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Fundamental and Computational Sciences Directorate

Staff information

Ljiljana Pasa Tolic

Science and Technology
Lab Fellow, Team Lead
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352

PNNL Publications

2017

  • Handakumbura P, KK Hixson, SO Purvine, GC Jansson, and L Pasa Tolic. 2017. "Plant iTRAQ-based proteomics." Current Protocols in Plant Biology 2(2):158-172.  doi:10.1002/cppb.20052
  • Walker LR, MM Tfaily, JB Shaw, NJ Hess, L Pasa Tolic, and DW Koppenaal. 2017. "Unambiguous Identification & Discovery of Bacterial Siderophores by Direct Injection 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Metallomics 9(1):82-92.  doi:10.1039/c6mt00201c
  • Zhou M, L Pasa Tolic, and DL Stenoien. 2017. "Profiling of Histone Post-translational Modifications in Mouse Brain with High Resolution Top Down Mass Spectrometry." Journal of Proteome Research 16(2):599-608.  doi:10.1021/acs.jproteome.6b00694
  • Smallwood HS, S Duan, M Morfouace, S Rezinciuc, BL Shulkin, A Shelat, EM Zink, S Milasta, R Bajracharya, AJ Oluwaseum, MF Roussel, DR Green, L Pasa Tolic, and PG Thomas. 2017. "Targeting Metabolic Reprogramming by Influenza Infection for Therapeutic Intervention." Cell Reports 19(8):1640-1653.  doi:10.1016/j.celrep.2017.04.039
  • Blair SL, AC Macmillan, GT Drozd, AH Goldstein, RK Chu, L Pasa Tolic, JB Shaw, N Tolic, P Lin, J Laskin, A Laskin, and S Nizkorodov. 2017. "Molecular Characterization of Organosulfur Compounds in Biodiesel and Diesel Fuel Secondary Organic Aerosol." Environmental Science & Technology 51(1):119-127.  doi:10.1021/acs.est.6b03304
  • Hess NJ, L Pasa Tolic, VL Bailey, and A Dohnalkova. 2017. "New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques." Rhizosphere 3(2):209-211.  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(9):1309-1316.  doi:10.1093/bioinformatics/btw806
  • Ledee DR, MA Kang, M Kajimoto, SO Purvine, HM Brewer, L Pasa Tolic, and MA Portman. 2017. "Quantitative cardiac phosphoproteomics profiling during ischemia-reperfusion in an immature swine model." American Journal of Physiology. Heart and Circulatory Physiology 313(1):H125-H137.  doi:10.1152/ajpheart.00842.2016
  • Park JK, PD Piehowski, CS Wilkins, M Zhou, JA Mendoza, GM Fujimoto, BC Gibbons, JB Shaw, Y Shen, AK Shukla, RJ Moore, T Liu, VA Petyuk, N Tolic, L Pasa Tolic, RD Smith, SH Payne, and S Kim. 2017. "Informed-Proteomics: Open Source Software Package for Top-down Proteomics." Nature Methods 14(9):909-914.  doi:10.1038/nmeth.4388
  • Romano CA, M Zhou, Y Song, VH Wysocki, A Dohnalkova, L Kovarik, L Pasa Tolic, and BM Tebo. 2017. "Biogenic manganese oxide nanoparticle formation by a multimeric multicopper oxidase Mnx." Nature Communications 8:746.  doi:10.1038/s41467-017-00896-8
  • Shen Y, N Tolic, PD Piehowski, AK Shukla, S Kim, R Zhao, Y Qu, EW Robinson, RD Smith, and L Pasa-Tolic. 2017. "High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics." Journal of Chromatography A 1498:99-110.  doi:10.1016/j.chroma.2017.01.008
  • Shen Y, N Tolic, PD Piehowski, AK Shukla, S Kim, R Zhao, Y Qu, EW Robinson, RD Smith, and L Pasa-Tolic. 2017. "High-Resolution Ultrahigh-PressurePhase Liquid Chromatography for To Long Column Reversed-p-Down Proteomics." Journal of Chromatography A 1498:99-110.  doi:10.1016/j.chroma.2017.01.008
  • Staley C, AP Ferrieri, MM Tfaily, Y Cui, RK Chu, P Wang, JB Shaw, CK Ansong, HM Brewer, AD Norbeck, LM Markillie, FP do Amaral, T Tuleski, T Pellizzaro, BJ Agtuca, RA Ferrieri, S Tringe, L Pasa Tolic, G Stacey, and M Sadowsky. 2017. "Diurnal Cycling of Rhizosphere Bacterial Communities is Associated with Shifts in Carbon Metabolism." Microbiome 5:Article No. 65.  doi:10.1186/s40168-017-0287-1
  • Stopka SA, BJ Agtuca, DW Koppenaal, L Pasa Tolic, G Stacey, A Vertes, and CR 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(2):340-354.  doi:10.1111/tpj.13569
  • Tfaily MM, RK Chu, JG Toyoda, N Tolic, EW Robinson, L Pasa Tolic, and NJ Hess. 2017. "Sequential extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry." Analytica Chimica Acta 972:54-61.  doi:10.1016/j.aca.2017.03.031
  • Yan J, M Zhou, J Gilbert, JJ Wolff, A Somogyi, RE Pedder, RS Quintyn, L Morrison, ML Easterling, L Pasa Tolic, and VH Wysocki. 2017. "Surface-induced dissociation of protein complexes in a hybrid Fourier transform ion cyclotron resonance mass spectrometer." Analytical Chemistry 89(1):895-901.  doi:10.1021/acs.analchem.6b03986
  • Zeiner CA, SO Purvine, EM Zink, L Pasa Tolic, DL Chaput, S Wu, CM Santelli, and CM Hansel. 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 106:61-75.  doi:10.1016/j.fgb.2017.06.004

