3791-3800. PNNL-SA-138847. doi:10.1021/acs.jproteome.8b00458 

Leduc R.D., V. Schwammle, M.R. Shortreed, A.J. Cesnik, S.K. Solntsev, J.B. Shaw, and M.J. Martin, et al. 2018. "ProForma: a Standard Proteoform Notation." Journal of Proteome Research 17, no. 3:1321-1325. PNNL-SA-133700. doi:10.1021/acs.jproteome.7b00851 

Naas A., L. Solden, A.D. Norbeck, H.M. Brewer, L. Hagen, I. Heggenes, and A. Mchardy, et al. 2018. "Candidatus Paraporphyromonas polyenzymogenes encodes multi-modular cellulases linked to the type IX secretion system." Microbiome 6. PNNL-SA-129531. doi:10.1186/s40168-018-0421-8 

Rivas-Ubach A., Y. Liu, T.S. Bianchi, N. Tolic, G.C. Jansson, and L. Pasa Tolic. 2018. "Moving beyond the van Krevelen diagram: A new stoichiometric approach for compound classification in organisms." Analytical Chemistry 90, no. 10:6152-6160. PNNL-SA-134250. doi:10.1021/acs.analchem.8b00529 

Shaw J.B., M. Gorshkov, Q. Wu, and L. Pasa Tolic. 2018. "High Speed Intact Protein Characterization Using 4X Frequency Multiplication, Ion Trap Harmonization, and 21 Tesla FTICR-MS." Analytical Chemistry 90, no. 9:5557-5562. PNNL-SA-133517. doi:10.1021/acs.analchem.7b04606 

Stopka S.A., R. Khattar, B.J. Agtuca, C.R. Anderton, L. Pasa Tolic, G. Stacey, and A. Vertes. 2018. "Metabolic Noise and Distinct Subpopulations Observed by Single Cell LAESI Mass Spectrometry of Plant Cells In situ." Frontiers in Plant Science 9. PNNL-SA-137441. doi:10.3389/fpls.2018.01646 

Velickovic D., R.K. Chu, A.A. Carrell, M. Thomas, L. Pasa Tolic, D.J. Weston, and C.R. Anderton. 2018. "Multimodal MSI in Conjunction with Broad Coverage Spatially Resolved MS2 Increases Confidence in Both Molecular Identification and Localization." Analytical Chemistry 90, no. 1:702-707. PNNL-SA-132227. doi:10.1021/acs.analchem.7b04319 

Velickovic D.S., B.J. Agtuca, S.A. Stopka, A. Vertes, D.W. Koppenaal, L. Pasa Tolic, and G. Stacey, et al. 2018. "Observed Metabolic Asymmetry Within Soybean Root Nodules Reflects Unexpected Complexity in Rhizobacteria-legume Metabolite Exchange." The ISME Journal 12, no. 9:2335-2338. PNNL-SA-127419. doi:10.1038/s41396-018-0188-8 

Yao Q., Z. Li, Y. Song, J. Wright, X. Guo, S.G. Tringe, and M.M. Tfaily, et al. 2018. "Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil." Nature Ecology & Evolution 2, no. 3:499-509. PNNL-SA-131384. doi:10.1038/s41559-017-0463-5 

Zhou M., J. Yan, C.A. Romano, B.M. Tebo, V.H. Wysocki, and L. Pasa Tolic. 2018. "Surface Induced Dissociation Coupled with High Resolution Mass Spectrometry Unveils Heterogeneity of a 211 kDa Multicopper Oxidase Protein Complex." Journal of the American Society for Mass Spectrometry 29, no. 4:723-733. PNNL-SA-124854. doi:10.1007/s13361-017-1882-x 

Zhu Y., R. Zhao, P.D. Piehowski, R.J. Moore, S. Lim, V.J. Orphan, and L. Pasa Tolic, et al. 2018. "Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples." International Journal of Mass Spectrometry 427. PNNL-SA-125645. doi:10.1016/j.ijms.2017.08.016 


Blair S.L., A.C. Macmillan, G.T. Drozd, A.H. Goldstein, R.K. Chu, L. Pasa Tolic, and J.B. Shaw, et al. 2017. "Molecular Characterization of Organosulfur Compounds in Biodiesel and Diesel Fuel Secondary Organic Aerosol." Environmental Science & Technology 51, no. 1:119-127. PNNL-SA-119437. doi:10.1021/acs.est.6b03304 

Handakumbura P., K.K. Hixson, S.O. Purvine, G.C. Jansson, and L. Pasa Tolic. 2017. "Plant iTRAQ-based proteomics." Current Protocols in Plant Biology 2, no. 2:158-172. PNNL-SA-123355. doi:10.1002/cppb.20052 

Hawely A.K., M. Torres Beltran, E. Zaikova, D.A. Walsh, A. Mueller, M. Scofield, and S. Kheirandish, et al. 2017. "A compendium of multi-omic sequence information from the Saanich Inlet water column." Scientific Data 4. PNNL-SA-121885. doi:10.1038/sdata.2017.160 

Hess N.J., L. Pasa Tolic, V.L. Bailey, and A. Dohnalkova. 2017. "New Understanding in Rhizosphere Processes Enabled by Advances in Molecular and Spatially Resolved Techniques." Rhizosphere 3, no. 2:209-211. PNNL-SA-124636. doi:10.1016/j.rhisph.2017.04.007 

Kou Q., S. Wu, N. Tolic, L. Pasa Tolic, Y. Liu, and X. Liu. 2017. "A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra." Bioinformatics 33, no. 9:1309-1316. PNNL-SA-123090. doi:10.1093/bioinformatics/btw806 

Ledee D.R., M.A. Kang, M. Kajimoto, S.O. Purvine, H.M. Brewer, L. Pasa Tolic, and M.A. Portman. 2017. "Quantitative cardiac phosphoproteomics profiling during ischemia-reperfusion in an immature swine model." American Journal of Physiology. Heart and Circulatory Physiology 313, no. 1:H125-H137. PNNL-SA-128530. doi:10.1152/ajpheart.00842.2016 

Park J., P.D. Piehowski, C.S. Wilkins, M. Zhou, J.A. Mendoza, G.M. Fujimoto, and B.C. Gibbons, et al. 2017. "Informed-Proteomics: Open Source Software Package for Top-down Proteomics." Nature Methods 14, no. 9:909-914. PNNL-SA-120171. doi:10.1038/nmeth.4388 

Rivas-Ubach A., J. Sardans, J.A. Hodar, J. Garcia-Porta, A.B. Guenther, L. Pasa Tolic, and M. Oravec, et al. 2017. "Close and Distant: Contrasting the Metabolism of Two Closely Related Subspecies of Scots Pine Under the Effects of Folivory and Summer Drought." Ecology and Evolution 7, no. 21:8976-8988. PNNL-SA-121524. doi:10.1002/ece3.3343 

Romano C.A., M. Zhou, Y. Song, V.H. Wysocki, A. Dohnalkova, L. Kovarik, and L. Pasa Tolic, et al. 2017. "Biogenic manganese oxide nanoparticle formation by a multimeric multicopper oxidase Mnx." Nature Communications 8. PNNL-SA-124759. doi:10.1038/s41467-017-00896-8 

Shen Y., N. Tolic, P.D. Piehowski, A.K. Shukla, S. Kim, R. Zhao, and Y. Qu, et al. 2017. "High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics." Journal of Chromatography A 1498. PNNL-SA-104738. doi:10.1016/j.chroma.2017.01.008 

Smallwood H.S., S. Duan, M. Morfouace, S. Rezinciuc, B.L. Shulkin, A. Shelat, and E.M. Zink, et al. 2017. "Targeting Metabolic Reprogramming by Influenza Infection for Therapeutic Intervention." Cell Reports 19, no. 8:1640-1653. PNNL-SA-127228. doi:10.1016/j.celrep.2017.04.039 

