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Fundamental and Computational Sciences Directorate

Staff information

Ljiljana

Ljiljana Pasa Tolic

Environmntl Molecular Sci Div
Lab Fellow, Team Lead, Chemist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352

Biography

Dr. Pasa-Tolic develops and implements the technology strategy to enable EMSL Sciences Areas in concert with the Chief Scientist, Deputy Directors and others. Responsible for instrument health, capability development, capital and non-capital instrument investment and instrument divestment. She also builds user communities in EMSL's Sciences Areas and leads outreach to the Department of Energy's Office of Biological and Environmental Research principal investigator community. As chief scientist for mass spectrometry, she develops and implements a strategic vision for that capability.

Research Interests

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

Education and Credentials

  • Graduated from the Shipley Capturing Federal Business Course, 2013
  • Graduated from the Emerging Leader Program, 2012
  • Graduated from the Management Skills Development Program, 2003
  • 1992 Ph.D., Chemistry, University of Zagreb, Zagreb, Croatia
  • 1989 M.S., Theoretical and Physical-Organic Chemistry, University of Zagreb, Zagreb, Croatia
  • 1986 B.S., Chemistry, University of Zagreb, Zagreb, Croatia

Affiliations and Professional Service

  • Member, American Chemical Society
  • Member, American Society for Mass Spectrometry (ASMS)
  • Member, ASMS Sanibel Committee, 2006
  • Treasurer, ASMS Sanibel Committee, 2007
  • Chair, ASMS Sanibel Committee, 2008
  • Nominated and unsuccessfully ran for ASMS Board of Directors, Member at Large for Education, 2006, and Secretary, 2011
  • Member, Ph.D. Thesis Committee, Ioana M. Barbu, Utrecht University, Netherlands, 2008
  • Member, Ph.D. Thesis Committee, Kamila Czornak, Utrecht University, Netherlands, 2012
  • Member, Ph.D. Thesis Committee, Dominique de Costa, Erasmus University Rotterdam, Netherlands, 2013
  • Reviewer, NCI: IMAT Program, 2006-2013
  • Reviewer, NCI: Innovations in Cancer Sample Preparation, 2006, 2007
  • Reviewer, NCI: Cancer Detection and Cancer Sample Preparation applications, 2006
  • Reviewer, NSF, Analytical and Surface Chemistry Program, 2005
  • Reviewer, NIH-NCRR Shared and High End Instrumentation, 2004-2012
  • Reviewer, NIH Bioanalytical Engineering and Chemistry Study Section, 2004
  • Reviewer, NCI: SBIR Program, 2004-2011
  • Conference co-organizer: Mass Spectrometry in Biology and Medicine, held during first week of July in Dubrovnik, Croatia, 2007-present.
  • Conference co-chair: ASMS 2013 Sanibel Conference on Top-Down Mass Spectrometry, January, 24-28, St. Pete Beach, FL
  • Scientific Committee member, European FT-MS workshop 2014
  • Member of the Board of Directors and a Member-at-Large; Consortium for Top-Down Proteomics; http://www.topdownproteomics.org/ 2012- present
  • Mass Spectrometry of Proteins and Peptides: Methods and Protocols, 2nd Edition (Methods in Molecular Biology), 2009, editor (with MS Lipton)
  • Special Issue of PROTEOMICS on “Top Down Proteomics”, 2013, Guest Editor (with C Masselon)
  • Participant, Kavli Futures Symposium “Microbiome Discussion: Decoding microbial networks”, organized by the Kavli Foundation, on January 21, 2015 at the National Academy of Sciences Building at 2101 Constitution Avenue NW, Washington, DC
  • Participant and invited speaker, National Science Foundation (NSF) sponsored workshop “Mass Spectrometry: Data to Knowledge”, Arlington, VA, May 11-12, 2015;
  • Participant, Forum on “Microbiome Innovation: Roadmap to the Future” organized by the White House Office of Science and Technology Policy, in conjunction with the U.S. Agency for International Development and DOE, September 25, 2015, in Washington, DC;
  • Advisory board member, The European project METASPACE on Bioinformatics for Spatial Metabolomics (Theodore Alexandrov, Principal Investigator (PI))
  • Reviewer, Nature Methods, Journal of Separation Science, Proteomics, Journal of Proteome Research, Analytica Chemica Acta, Analytical Biochemistry, Electrophoresis, Nature Methods, Molecular & Cellular Proteomics, Rapid Communications in Mass Spectrometry, Analytical Chemistry, Journal of the American Chemical Society, Journal of the American Society for Mass Spectrometry, 1995 to present

Awards and Recognitions

  • “The 1988 International Institute in Quantum Chemistry and Solid State Theory” Attendance Award, University of Florida, Gainesville, 1988
  • PNNL Outstanding Performance Award (four times), 1998-2000
  • PNNL Key Contributor Award (two times), 2002, 2003
  • Systems Biology Fellows Mentor Award, 2007
  • EMSL Director’s Award, 2010
  • PNNL’s Earth and Biological Sciences Directorate “BESTies” Award, 2015
  • 2007 Outstanding Merit Award, International Immunology
  • Spectrometry Global Impact Celebration, 2015 award recipient

PNNL Publications

2018

  • 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
  • Naas A., L. Solden, A.D. Norbeck, H.M. Brewer, L. Hagen, I. Heggenes, and A.C. Mchardy, et al. 2018. "Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the Type IX secretion system." Microbiome 6, no. 1:Article No. 44. PNNL-SA-133703. doi:10.1186/s40168-018-0421-8
  • 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

2017

  • 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

2016

  • 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
  • Zhou M., S. Wu, D.L. Stenoien, Z. Zhang, L. Connolly, M. Freitag, and L. Pasa-Tolic. 2016. "Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry." In Methods in Molecular Biology: Eukaryotic transcriptional and post-transcriptional gene expression regulation, edited by N Wajapeyee and R Gupta. 153-168. New York, New York:Springer. PNNL-SA-113153. doi:10.1007/978-1-4939-6518-2_12

2015

  • 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

2014

  • 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

2013

  • 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

2012

  • 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

2011

  • 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.
  • 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.
  • 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

2010

  • 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.

2009

  • 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: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

2008

  • 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.

2007

  • 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: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

2006

  • 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

2005

  • 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

2004

  • 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.

2003

  • 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.

2002

  • 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.

2001

  • 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.

2000

  • 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.

1999

  • 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.

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