2016

  • Shaw JB, EW Robinson, and L Pasa-Tolic. 2016. "Vacuum Ultraviolet Photodissociation and Fourier Transform-Ion Cyclotron Resonance (FT-ICR) Mass Spectrometry: Revisited." Analytical Chemistry 88(6):3019-3023.  doi:10.1021/acs.analchem.6b00148
  • Shaw JB, TY Lin, FE Leach, III, AV Tolmachev, N Tolic, EW Robinson, DW Koppenaal, and L Pasa Tolic. 2016. "21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Greatly Expands Mass Spectrometry Toolbox." Journal of the American Society for Mass Spectrometry 27(12):1929-1936.  doi:10.1007/s13361-016-1507-9
  • Zhou M, S Wu, DL Stenoien, Z Zhang, L Connolly, M Freitag, and L Pasa-Tolic. 2016. "Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry." Chapter 12 in Methods in Molecular Biology: Eukaryotic transcriptional and post-transcriptional gene expression regulation, vol. 1507, ed. N Wajapeyee and R Gupta, pp. 153-168.  Springer, NEW YORK, NY.  doi:10.1007/978-1-4939-6518-2_12
  • Anderton CR, RK Chu, N Tolic, AV 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(3):556-559.  doi:10.1007/s13361-015-1324-6
  • Kou Q, B Zhu, S Wu, CK 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(8):2422-2432.  doi:10.1021/acs.jproteome.5b01098
  • Valdes-Lopez O, JM Batek Rios, N Gomez-Hernandez, CT Nguyen, MC Isidra-Arellano, N Zhang, T Joshi, D Xu, KK Hixson, KK Weitz, JT Aldrich, L Pasa-Tolic, and G Stacey. 2016. "Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles." Frontiers in Plant Science 7:Article No. 517.  doi:10.3389/fpls.2016.00517
  • Vyatkina K, S Wu, LJ Dekker, MM vanDuijn, X Liu, N Tolic, TM Luider, L Pasa Tolic, and PA Pevzner. 2016. "Top-down analysis of protein samples by de novo sequencing techniques." Bioinformatics 32(18):2753-2759.  doi:10.1093/bioinformatics/btw307
  • Zeiner CA, SO Purvine, EM Zink, L Pasa Tolic, DL Chaput, S Haridas, S Wu, KM LaButti, IV Grigoriev, B Henrissat, CM Santelli, and CM Hansel. 2016. "Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi." PLoS One 11(7):Article No. e0157844.  doi:10.1371/journal.pone.0157844