Staley C., A.P. Ferrieri, M.M. Tfaily, Y. Cui, R.K. Chu, P. Wang, and J.B. Shaw, et al. 2017. "Diurnal Cycling of Rhizosphere Bacterial Communities is Associated with Shifts in Carbon Metabolism." Microbiome 5. PNNL-SA-121718. doi:10.1186/s40168-017-0287-1 

Stopka S.A., B.J. Agtuca, D.W. Koppenaal, L. Pasa Tolic, G. Stacey, A. Vertes, and C.R. Anderton. 2017. "Laser Ablation Electrospray Ionization Mass Spectrometry with Ion Mobility Separation Reveals Metabolites and Lipids in the Symbiotic Interactions of Soybean Roots and Rhizobia." The Plant Journal 91, no. 2:340-354. PNNL-SA-121531. doi:10.1111/tpj.13569 

Tfaily M.M., R.K. Chu, J.G. Toyoda, N. Tolic, E.W. Robinson, L. Pasa Tolic, and N.J. Hess. 2017. "Sequential extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry." Analytica Chimica Acta 972. PNNL-SA-125053. doi:10.1016/j.aca.2017.03.031 

Tolic N., Y. Liu, A.V. Liyu, Y. Shen, M.M. Tfaily, E.B. Kujawinski, and K. Longnecker, et al. 2017. "Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultra-High Resolution Mass Spectra." Analytical Chemistry 89, no. 23:12659-12665. PNNL-SA-128094. doi:10.1021/acs.analchem.7b03318 

Walker L.R., M.M. Tfaily, J.B. Shaw, N.J. Hess, L. Pasa Tolic, and D.W. Koppenaal. 2017. "Unambiguous Identification & Discovery of Bacterial Siderophores by Direct Injection 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Metallomics 9, no. 1:82-92. PNNL-SA-121375. doi:10.1039/c6mt00201c 

Yan J., M. Zhou, J. Gilbert, J.J. Wolff, A. Somogyi, R.E. Pedder, and R.S. Quintyn, et al. 2017. "Surface-induced dissociation of protein complexes in a hybrid Fourier transform ion cyclotron resonance mass spectrometer." Analytical Chemistry 89, no. 1:895-901. PNNL-SA-121761. doi:10.1021/acs.analchem.6b03986 

Zeiner C.A., S.O. Purvine, E.M. Zink, L. Pasa Tolic, D.L. Chaput, S. Wu, and C.M. Santelli, et al. 2017. "Quantitative iTRAQ-based secretome analysis reveals species-specific and temporal shifts in carbon utilization strategies among manganese(II)-oxidizing Ascomycete fungi." Fungal Genetics and Biology : FG & B 106. PNNL-SA-122328. doi:10.1016/j.fgb.2017.06.004 

Zhou M., L. Pasa Tolic, and D.L. Stenoien. 2017. "Profiling of Histone Post-translational Modifications in Mouse Brain with High Resolution Top Down Mass Spectrometry." Journal of Proteome Research 16, no. 2:599-608. PNNL-SA-119705. doi:10.1021/acs.jproteome.6b00694 


Anderton C.R., R.K. Chu, N. Tolic, A.V. Creissen, and L. Pasa-Tolic. 2016. "Utilizing a Robotic Sprayer for High Lateral and Mass Resolution MALDI FT-ICR MSI of Microbial Cultures." Journal of the American Society for Mass Spectrometry 27, no. 3:556-559. PNNL-SA-115142. doi:10.1007/s13361-015-1324-6 

Kou Q., B. Zhu, S. Wu, C.K. Ansong, N. Tolic, L. Pasa Tolic, and X. Liu. 2016. "Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore." Journal of Proteome Research 15, no. 8:2422-2432. PNNL-SA-119698. doi:10.1021/acs.jproteome.5b01098 

Shaw J.B., E.W. Robinson, and L. Pasa-Tolic. 2016. "Vacuum Ultraviolet Photodissociation and Fourier Transform-Ion Cyclotron Resonance (FT-ICR) Mass Spectrometry: Revisited." Analytical Chemistry 88, no. 6:3019-3023. PNNL-SA-114531. doi:10.1021/acs.analchem.6b00148 

Shaw J.B., T. Lin, F.E. Leach, A.V. Tolmachev, N. Tolic, E.W. Robinson, and D.W. Koppenaal, et al. 2016. "21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Greatly Expands Mass Spectrometry Toolbox." Journal of the American Society for Mass Spectrometry 27, no. 12:1929-1936. PNNL-SA-121061. doi:10.1007/s13361-016-1507-9 

Tolic N., M.M. Tfaily, Y. Shen, R.K. Chu, T.L. Fillmore, R. Zhao, and K.J. Bloodsworth, et al. 2016. "Soil Organic Matter (SOM): Mass Spectrometry Data Analysis." In Encyclopedia of Soil Science, Third Edition, edited by R Lal. Boca Raton, Florida:CRC Press. PNNL-SA-117244. doi:10.1081/E-ESS3-120053757 

Valdes-Lopez O., J.M. Batek Rios, N. Gomez-Hernandez, C.T. Nguyen, M.C. Isidra-Arellano, N. Zhang, and T. Joshi, et al. 2016. "Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles." Frontiers in Plant Science 7. PNNL-SA-114787. doi:10.3389/fpls.2016.00517 

Vyatkina K., S. Wu, L.J. Dekker, M.M. vanDuijn, X. Liu, N. Tolic, and T.M. Luider, et al. 2016. "Top-down analysis of protein samples by de novo sequencing techniques." Bioinformatics 32, no. 18:2753-2759. PNNL-SA-119182. doi:10.1093/bioinformatics/btw307 

Zeiner C.A., S.O. Purvine, E.M. Zink, L. Pasa Tolic, D.L. Chaput, S. Haridas, and S. Wu, et al. 2016. "Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi." PLoS One 11, no. 7:Article No. e0157844. PNNL-SA-121069. doi:10.1371/journal.pone.0157844 


Lin T., G.A. Anderson, R.V. Norheim, S.A. Prost, B.L. Lamarche, F.E. Leach, and K.J. Auberry, et al. 2015. "An Adaptable Multiple Power Source for Mass Spectrometry and other Scientific Instruments." Review of Scientific Instruments 86, no. 9:Article No. 094102. PNNL-SA-110063. doi:10.1063/1.4930967 

Lu J., K. Chughtai, S.O. Purvine, Z.M. Bhujwalla, V. Raman, L. Pasa-Tolic, and R.M. Heeren, et al. 2015. "MALDI-mass spectrometric imaging revealing hypoxia-driven lipids and proteins in a breast tumor model." Analytical Chemistry 87, no. 12:5947-5956. PNNL-SA-110776. doi:10.1021/ac504503x 

Ream T.S., J.R. Haag, F. Pontvianne, C.D. Nicora, A.D. Norbeck, L. Pasa-Tolic, and C.S. Pikaard. 2015. "Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III- specific forms of the AC40 subunit, and alternative C53 subunits." Nucleic Acids Research 43, no. 8:4163-4178. PNNL-SA-108415. doi:10.1093/nar/gkv247 

Tfaily M.M., R.K. Chu, N. Tolic, K.M. Roscioli, C.R. Anderton, L. Pasa-Tolic, and E.W. Robinson, et al. 2015. "Advanced solvent based methods for molecular characterization of soil organic matter by high-resolution mass spectrometry." Analytical Chemistry 87, no. 10:5206-5215. PNNL-SA-107718. doi:10.1021/acs.analchem.5b00116 

Vyatkina K., S. Wu, L.J. Dekker, M.M. vanDuijn, X. Liu, N. Tolic, and M. Dvorkin, et al. 2015. "De novo sequencing of peptides from top-down tandem mass spectra." Journal of Proteome Research 14, no. 11:4450-4462. PNNL-SA-103863. doi:10.1021/pr501244v 