2015

  • Lin TY, GA Anderson, RV Norheim, SA Prost, BL Lamarche, FE Leach, III, KJ Auberry, RD Smith, DW Koppenaal, EW Robinson, and L Pasa-Tolic. 2015. "An Adaptable Multiple Power Source for Mass Spectrometry and other Scientific Instruments." Review of Scientific Instruments 86(9):Article No. 094102.  doi:10.1063/1.4930967
  • Lu J, K Chughtai, SO Purvine, ZM Bhujwalla, V Raman, L Pasa-Tolic, RM Heeren, and K Glunde. 2015. "MALDI-mass spectrometric imaging revealing hypoxia-driven lipids and proteins in a breast tumor model." Analytical Chemistry 87(12):5947-5956.  doi:10.1021/ac504503x
  • Ream TS, JR Haag, F Pontvianne, CD Nicora, AD Norbeck, L Pasa-Tolic, and CS 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(8):4163-4178.  doi:10.1093/nar/gkv247
  • Tfaily MM, RK Chu, N Tolic, KM Roscioli, CR Anderton, L Pasa-Tolic, EW Robinson, and NJ Hess. 2015. "Advanced solvent based methods for molecular characterization of soil organic matter by high-resolution mass spectrometry." Analytical Chemistry 87(10):5206-5215.  doi:10.1021/acs.analchem.5b00116
  • Vyatkina K, S Wu, LJ Dekker, MM vanDuijn, X Liu, N Tolic, M Dvorkin, S Alexandrova, TN Luider, L Pasa-Tolic, and PA Pevzner. 2015. "De novo sequencing of peptides from top-down tandem mass spectra." Journal of Proteome Research 14(11):4450-4462.  doi:10.1021/pr501244v

2014

  • Pasa-Tolic L, and C Masselon. 2014. "Shining a spotlight on intact proteins." Proteomics 14(10):1125-1127.  doi:10.1002/pmic.201470073
  • Anderson JC, Y Wan, YM Kim, L Pasa-Tolic, TO Metz, and SC 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(18):6846-6851.  doi:10.1073/pnas.1403248111
  • Cao L, N Tolic, Y Qu, D Meng, R Zhao, Q Zhang, RJ Moore, EM Zink, MS Lipton, L Pasa-Tolic, and S Wu. 2014. "Characterization of intact N- and O-linked glycopeptides using higher energy collisional dissociation." Analytical Biochemistry 452:96-102.  doi:10.1016/j.ab.2014.01.003
  • Dang X, J Scotcher, S Wu, RK Chu, N Tolic, I Ntai, P Thomas, RT Fellers , BP Early, Y Zheng, KR Durbin, RD LeDuc, JJ Wolff, CJ Thompson, J Pan, J Han, JB Shaw, JP Salisbury, M Easterling, CH Borchers, JS Brodbelt, J Agar, L Pasa-Tolic, N Kelleher, and NL Young. 2014. "The first pilot project of the consortium for top-down proteomics: A status report." Proteomics 14(10):1130-1140.  doi:10.1002/pmic.201300438
  • Debord JD, DF Smith, CR Anderton, RM Heeren, L Pasa-Tolic, RH Gomer, and FA Fernandez-Lima. 2014. "Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams." PLoS One 9(6):e99319.  doi:10.1371/journal.pone.0099319
  • Dekker LJ, S Wu, MM vanDuijn, N Tolic, C Stingl, R Zhao, TN Luider, and L Pasa-Tolic. 2014. "An integrated top-down and bottom-up proteomic approach to characterize the antigen binding fragment of antibodies." Proteomics 14(10):1239-1248.  doi:10.1002/pmic.201300366
  • Haag JR, B Brower-Toland, EK Krieger, L Sidorenko, CD Nicora, AD Norbeck, A Irsigler, H LaRue, J Brzeski, KA Mcginnis, S Ivashuta, L Pasa-Tolic, VL Chandler, and CS Pikaard. 2014. "Functional Diversification of Maize RNA Polymerase IV and V subtypes via Alternative Catalytic Subunits." Cell Reports 9(1):378-390.  doi:10.1016/j.celrep.2014.08.067
  • Hawley AK, HM Brewer, AD Norbeck, L Pasa-Tolic, and SJ 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(31):11395-11400.  doi:10.1073/pnas.1322132111
  • Hengel S, JT Aldrich, KM Waters, L Pasa-Tolic, and DL Stenoien. 2014. "Quantitative Proteomic Profiling of Low Dose Ionizing Radiation Effects in a Human Skin Model." Proteomes 2(3):382-398.  doi:10.3390/proteomes2030382
  • Leach FE, III, RV Norheim, GA 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(12):2069-2072.  doi:10.1007/s13361-014-0952-6
  • Mohimani H, R Kersten, W Liu, M Wang, SO Purvine, S Wu, HM Brewer, L Pasa-Tolic, N Bandeira, BS Moore, PA Pevzner, and PC Dorrestein. 2014. "Automated genome mining of ribosomal peptide natural products." ACS Chemical Biology 9(7):1545-1551.  doi:10.1021/cb500199h
  • Nakayasu ES, S Wu, MA Sydor, AK Shukla, KK Weitz, RJ Moore, KK Hixson, JS Kim, VA Petyuk, ME Monroe, L Pasa-Tolic, W Qian, RD Smith, JN Adkins, and C Ansong. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014:Article No. 730725.  doi:10.1155/2014/730725
  • Qu Y, J Feng, S Deng, L Cao, Q Zhang, R Zhao, Z Zhang, Y Jiang, EM Zink, SE Baker, MS Lipton, L Pasa-Tolic, JZ Hu, and S Wu. 2014. "Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection." Fungal Genetics and Biology : FG & B 72:207-215.  doi:10.1016/j.fgb.2014.08.001
  • Shen Y, L Pasa-Tolic, EW Robinson, JN Adkins, and RD Smith. 2014. "New challenges for proteomics technologies: a mini perspective review." Austin Journal of Proteomics, Bioinformatics & Genomics 1(1):Article No. 3. 
  • Wu S, JN Brown, N Tolic, D Meng, X Liu, H Zhang, R Zhao, RJ Moore, PA Pevzner, RD Smith, and L Pasa-Tolic. 2014. "Quantitative Analysis of Human Salivary Gland-Derived Intact Proteome Using Top-Down Mass Spectrometry." Proteomics 14(10):1211-1222.  doi:10.1002/pmic.201300378

2013

  • Ansong C, S Wu, D Meng, X Liu, HM Brewer, BLD Kaiser, ES Nakayasu, JR Cort, PA Pevzner, RD Smith, F Heffron, JN Adkins, and L Pasa-Tolic. 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(25):10153-10158.  doi:10.1073/pnas.1221210110
  • D'haeseleer P, JM Gladden, M Allgaier, P Chain, SG Tringe, S Malfatti, JT Aldrich, CD Nicora, EW Robinson, L Pasa-Tolic, P Hugenholtz, BA Simmons, and SW Singer. 2013. "Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass." PLoS One 8(7):e68465.  doi:10.1371/journal.pone.0068465
  • Duijvesz D, KE Burnum-Johnson, MA Gritsenko, M Hoogland, MS Vredenbregt-van den Berg, R Willemsen, TN Luider, L Pasa-Tolic, and G Jenster. 2013. "Proteomic Profiling of Exosomes Leads to the Identification of Novel Biomarkers for Prostate Cancer." PLoS One 8(12):Article No. e82589.  doi:10.1371/journal.pone.0082589
  • Halim MF, F Pfeiffer, J Zou, A Frisch, DH Haft, S Wu, N Tolic, HM Brewer, SH Payne, L Pasa-Tolic, and M Pohlschroder. 2013. "Haloferax volcanii archaeosortase is required for motility, mating, and C-terminal processing of the S-layer glycoprotein." Molecular Microbiology 88(6):1164-1175.  doi: 10.1111/mmi.12248
  • Hawley AK, S Kheirandish, A Mueller, HTC Leung, AD Norbeck, HM Brewer, L Pasa-Tolic, and SJ Hallam. 2013. "Molecular Tools for Investigating Microbial Community Structure and Function in Oxygen-Deficient Marine Waters." Chapter 16 in Methods in Enzymology: Microbial Metagenomics, Metatranscriptomics, and Metaproteomics, vol. 531, ed. EF DeLong, pp. 305-329.  Academic Press, San Diego, CA. 
  • Isanapong J, S Hambright, AG Willis, A Boonmee, SJ Callister, KE Burnum-Johnson, L Pasa-Tolic, CD Nicora, JT Wertz, T Schmidt, and JL Rodrigues. 2013. "Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium." The ISME Journal 7(9):1803-1813.  doi:10.1038/ismej.2013.74
  • Liu X, SM Hengel, S Wu, N Tolic, L Pasa-Tolic, and PA Pevzner. 2013. "Identification of Ultramodified Proteins Using Top-Down Mass Spectra." Journal of Proteome Research 12(12):5830-8.  doi:10.1021/pr400849y
  • Liu X, SM Hengel, S Wu, N Tolic, L Pasa-Tolic, and PA 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, vol. 7821, ed. M Deng, et al, pp. 132-144.  Springer , Berlin, Germany.  doi:10.1007/978-3-642-37195-0_11
  • Qu Y, S Wu, R Zhao, EM Zink, DJ Orton, RJ Moore, D Meng, TRW Clauss, JT Aldrich, MS Lipton, and L Pasa-Tolic. 2013. "Automated Immobilized Metal Affinity Chromatography System for Enrichment of Escherichia coli Phosphoproteome." Electrophoresis 34(11):1619-1626.  doi:10.1002/elps.201200628
  • Smith DF, A Kiss, FE Leach, III, EW Robinson, L Pasa-Tolic, and RM 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(18):6069-6076.  doi:10.1007/s00216-013-7048-1
  • Wu S, RN Brown, SH Payne, D Meng, R Zhao, N Tolic, L Cao, AK Shukla, ME Monroe, RJ Moore, MS Lipton, and L Pasa-Tolic. 2013. "Top-down characterization of the post-translationally modified intact periplasmic proteome of the bacterium Novosphingobium aromaticivorans ." International Journal of Proteomics 2013:279590.  doi:10.1155/2013/279590