Anderson J.C., Y. Wan, Y. Kim, L. Pasa-Tolic, T.O. Metz, and S.C. Peck. 2014. "Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against Pseudomonas syringae." Proceedings of the National Academy of Sciences of the United States of America 111, no. 18:6846-6851. PNNL-SA-97264. doi:10.1073/pnas.1403248111 

Cao L., N. Tolic, Y. Qu, D. Meng, R. Zhao, Q. Zhang, and R.J. Moore, et al. 2014. "Characterization of intact N- and O-linked glycopeptides using higher energy collisional dissociation." Analytical Biochemistry 452. PNNL-SA-99189. doi:10.1016/j.ab.2014.01.003 

Dang X., J. Scotcher, S. Wu, R.K. Chu, N. Tolic, I. Ntai, and P. Thomas, et al. 2014. "The first pilot project of the consortium for top-down proteomics: A status report." Proteomics 14, no. 10:1130-1140. PNNL-SA-102713. doi:10.1002/pmic.201300438 

Debord J., D.F. Smith, C.R. Anderton, R.M. Heeren, L. Pasa-Tolic, R.H. Gomer, and F.A. Fernandez-Lima. 2014. "Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams." PLoS One 9, no. 6:e99319. PNNL-SA-101216. doi:10.1371/journal.pone.0099319 

Dekker L.J., S. Wu, M.M. vanDuijn, N. Tolic, C. Stingl, R. Zhao, and T.n. Luider, et al. 2014. "An integrated top-down and bottom-up proteomic approach to characterize the antigen binding fragment of antibodies." Proteomics 14, no. 10:1239-1248. PNNL-SA-101637. doi:10.1002/pmic.201300366 

Haag J.R., B. Brower-Toland, E.K. Krieger, L. Sidorenko, C.D. Nicora, A.D. Norbeck, and A. Irsigler, et al. 2014. "Functional Diversification of Maize RNA Polymerase IV and V subtypes via Alternative Catalytic Subunits." Cell Reports 9, no. 1:378-390. PNNL-SA-105690. doi:10.1016/j.celrep.2014.08.067 

Hawley A.K., H.M. Brewer, A.D. Norbeck, L. Pasa-Tolic, and S.J. Hallam. 2014. "Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes." Proceedings of the National Academy of Sciences of the United States of America 111, no. 31:11395-11400. PNNL-SA-100391. doi:10.1073/pnas.1322132111 

Hengel S., J.T. Aldrich, K.M. Waters, L. Pasa-Tolic, and D.L. Stenoien. 2014. "Quantitative Proteomic Profiling of Low Dose Ionizing Radiation Effects in a Human Skin Model." Proteomes 2, no. 3:382-398. PNNL-SA-102010. doi:10.3390/proteomes2030382 

Leach F.E., R.V. Norheim, G.A. Anderson, and L. Pasa-Tolic. 2014. "Application of Printed Circuit Board Technology to FT-ICR MS Analyzer Cell Construction and Prototyping." Journal of the American Society for Mass Spectrometry 25, no. 12:2069-2072. PNNL-SA-107383. doi:10.1007/s13361-014-0952-6 

Mohimani H., R. Kersten, W. Liu, M. Wang, S.O. Purvine, S. Wu, and H.M. Brewer, et al. 2014. "Automated genome mining of ribosomal peptide natural products." ACS Chemical Biology 9, no. 7:1545-1551. PNNL-SA-99212. doi:10.1021/cb500199h 

Nakayasu E.S., S. Wu, M.A. Sydor, A.K. Shukla, K.K. Weitz, R.J. Moore, and K.K. Hixson, et al. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014. PNNL-SA-96571. doi:10.1155/2014/730725 

Pasa-Tolic L., and C. Masselon. 2014. "Shining a spotlight on intact proteins." Proteomics 14, no. 10:1125-1127. PNNL-SA-103862. doi:10.1002/pmic.201470073 

Qu Y., J. Feng, S. Deng, L. Cao, Q. Zhang, R. Zhao, and Z. Zhang, et al. 2014. "Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection." Fungal Genetics and Biology : FG & B 72. PNNL-SA-101957. doi:10.1016/j.fgb.2014.08.001 

Shen Y., L. Pasa-Tolic, E.W. Robinson, J.N. Adkins, and R.D. Smith. 2014. "New challenges for proteomics technologies: a mini perspective review." Austin Journal of Proteomics, Bioinformatics & Genomics 1, no. 1:Article No. 3. PNNL-SA-106057. 

Wu S., J.N. Brown, N. Tolic, D. Meng, X. Liu, H. Zhang, and R. Zhao, et al. 2014. "Quantitative Analysis of Human Salivary Gland-Derived Intact Proteome Using Top-Down Mass Spectrometry." Proteomics 14, no. 10:1211-1222. PNNL-SA-83095. doi:10.1002/pmic.201300378 


Ansong C., S. Wu, D. Meng, X. Liu, H.M. Brewer, B. Kaiser, and E.S. Nakayasu, et al. 2013. "Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions." Proceedings of the National Academy of Sciences of the United States of America 110, no. 25:10153-10158. PNNL-SA-92306. doi:10.1073/pnas.1221210110 

D'haeseleer P., J.M. Gladden, M. Allgaier, P. Chain, S.G. Tringe, S. Malfatti, and J.T. Aldrich, et al. 2013. "Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass." PLoS One 8, no. 7:e68465. PNNL-SA-98320. doi:10.1371/journal.pone.0068465 

Duijvesz D., K.E. Burnum-Johnson, M.A. Gritsenko, M. Hoogland, M.S. Vredenbregt-van den Berg, R. Willemsen, and T.n. Luider, et al. 2013. "Proteomic Profiling of Exosomes Leads to the Identification of Novel Biomarkers for Prostate Cancer." PLoS One 8, no. 12:Article No. e82589. PNNL-SA-88219. doi:10.1371/journal.pone.0082589 

Halim M.F., F. Pfeiffer, J. Zou, A. Frisch, D.H. Haft, S. Wu, and N. Tolic, et al. 2013. "Haloferax volcanii archaeosortase is required for motility, mating, and C-terminal processing of the S-layer glycoprotein." Molecular Microbiology 88, no. 6:1164-1175. PNNL-SA-93808. doi:10.1111/mmi.12248 

Hawley A.K., S. Kheirandish, A. Mueller, H.C. Leung, A.D. Norbeck, H.M. Brewer, and L. Pasa-Tolic, et al. 2013. "Molecular Tools for Investigating Microbial Community Structure and Function in Oxygen-Deficient Marine Waters." In Methods in Enzymology: Microbial Metagenomics, Metatranscriptomics, and Metaproteomics, edited by EF DeLong. 305-329. San Diego, California:Academic Press. PNNL-SA-100374. 

Isanapong J., S. Hambright, A.G. Willis, A. Boonmee, S.J. Callister, K.E. Burnum-Johnson, and L. Pasa-Tolic, et al. 2013. "Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium." The ISME Journal 7, no. 9:1803-1813. PNNL-SA-98615. doi:10.1038/ismej.2013.74 

Liu X., S.M. Hengel, S. Wu, N. Tolic, L. Pasa-Tolic, and P.A. Pevzner. 2013. "Identification of Ultramodified Proteins Using Top-Down Mass Spectra." Journal of Proteome Research 12, no. 12:5830-8. PNNL-SA-94025. doi:10.1021/pr400849y 

Liu X., S.M. Hengel, S. Wu, N. Tolic, L. Pasa-Tolic, and P.A. Pevzner. 2013. "Identification of ultramodified proteins using top-down spectra." In Research in Computational Molecular Biology: 17th Annual International Conference, April 7-10, 2013, Beijing, China. Lecture Notes in Computer Science, edited by M Deng, et al, 7821, 132-144. Berlin:Springer. PNNL-SA-93057. doi:10.1007/978-3-642-37195-0_11 