2012

  • Brechenmacher L, TH Nguyen, KK Hixson, M Libault, JT Aldrich, L Pasa-Tolic, and G Stacey. 2012. "Identification of soybean proteins from a single cell type: The root hair." Proteomics 12(22):3365-3373.  doi:10.1002/pmic.201200160
  • Haag JR, TS Ream, M Marasco, CD Nicora, AD Norbeck, L Pasa-Tolic, and CS 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(5):811-8.  doi:10.1016/j.molcel.2012.09.027
  • Hengel SM, EA Floyd, ES Baker, R Zhao, S Wu, and L Pasa-Tolic. 2012. "Evaluation of SDS depletion using an affinity spin column and IMS-MS detection." Proteomics 12(21):3138-3142.  doi:10.1002/pmic.201200168
  • Marshall KE, EW Robinson, SM Hengel, L Pasa-Tolic, and G Roesijadi. 2012. "FRET Imaging of Diatoms Expressing a Biosilica-Localized Ribose Sensor." PLoS One 7(3):e33771 1-8.  doi:10.1371/journal.pone.0033771
  • Nguyen TH, L Brechenmacher, JT Aldrich, TRW Clauss, MA Gritsenko, KK Hixson, M Libault, K Tanaka, F Yang, Q Yao, L Pasa-Tolic, D Xu, HT Nguyen, and G Stacey. 2012. "Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum." Molecular & Cellular Proteomics. MCP 11(11):1140-1155.  doi:10.1074/mcp.M112.018028
  • Payne SH, S Bonissone, S Wu, RN Brown, D Ivankov, D Frishman, L Pasa-Tolic, RD Smith, and PA Pevzner. 2012. "Unexpected Diversity of Signal Peptides in Prokaryotes." mBio 3(6):Article No. e00339-12.  doi:10.1128/mBio.00339-12
  • Perera RM, C Riley, G Isaac, A Hopf- Jannasch, RJ Moore, KK Weitz, L Pasa-Tolic, TO Metz, J Adamec, and RJ Kuhn. 2012. "Dengue Virus Infection Perturbs Lipid Homeostasis in Infected Mosquito Cells." PLoS Pathogens 8(3):Article No. e1002584.  doi:10.1371/journal.ppat.1002584
  • Petrus AK, KS Swithers, CR Ranjit, S Wu, HM Brewer, JP Gogarten, L Pasa-Tolic, and KM Noll. 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(6):e40236.  doi:10.1371/journal.pone.0040236
  • Petrus AK, KS Swithers, CR Ranjit, S Wu, HM Brewer, JP Gogarten, L Pasa-Tolic, and KM Noll. 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(6):e40236.  doi:10.1371/journal.pone.0040236
  • Shi T, TL Fillmore, X Sun, R Zhao, AA Schepmoes, M Hossain, F Xie, S Wu, JS Kim, NJ Jones, RJ Moore, L Pasa-Tolic, J Kagan, KD Rodland, T Liu, K Tang, DG Camp, II, RD Smith, and W Qian. 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(38):15395-15400.  doi:10.1073/pnas.1204366109
  • Smith DF, A Kharchenko, M Konijnenburg, I Klinkert, L Pasa-Tolic, and RM Heeren. 2012. "Advanced Mass Calibration and Visualization for FT-ICR Mass Spectrometry Imaging." Journal of the American Society for Mass Spectrometry 23(11):1865-1872.  doi:10.1007/s13361-012-0464-1
  • Tian Z, N Tolic, R Zhao, RJ Moore, SM Hengel, EW Robinson, DL Stenoien, S Wu, RD Smith, and L Pasa-Tolic. 2012. "Enhanced top-down characterization of histone post-translational modifications ." Genome Biology 13(10):R86.  doi:10.1186/gb-2012-13-10-r86
  • Tolmachev AV, EW Robinson, RD Smith, FE Leach, III, JH Futrell, and L Pasa-Tolic. 2012. "A Conceptual Approach for FT-ICR cell Harmonization Utilizing External Shim Electrodes ." International Journal of Mass Spectrometry 325-327:45-50.  doi:10.1016/j.ijms.2012.06.027
  • Tolmachev AV, EW Robinson, S Wu, RD Smith, JH Futrell, and L Pasa-Tolic. 2012. "Angular Averaged Profiling of the Radial Electric Field in Compensated FTICR Cells." Journal of the American Society for Mass Spectrometry 23(7):1169-1172.  doi:10.1007/s13361-012-0395-x