Qu Y., S. Wu, R. Zhao, E.M. Zink, D.J. Orton, R.J. Moore, and D. Meng, et al. 2013. "Automated Immobilized Metal Affinity Chromatography System for Enrichment of Escherichia coli Phosphoproteome." Electrophoresis 34, no. 11:1619-1626. PNNL-SA-92228. doi:10.1002/elps.201200628 

Smith D.F., A. Kiss, F.E. Leach, E.W. Robinson, L. Pasa-Tolic, and R.M. Heeren. 2013. "High Mass Accuracy and High Mass Resolving Power FT-ICR Secondary Ion Mass Spectrometry for Biological Tissue Imaging." Analytical and Bioanalytical Chemistry 405, no. 18:6069-6076. PNNL-SA-94322. doi:10.1007/s00216-013-7048-1 

Wu S., R.N. Brown, S.H. Payne, D. Meng, R. Zhao, N. Tolic, and L. Cao, et al. 2013. "Top-down characterization of the post-translationally modified intact periplasmic proteome of the bacterium Novosphingobium aromaticivorans." International Journal of Proteomics 2013. PNNL-SA-91327. doi:10.1155/2013/279590 


Brechenmacher L., T.H. Nguyen, K.K. Hixson, M. Libault, J.T. Aldrich, L. Pasa-Tolic, and G. Stacey. 2012. "Identification of soybean proteins from a single cell type: The root hair." Proteomics 12, no. 22:3365-3373. PNNL-SA-86320. doi:10.1002/pmic.201200160 

Haag J.R., T.S. Ream, M. Marasco, C.D. Nicora, A.D. Norbeck, L. Pasa-Tolic, and C.S. Pikaard. 2012. "In vitro transcription activities of Pol IV, Pol V and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing." Molecular Cell 48, no. 5:811-8. PNNL-SA-90501. doi:10.1016/j.molcel.2012.09.027 

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 

Marshall K.E., E.W. Robinson, S.M. Hengel, L. Pasa-Tolic, and G. Roesijadi. 2012. "FRET Imaging of Diatoms Expressing a Biosilica-Localized Ribose Sensor." PLoS One 7, no. 3:e33771 1-8. PNNL-SA-84370. doi:10.1371/journal.pone.0033771 

Nguyen T.H., L. Brechenmacher, J.T. Aldrich, T.R. Clauss, M.A. Gritsenko, K.K. Hixson, and M. Libault, et al. 2012. "Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum." Molecular & Cellular Proteomics. MCP 11, no. 11:1140-1155. PNNL-SA-86415. doi:10.1074/mcp.M112.018028 

Payne S.H., S. Bonissone, S. Wu, R.N. Brown, D. Ivankov, D. Frishman, and L. Pasa-Tolic, et al. 2012. "Unexpected Diversity of Signal Peptides in Prokaryotes." mBio 3, no. 6:Article No. e00339-12. PNWD-SA-9881. doi:10.1128/mBio.00339-12 

Perera R.M., C. Riley, G. Isaac, A. Hopf- Jannasch, R.J. Moore, K.K. Weitz, and L. Pasa-Tolic, et al. 2012. "Dengue Virus Infection Perturbs Lipid Homeostasis in Infected Mosquito Cells." PLoS Pathogens 8, no. 3:Article No. e1002584. PNNL-SA-83173. doi:10.1371/journal.ppat.1002584 

Petrus A.K., K.S. Swithers, C.R. Ranjit, S. Wu, H.M. Brewer, J. Gogarten, and L. Pasa-Tolic, et al. 2012. "Genes for the major structural components of Thermotogales species' togas revealed by proteomic and evolutionary analyses of OmpA and OmpB homologs." PLoS One 7, no. 6:e40236. PNNL-SA-84820. doi:10.1371/journal.pone.0040236 

Shi T., T.L. Fillmore, X. Sun, R. Zhao, A.A. Schepmoes, M. Hossain, and F. Xie, et al. 2012. "Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum." Proceedings of the National Academy of Sciences of the United States of America 109, no. 38:15395-15400. PNNL-SA-83776. doi:10.1073/pnas.1204366109 

Smith D.F., A. Kharchenko, M. Konijnenburg, I. Klinkert, L. Pasa-Tolic, and R.M. Heeren. 2012. "Advanced Mass Calibration and Visualization for FT-ICR Mass Spectrometry Imaging." Journal of the American Society for Mass Spectrometry 23, no. 11:1865-1872. PNNL-SA-93060. doi:10.1007/s13361-012-0464-1 

Tian Z., N. Tolic, R. Zhao, R.J. Moore, S.M. Hengel, E.W. Robinson, and D.L. Stenoien, et al. 2012. "Enhanced top-down characterization of histone post-translational modifications." Genome Biology 13, no. 10:R86. PNNL-SA-90867. doi:10.1186/gb-2012-13-10-r86 

Tolmachev A.V., E.W. Robinson, R.D. Smith, F.E. Leach, J.H. 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. PNNL-SA-89137. doi:10.1016/j.ijms.2012.06.027 

Tolmachev A.V., E.W. Robinson, S. Wu, R.D. Smith, J.H. 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, no. 7:1169-1172. PNNL-SA-86041. doi:10.1007/s13361-012-0395-x 


Ahring B.K., N.S. Baliga, J.R. Frederickson, S. Kaplan, H.B. Pakrasi, J.G. Pounds, and I. shah, et al. 2011. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP). PNNL-20717. Richland, WA: Pacific Northwest National Laboratory. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP) 

Brown G.E., A. Chaka, D.K. Shuh, E.E. Roden, C.J. Werth, N.J. Hess, and A.R. Felmy, et al. 2011. EMSL Geochemistry, Biogeochemistry and Subsurface Science-Science Theme Advisory Panel Meeting. PNNL-20601. Richland, WA: Pacific Northwest National Laboratory. EMSL Geochemistry, Biogeochemistry and Subsurface Science-Science Theme Advisory Panel Meeting 

Hallam S.J., A.P. Page, L. Constan, Y.C. Song, A.D. Norbeck, H.M. Brewer, and L. Pasa-Tolic. 2011. "Molecular tools for investigating ANME community structure and function." In Methods in Enzymology, Part A, edited by AC Rosenzweig and SW Ragsdale. 75-90. Amsterdam:Elsevier/Academic Press. PNNL-SA-75404. 

Lopez-Ferrer D., K. Petritis, E.W. Robinson, K.K. Hixson, Z. Tian, J. Lee, and S. Lee, et al. 2011. "Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics." Molecular & Cellular Proteomics. MCP 10, no. 2. PNNL-SA-71649. doi:10.1074/mcp.M110.001479 

Parnell J.J., S.J. Callister, G. Rompato, C.D. Nicora, L. Pasa-Tolic, A. Williamson, and M.E. Pfrender. 2011. "Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock." Scientific Reports 1. PNNL-SA-74290. doi:10.1038/srep00025 

Smith D.F., E.W. Robinson, A.V. Tolmachev, R.M. Heeren, and L. Pasa-Tolic. 2011. "C60 Secondary Ion Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Analytical Chemistry 83, no. 24:9552-9556. PNNL-SA-82567. doi:10.1021/ac2023348 

Tolmachev A.V., E.W. Robinson, S. Wu, R.D. Smith, and L. Pasa-Tolic. 2011. "Trapping radial electric field optimization in compensated FTICR Cells." Journal of the American Society for Mass Spectrometry 22, no. 8:1334-1342. PNNL-SA-77848. doi:10.1007/s13361-011-0167-z 

Wu S., N. Tolic, Z. Tian, E.W. Robinson, and L. Pasa-Tolic. 2011. "An integrated top-down and bottom-up strategy for characterization protein isoforms and modifications." In Bioinformatics for Comparative Proteomics: Methods in Molecular Biology, edited by CH Wu and C Chen. 291-304. New York, New York:Springer. PNNL-SA-68814. 

Zhang H., F. Yang, W. Qian, R.N. Brown, Y. Wang, E.D. Merkley, and J.H. Park, et al. 2011. "Identification of c-Type Heme-Containing Peptides Using Non-Activated Immobilized Metal Affinity Cchromatography Resin Enrichment and Higher-Energy Collisional Dissociation." Analytical Chemistry 83, no. 19:7260-7268. PNNL-SA-77198. doi:10.1021/ac2000829 


Hixson K.K., D. Lopez-Ferrer, E.W. Robinson, and L. Pasa-Tolic. 2010. "Proteomics." In Encyclopedia of Spectroscopy and Spectrometry, 2nd edition, edited by J Lindon, GE Trantor, D Koppenaal. 2280-2288. Amsterdam:Academic Press. PNNL-SA-62501. 

Liu M., J. Hou, L. Huang, X. Huang, T.H. Heibeck, R. Zhao, and L. Pasa-Tolic, et al. 2010. "Site-Specific Proteomics Approach for Study Protein S-Nitrosylation." Analytical Chemistry 82, no. 17:7160-7168. PNNL-SA-75223. doi:10.1021/ac100569d 

Lourette N.M., H.S. Smallwood, S. Wu, E.W. Robinson, T.C. Squier, R.D. Smith, and L. Pasa-Tolic. 2010. "A Top-Down LC-FTICR MS-Based Strategy for Characterizing Oxidized Calmodulin in Activated Macrophages." Journal of the American Society for Mass Spectrometry 21, no. 6:930-939. PNNL-SA-69765. 

Mercer R., S.J. Callister, M.S. Lipton, L. Pasa-Tolic, H. Strnad, V. Paces, and J.T. Beatty, et al. 2010. "Loss of the Response Regulator CtrA Causes Pleiotropic Effects on Gene Expression but Does Not Affect Growth Phase Regulation in Rhodobacter capsulatus." Journal of Bacteriology 192, no. 11:2701-2710. PNNL-SA-69016. doi:10.1128/JB.00160-10 

Tian Z., R. Zhao, N. Tolic, R.J. Moore, D.L. Stenoien, E.W. Robinson, and R.D. Smith, et al. 2010. "Two-dimensional liquid chromatography system for online top-down mass spectrometry." Proteomics 10, no. 20:3610-3620. PNNL-SA-73468. doi:10.1002/pmic.201000367 

Vomaske J., S.M. Varnum, R. Melnychuk, P. Smith, L. Pasa-Tolic, J.I. Shutthanandan, and D.N. Streblow. 2010. "HCMV pUS28 initiates pro-migratory signaling via activation of Pyk2 kinase." Herpesviridae 1, no. 1:Article No.: 2. PNNL-SA-71328. doi:10.1186/2042-4280-1-2 

Zhang H., R.N. Brown, W. Qian, M.E. Monroe, S.O. Purvine, R.J. Moore, and M.A. Gritsenko, et al. 2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9, no. 5:2160-2169. PNNL-SA-67314. 


Ream T.S., J.R. Haag, A.T. Wierzbicki, C.D. Nicora, A.D. Norbeck, J. Zhu, and G. Hagen, et al. 2009. "Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II." Molecular Cell 33, no. 2:192-203. PNNL-SA-75446. doi:10.1016/j.molcel.2008.12.015 

Ream T.S., J.R. Haag, A.T. Wierzbicki, C.D. Nicora, A.D. Norbeck, J.K. Zhu, and G. Hagen, et al. 2009. "Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II." Molecular Cell 33, no. 2:192-203. PNNL-SA-62481. doi:10.1016/j.molcel.2008.12.015 

Springer D.L., J.H. Miller, S.L. Spinelli, L. Pasa-Tolic, S.O. Purvine, D.S. Daly, and R.C. Zangar, et al. 2009. "Platelet Proteome Changes Associated with Diabetes and During Platelet Storage for Transfusion." Journal of Proteome Research 8, no. 5:2261-2272. PNWD-SA-8399. 

Tolmachev A.V., E.W. Robinson, S. Wu, L. Pasa-Tolic, and R.D. Smith. 2009. "FT-ICR MS optimization for the analysis of intact proteins." International Journal of Mass Spectrometry 287, no. 1-3 SP ISS:32-38. PNNL-SA-61301. doi:10.1016/j.ijms.2008.10.010 

Umar A., H. Kang, A.M. Timmermans, M.P. Look, M.E. Meijer-van Gelder, M.A. den Bakker, and N. Jaitly, et al. 2009. "Identification of a putative protein profile associating with tamoxifen therapy resistance in breast cancer." Molecular & Cellular Proteomics. MCP 8, no. 6:1278-1294. PNNL-SA-63534. doi:10.1074/mcp.M800493-MCP200 

Wu S., F. Yang, R. Zhao, N. Tolic, E.W. Robinson, D.G. Camp, and R.D. Smith, et al. 2009. "An integrated workflow for characterizing intact phosphoproteins from complex mixtures." Analytical Chemistry 81, no. 11:4210-4219. PNNL-SA-63139. doi:10.1021/ac802487q 

Wu S., N.M. Lourette, N. Tolic, R. Zhao, R. Robinson, A.V. Tolmachev, and R.D. Smith, et al. 2009. "An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications." Journal of Proteome Research 8, no. 3:1347-1357. PNNL-SA-58633. 

Yang F., S. Wu, D.L. Stenoien, R. Zhao, M.E. Monroe, M.A. Gritsenko, and S.O. Purvine, et al. 2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ-labeled phosphopeptides." Analytical Chemistry 81, no. 10:4137-4143. PNNL-SA-63701. doi:10.1021/ac802605m 


Brewer H.M., A.D. Norbeck, J.N. Adkins, N.P. Manes, C. Ansong, L. Shi, and Y. Rikihisa, et al. 2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." Journal of Biomolecular Techniques:JBT 19, no. 5:285-295. PNNL-SA-60633. 

Lopez-Ferrer D., K. Petritis, N.M. Lourette, B.H. Clowers, K.K. Hixson, T.H. Heibeck, and D.C. Prior, et al. 2008. "Fast On-Line Digestion System for Protein Characterization." Analytical Chemistry 80, no. 23:8930-8936. PNWD-SA-8189. doi:10.1021/ac800927v 

Pasa-Tolic L., J.M. Jacobs, W. Qian, and R.D. Smith. 2008. "Quantitative Proteomics using Nano-LC with High Accuracy Mass Spectrometry." In Clinical Proteomics: From Diagnosis to Therapy, edited by JE Van Eyk and MJ Dunn. 89-100. Weinheim:Wiley-VCH. PNNL-SA-51867. 

Shen Y., N. Tolic, K.K. Hixson, S.O. Purvine, L. Pasa-Tolic, W. Qian, and J.N. Adkins, et al. 2008. "Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags." Analytical Chemistry 80, no. 6:1871-82. PNNL-SA-56012. doi:10.1021/ac702328x 

Tolmachev A.V., E.W. Robinson, S. Wu, H. Kang, N.M. Lourette, L. Pasa-Tolic, and R.D. Smith. 2008. "Trapped-ion cell with improved DC potential harmonicity for FT-ICR MS." Journal of the American Society for Mass Spectrometry 19, no. 4:586 - 597. PNNL-SA-57299. doi:10.1016/j.jasms.2008.01.006 

Umar A., M. Jaremko, P.C. Burgers, T.M. Luider, T.M. Luider, J.A. Foekens, and L. Pasa-Tolic. 2008. "High-throughput proteomics of breast carcinoma cells: a focus on FTICR-MS." Expert Review of Proteomics 2008 Jun;5, no. 3:445-55. PNNL-SA-59969. 


Kang H., L. Pasa-Tolic, and R.D. Smith. 2007. "Targeted Tandem Mass Spectrometry for High-Throughput Comparative Proteomics Employing NanoLC-FTICR MS with External Ion Dissociation." Journal of the American Society for Mass Spectrometry 18, no. 7:1332-1343. PNNL-SA-54095. doi:10.1016/j.jasms.2007.04.011 

Sharma S., D.C. Simpson, N. Tolic, N. Jaitly, A.M. Mayampurath, R.D. Smith, and L. Pasa-Tolic. 2007. "Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry." Journal of Proteome Research 6, no. 2:602-610. PNNL-SA-50906. doi:10.1021/pr060354a 

Smallwood H.S., N.M. Lourette, C.B. Boschek, D.J. Bigelow, R.D. Smith, L. Pasa-Tolic, and T.C. Squier. 2007. "Identification of a Denitrase Activity Against Calmodulin in Activated Macrophages Using High-Field Liquid Chromatography - FTICR Mass Spectrometry." Biochemistry 46, no. 37:10498-10505. PNWD-SA-7801. 

Umar A., T.n. Luider, J.A. Foekens, and L. Pasa-Tolic. 2007. "NanoLC-FT-ICR MS improves proteome coverage attainable for ~3000 laser microdissected breast carcinoma cells." Proteomics 7, no. 2:323-329. PNNL-SA-49906. doi:10.1002/pmic.200600293 


Lipton M.S., M.F. Romine, M.E. Monroe, D.A. Elias, L. Pasa-Tolic, G.A. Anderson, and D.J. Anderson, et al. 2006. "AMT Tag Approach to Proteomic Characterization of Deinococcus Radiodurans and Shewanella Oneidensis." In Microbial Proteomics, Methods of Biochemical Analysis, edited by I. Humphery-Smith and M. Hecker. 113-134. Hoboken, New Jersey:John Wiley & Sons, Inc. PNNL-SA-42692. 

Simpson D.C., S. Ahn, L. Pasa-Tolic, B. Bogdanov, H.M. Mottaz, A.N. Vilkov, and G.A. Anderson, et al. 2006. "Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling." Electrophoresis 27, no. 13:2722-2733. PNNL-SA-46424. doi:10.1002/elps.200600037 

Simson D.C., S. Ahn, L. Pasa-Tolic, B. Bogdanov, H.M. Brewer, A.N. Vilkov, and G.A. Anderson, et al. 2006. "Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling." Electrophoresis 27, no. 13:2722-2733. PNNL-SA-49244. doi:10.1002/elps.200600037 

Zhang Y., Y. Song, F. Yin, E. Broderick, E. Broderick, K. Siegel, and A. Goddard, et al. 2006. "Structural Studies of V?2Vd2 T Cell Phosphoantigens." Chemistry & Biology 13, no. 9:985-992. PNNL-SA-52023. doi:10.1016/j.chembiol.2006.08.007 


Huang Y., J.M. Triscari, G.C. Tseng, L. Pasa-Tolic, M.S. Lipton, R.D. Smith, and V.H. Wysocki. 2005. "Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns." Analytical Chemistry 77, no. 18:5800-5813. PNNL-SA-45900. 

Kolker E., A.F. Picone, M.Y. Galperin, M.F. Romine, R. Higdon, K.S. Makarova, and N. Kolker, et al. 2005. "Global Profiling of Shewanella oneidensis MR-1: Expression of Hypothetical Genes and Improved functional annotations." Proceedings of the National Academy of Sciences of the United States of America 102, no. 6:2099-2104. PNNL-SA-43139. 

Masselon C.D., L. Pasa-Tolic, N. Tolic, G.A. Anderson, B. Bogdanov, A.N. Vilkov, and Y. Shen, et al. 2005. "Targeted Comparative Proteomics by Liquid Chromatography - Tandem Fourier ion cyclotron resonance Mass Spectrometry." Analytical Chemistry 77, no. 2:400-406. PNNL-SA-42470. 

Yang F., B. Bogdanov, E.F. Strittmatter, A.N. Vilkov, M.A. Gritsenko, L. Shi, and D.A. Elias, et al. 2005. "Characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in Shewanella oneidenis cytochromes using mass spectrometry." Journal of Proteome Research 4, no. 3:846-854. PNNL-SA-43808. doi:10.1021/pr0497475 


Gorshkov M.V., C.D. Masselon, E.N. Nikolaev, H.R. Udseth, L. Pasa-Tolic, and R.D. Smith. 2004. "Consideration for Electron Capture Dissociation Efficiency in FTICR Mass Spectrometry." International Journal of Mass Spectrometry 234, no. 1-3:131-136. PNNL-SA-39793. 

Huang Y., J.M. Triscari, L. Pasa-Tolic, G.A. Anderson, M.S. Lipton, R.D. Smith, and V.H. Wysocki. 2004. "Dissociation Behavior of Doubly-Charged Tryptic Peptides: Correlation of Gas-Phase Cleavage Abundance with Ramachandran Plots." Journal of the American Chemical Society 126, no. 10:3034-3035. PNNL-SA-43138. 

Martinovic S., L. Pasa-Tolic, and R.D. Smith. 2004. "Capillary Isoelectric Focusing-Mass Spectrometry of Proteins and Protein Complexes." In Capillary Electrophoresis of Proteins and Peptides: Methods in Molecular Biology, edited by MA Strege and AL Lagu. 291-304. Totowa, New Jersey:Human Press. PNNL-SA-37970. 

Pasa-Tolic L., C.D. Masselon, R.C. Barry, Y. Shen, and R.D. Smith. 2004. "Proteomic Analyses using an Accurate Mass and Time Tag Strategy." BioTechniques 37, no. 4:621-636. PNNL-SA-42437. 

Shen Y., N. Tolic, C.D. Masselon, L. Pasa-Tolic, D.G. Camp, G.A. Anderson, and R.D. Smith, et al. 2004. "Nanoscale Proteomics." Analytical and Bioanalytical Chemistry 378, no. 4:1037-1045. PNNL-SA-39154. 

Shen Y., N. Tolic, C.D. Masselon, L. Pasa-Tolic, D.G. Camp, K.K. Hixson, and R. Zhao, et al. 2004. "Ultrasensitive Proteomics using High-Efficiency on-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS." Analytical Chemistry 76, no. 1:144-154. PNNL-SA-38244. 

Tolmachev A.V., A.N. Vilkov, B. Bogdanov, L. Pasa-Tolic, C.D. Masselon, and R.D. 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, no. 11:1616-1628. PNNL-SA-41836. 

Varnum S.M., D.N. Streblow, M.E. Monroe, P. Smith, K.J. Auberry, L. Pasa-Tolic, and D. Wang, et al. 2004. "Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome." Journal of Virology 78, no. 20:10960-10966. PNNL-SA-43398. 

Vilkov A.N., B. Bogdanov, L. Pasa-Tolic, D.C. Prior, G.A. Anderson, C.D. Masselon, and R.J. Moore, et al. 2004. "Tailored Noise Waveform/ Collision-Induced Dissociation of Ions Stored in a Linear Ion Trap Combined with Liquid Chromatography/Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Rapid Communications in Mass Spectrometry 18, no. 22:2682-2690. PNNL-SA-42697. 


Curic M., D. Babic, L. Pasa-Tolic, V. Butkovic, J. Plavec, and L. Tusek-Bozic. 2003. "Synthesis and Characterisation of Pd(II) Complexes with a Derivative of Aminoazobenzene - Dynamic H-1-NMR Study of Cyclopalladation Reactions in DMF." Journal of Organometallic Chemistry 687, no. 1:85-99. PNNL-SA-40331. 

Masselon C.D., L. Pasa-Tolic, S. Lee, L. Li, G.A. Anderson, R. Harkewicz, and R.D. Smith. 2003. "Identification of Tryptic Peptides from Large Databases using Multiplexed Tandem Mass Spectrometry: Simulations and Experimental Results." Proteomics 3, no. 7:1279-1286. PNWD-SA-5898. 

Mohan D., L. Pasa-Tolic, C.D. Masselon, N. Tolic, B. Bogdanov, K.K. Hixson, and R.D. Smith, et al. 2003. "Integration of Electrokinetic-Based Multidimensional Separations/Concentration Platform with electrospray ionization-Fourier transform ion cyclotron resonance-mass spectrometry for Proteome Analysis of Shewanella Oneidensis." Analytical Chemistry 75, no. 17:4432-4440. PNNL-SA-39340. 

Petritis K., L.J. Kangas, P.L. Ferguson, G.A. Anderson, L. Pasa-Tolic, M.S. Lipton, and K.J. Auberry, et al. 2003. "Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses." Analytical Chemistry 75, no. 5:1039-1048. PNNL-SA-37767. 

Shen Y., R.J. Moore, R. Zhao, J. Blonder, D.L. Auberry, C.D. Masselon, and L. Pasa-Tolic, et al. 2003. "High-Efficiency On-Line Solid-Phase Extraction Coupling to 15-150 um I.D. Column Liquid Chromatography for Proteomic Analysis." Analytical Chemistry 75, no. 14:3596-3605. PNNL-SA-38207. 

Tolmachev A.V., A.N. Vilkov, L. Pasa-Tolic, H.R. Udseth, and R.D. 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, no. 11:1229-1235. PNNL-SA-38354. 


Berger S.J., S. Lee, G.A. Anderson, L. Pasa-Tolic, N. Tolic, Y. Shen, and R. Zhao, et al. 2002. "High-Throughput Global Peptide Proteomic Analysis by Combining Stable Isotope Amino Acid Labeling and Data-Dependent Multiplexed-MS/MS." Analytical Chemistry 74, no. 19:4994-5000. PNNL-SA-39339. 

Blonder J., M.B. Goshe, R.J. Moore, L. Pasa-Tolic, C.D. Masselon, M.S. Lipton, and R.D. Smith. 2002. "Enrichment of Integral Membrane Proteins for Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry." Journal of Proteome Research 1, no. 4:351-360. PNNL-SA-36193. 

Harkewicz R., M.E. Belov, G.A. Anderson, L. Pasa-Tolic, C.D. Masselon, D.C. Prior, and H.R. Udseth, et al. 2002. "ESI-FTICR Mass Spectrometry Employing Data-Dependent External Ion Selection and Accumulation." Journal of the American Society for Mass Spectrometry 13, no. 2:144-154. PNNL-SA-34711. 

Lee S., S.J. Berger, S. Martinovic, L. Pasa-Tolic, G.A. Anderson, Y. Shen, and R. Zhao, et al. 2002. "Direct Mass Spectrometric Analysis of Intact Proteins of the Yeast Large Ribosomal Subunit using Capillary LC/FTICR." Proceedings of the National Academy of Sciences of the United States of America 99, no. 9:5942-5947. PNWD-SA-5450. 

Lipton M.S., L. Pasa-Tolic, G.A. Anderson, D.J. Anderson, D.L. Auberry, J.R. Battista, and M.J. Daly, et al. 2002. "Global Analysis of Deinococcus Radiodurans Proteome by Csing Accurate Mass Tags." Proceedings of the National Academy of Sciences of the United States of America 99, no. 17:11049-11054. PNNL-SA-35211. 

Martinovic S., T.D. Veenstra, G.A. Anderson, L. Pasa-Tolic, and R.D. Smith. 2002. "Selective Incorporation Acids for Identification Proteome-wide Level." Journal of Mass Spectrometry 37, no. 1:99-107. PNWD-SA-5482. 

Pasa-Tolic L., M.S. Lipton, C.D. Masselon, G.A. Anderson, Y. Shen, N. Tolic, and R.D. Smith. 2002. "Gene expression profiling using advanced mass spectrometric approaches." Journal of Mass Spectrometry 37, no. 12:1185-1198. PNWD-SA-5864. 

Pasa-Tolic L., R. Harkewicz, G.A. Anderson, N. Tolic, Y. Shen, R. Zhao, and B.D. Thrall, et al. 2002. "Increased Proteome Coverage for Quantitative Peptide Abundance Measurements Based upon High Performance Separations and DREAMS FTICR Mass Spectrometry." Journal of the American Society for Mass Spectrometry 13, no. 8:954-963. PNNL-SA-35815. 

Smith R.D., G.A. Anderson, M.S. Lipton, C.D. Masselon, L. Pasa-Tolic, Y. Shen, and H.R. Udseth. 2002. "The Use of Accurate Mass Tags for High-Throughput Microbial Proteomics." OMICS. A Journal of Integrative Biology 6, no. 1:61-90. PNNL-SA-36632. 

Smith R.D., G.A. Anderson, M.S. Lipton, L. Pasa-Tolic, Y. Shen, T.P. Conrads, and T.D. Veenstra, et al. 2002. "An Accurate Mass Tag Strategy for Quantitative and High-Throughput Proteome Measurements." Proteomics 2. PNNL-SA-34714. 

Smith R.D., G.A. Anderson, T.P. Conrads, C.D. Masselon, M.S. Lipton, L. Pasa-Tolic, and T.D. Veenstra. 2002. "Advanced Mass Spectrometric Approaches for Rapid and Quantitative Proteomics." In Applied Electrospray Mass Spectrometry, edited by BN Pramanik,, AK Ganguly & ML Gross. 307-360. New York, New York: Marcel Dekker. PNNL-SA-33075. 


Conrads T.P., K. Alving, T.D. Veenstra, M.E. Belov, G.A. Anderson, D.J. Anderson, and M.S. Lipton, et al. 2001. "Quantitative Analysis of Bacterial and Mammalian Proteomes using a Combination of Cysteine Affinity Tags and 15N-Metabolic Labeling." Analytical Chemistry 73, no. 9:2132-2139. PNNL-SA-34135. 

Kane R.S., P.T. Glink, R.G. Chapman, J.C. Mcdonald, P.K. Jensen, H. Gao, and L. Pasa-Tolic, et al. 2001. "Basicity of the Amino Groups of the Aminoglycoside Amikacin Using Capillary Electrophoresis and coupled CE-MS-MS techniques." Analytical Chemistry 73, no. 16:4028-4036. PNNL-SA-34179. 

Li L., C.D. Masselon, G.A. Anderson, L. Pasa-Tolic, S. Lee, Y. Shen, and R. Zhao, et al. 2001. "High-Throughput Peptide Identification from Protein Digests Using Data-Dependent Multiplexed Tandem FTICR Mass Spectrometry Coupled with Capillary Liquid Chromatography." Analytical Chemistry 73, no. 14:3312-3322. PNWD-SA-5251. 

Shen Y., N. Tolic, R. Zhao, L. Pasa-Tolic, L. Li, S.J. Berger, and R. Harkewicz, et al. 2001. "High-Throughput Proteomics Using High Efficiency Multiple-Capillary Liquid Chromatography With On-Line High-Performance ESI FTICR Mass Spectrometry." Analytical Chemistry 73, no. 13:3011-3021. PNNL-SA-33921. 

Shen Y., R. Zhao, M.E. Belov, T.P. Conrads, G.A. Anderson, K. Tang, and L. Pasa-Tolic, et al. 2001. "Packed Capillary Reversed-Phase Liquid Chromatography with High Performance Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Proteomics." Analytical Chemistry 73, no. 8:1766-1775. PNNL-SA-34100. 

Smith R.D., L. Pasa-Tolic, M.S. Lipton, P.K. Jensen, G.A. Anderson, Y. Shen, and T.P. Conrads, et al. 2001. "Rapid quantitative measurements of proteomes by Fourier transform ion cyclotron resonance mass spectrometry." Electrophoresis 22. PNNL-SA-35082. 


Bruce J.E., G.A. Anderson, M.D. Brands, L. Pasa-Tolic, and R.D. Smith. 2000. "Obtaining More Accurate Fourier Transform Ion Cyclotron Resonance Mass Measurements Without Internal Standards Using Multiply Charged Ions." Journal of the American Society for Mass Spectrometry 11, no. 5:416-421. PNNL-SA-32245. 

Conrads T.P., G.A. Anderson, T.D. Veenstra, L. Pasa-Tolic, and R.D. Smith. 2000. "Utility of Accurate Mass Tags for Proteome-Wide Protein Identification." Analytical Chemistry 72, no. 14:3349-3354. PNNL-SA-32770. 

Gao H., Y. Shen, T.D. Veenstra, R. Harkewicz, G.A. Anderson, J.E. Bruce, and L. Pasa-Tolic, et al. 2000. "Two Dimensional Electrophoretic/Chromatographic Separations Combined with Electrospray Ionization FTICR Mass Spectrometry for High Throughput Proteome Analysis." Journal of Microcolumn Separations 12, no. 7:383-390. PNNL-SA-32592. 

Goodlet D.R., J.E. Bruce, G.A. Anderson, B. Rist, L. Pasa-Tolic, O.N. Fiehn, and R.D. Smith, et al. 2000. "Protein Identification with a Single Accurate Mass of a Cysteine-Containing Peptide and Constrained Database Searching." Analytical Chemistry 72, no. 6:1112-1118. PNNL-SA-32976. 

Jensen P.K., L. Pasa-Tolic, K.K. Peden, S. Martinovic, M.S. Lipton, G.A. Anderson, and N. Tolic, et al. 2000. "Mass Spectrometric Detection for Capillary Isoelectric Focusing Separations of Complex Protein Mixtures." Electrophoresis 21, no. 7:1372-1380. PNNL-SA-32088. 

Maier C., X. Yan, M.E. Harder, M.I. Schimerlik, L. Pasa-Tolic, and R.D. Smith. 2000. "Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometric Analysis of the Recombinant Human Macrophage Colony Stimulating Factor Beta and Derivatives." Journal of the American Society for Mass Spectrometry 11, no. 3:237-243. PNNL-SA-34431. 

Martinovic S., L. Pasa-Tolic, C.D. Masselon, P.K. Jensen, C.L. Stone, and R.D. Smith. 2000. "Characterization of Human Alcohol Dehydrogenase Isoenzymes by Capillary Isoelectric Focusing-Mass Spectrometry." Electrophoresis 21, no. 12:2368-2375. PNNL-SA-32630. 

Martinovic S., S.J. Berger, L. Pasa-Tolic, and R.D. Smith. 2000. "Separation and Detection of Intact Noncovalent Protein Complexes from Mixtures by On-Line Capillary Isoelectric Focusing-Mass Spectrometry." Analytical Chemistry 72, no. 21:5356-5360. PNNL-SA-33036. 

Masselon C.D., G.A. Anderson, R. Harkewicz, J.E. Bruce, L. Pasa-Tolic, and R.D. Smith. 2000. "Accurate Mass Multiplexed Tandem Mass Spectrometry for High-Throughput Polypeptide Identification from Mixtures." Analytical Chemistry 72, no. 8:1918-1924. PNNL-SA-32241. 

Veenstra T.D., S. Martinovic, G.A. Anderson, L. Pasa-Tolic, and R.D. Smith. 2000. "Proteome Analysis using Selective Incorporation of Isotopically Labeled Amino Acids." Journal of the American Society for Mass Spectrometry 11, no. 1:78-82. PNNL-SA-32093. 

Wunschel D.S., L. Pasa-Tolic, B. Feng, and R.D. Smith. 2000. "Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Analysis of Large Polymerases Chain Reaction Products." Journal of the American Society for Mass Spectrometry 11, no. 4:333-337. PNNL-SA-33317. 

Zhang C., F. Xiang, L. Pasa-Tolic, G.A. Anderson, T.D. Veenstra, and R.D. Smith. 2000. "Stepwise Mobilization of Focused Proteins in Capillary Isoelectric Focusing Mass Spectrometry." Analytical Chemistry 72, no. 7:1462-1468. PNNL-SA-31558. 


Feng B., D.S. Wunschel, C.D. Masselon, L. Pasa-Tolic, and R.D. Smith. 1999. "Retrieval of DNA using Soft-Landing after Mass Analysis by ESI-FTICR for Enzymatic Manipulation." Journal of the American Chemical Society 121, no. 38:8961-8962. PNNL-SA-32087. 

Gorshkov M.V., L. Pasa-Tolic, and R.D. Smith. 1999. "Pressure Limited Sustained Off-Resonance Irradiation for Collision-Activated Dissociation in Fourier Transform Mass Spectrometry." Journal of the American Society for Mass Spectrometry 10. PNWD-SA-30523. 

Jensen P.K., L. Pasa-Tolic, G.A. Anderson, J.A. Horner, M.S. Lipton, J.E. Bruce, and R.D. Smith. 1999. "Probing Proteomes Using Capillary Isoelectric Focusing-Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Analytical Chemistry 71, no. 11:2076-2084. PNNL-SA-30888. 

Li L., R.W. Garden, P.D. Floyd, T.P. Moroz, J.M. Gleeson, J.V. Sweedler, and L. Pasa-Tolic, et al. 1999. "Egg-Laying Hormone Peptides in the Aplysiidae Family." Journal of Experimental Biology 202. PNWD-SA-5269. 

Pasa-Tolic L., P.K. Jensen, G.A. Anderson, M.S. Lipton, K.K. Peden, S. Martinovic, and N. Tolic, et al. 1999. "High Throughput Proteome-Wide Precision Measurements of Protein Expression using Mass Spectrometry." Journal of the American Chemical Society 121, no. 34:7949-7950. PNNL-SA-31133. 

Xu N., L. Pasa-Tolic, R.D. Smith, S. Ni, and B.D. Thrall. 1999. "Electrospray Ionization-Mass Spectrometry Study of the Interaction of Cisplatin-Adducted Oligonucleotides with Human XPA Minimal Binding Domain Protein." Analytical Biochemistry 272, no. 1:26-33. PNNL-SA-30454. 


Gorshkov M.V., L. Pasa-Tolic, H.R. Udseth, G.A. Anderson, B.M. Huang, J.E. Bruce, and D.C. Prior, et al. 1998. "Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry at 11.5 Tesla: Instrument Design and Initial Results." Journal of the American Society for Mass Spectrometry 9, no. 7:692-700. PNNL-SA-29660. doi:10.1016/S1044-0305(98)00037-3 

Pasa-Tolic L., A.C. Harms, G.A. Anderson, R.D. Smith, A. Willie, and M. Jorns. 1998. "Electrospray Ionization-Mass Spectrometry Characterization of Heterotetrameric Sarcosine Oxidase." Journal of the American Society for Mass Spectrometry 9, no. 5:510-515. PNNL-SA-29159. doi:10.1016/S1044-0305(98)00011-7 

Pasa-Tolic L., J.E. Bruce, Q.P. Lei, G.A. Anderson, and R.D. Smith. 1998. "In-Trap Cleanup of Proteins from Electrospray Ionization Using Soft Sustained Off-Resonance Irradiation with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Analytical Chemistry 70, no. 2:405-408. PNNL-SA-30183. doi:10.1021/ac970828c 

Yang L., C.S. Lee, S.A. Hofstadler, L. Pasa-Tolic, and R.D. Smith. 1998. "Capillary Isoelectric Focusing-Electropsray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Protein Characterization." Analytical Chemistry 70, no. 15:3235-3241. PNNL-SA-29818. 


Gorshkov M.V., L. Pasa-Tolic, J.E. Bruce, G.A. Anderson, and R.D. Smith. 1997. "A Dual Trap Design and its Application in Electrospray Ionization FTICR Mass Spectrometry." Analytical Chemistry 69, no. 7:1307-1314. PNNL-SA-28152. 


Muddiman D.C., D.S. Wunschel, C. Liu, L. Pasa-Tolic, K.F. Fox, A. Fox, and G.A. Anderson, et al. 1996. "Characterization of PCR Products From Bacilli Using Electrospray Ionization FTICR Mass Spectrometry." Analytical Chemistry 68, no. 21:3705-3712. PNNL-SA-27875.