2011

  • Lopez-Ferrer D, K Petritis, EW Robinson, KK Hixson, Z Tian, JH Lee, SW Lee, N Tolic, KK Weitz, ME Belov, RD Smith, and L Pasa-Tolic. 2011. "Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics." Molecular & Cellular Proteomics. MCP 10(2):, doi:10.1074/mcp.M110.001479
  • Ahring BK, NS Baliga, JR Frederickson, S Kaplan, HB Pakrasi, JG Pounds, I shah, S Slater, G Stacey, KJ Auberry, DR Baer, DML Brown, DE Cowley, DW Hoyt, DW Koppenaal, BE Linggi, KT Mueller, G Orr, EW Robinson, RG Teller, HS Wiley, NJ Hess, L Pasa-Tolic, KM Waters, and KD Rodland. 2011. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP)PNNL-20717, Pacific Northwest National Laboratory, Richland, WA. 
  • Brown GE, A Chaka, DK Shuh, EE Roden, CJ Werth, NJ Hess, AR Felmy, KM Rosso, DR Baer, VL Bailey, ME Bowden, JW Grate, DW Hoyt, LR Kuprat, AS Lea, KT Mueller, M Oostrom, G Orr, L Pasa-Tolic, C Plata, EW Robinson, RG Teller, S Thevuthasan, H Wang, HS Wiley, and MJ Wilkins. 2011. EMSL Geochemistry, Biogeochemistry and Subsurface Science-Science Theme Advisory Panel MeetingPNNL-20601, Pacific Northwest National Laboratory, Richland, WA. 
  • Hallam SJ, AP Page, L Constan, YC Song, AD Norbeck, HM Brewer, and L Pasa-Tolic. 2011. "Molecular tools for investigating ANME community structure and function." Chapter 4 in Methods in Enzymology, Part A, vol. 494, ed. AC Rosenzweig and SW Ragsdale, pp. 75-90.  Elsevier/Academic Press, Amsterdam, Netherlands. 
  • Parnell JJ, SJ Callister, G Rompato, CD Nicora, L Pasa-Tolic, A Williamson, and ME Pfrender. 2011. "Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock." Scientific Reports 1:Article No. 25.  doi:10.1038/srep00025
  • Smith DF, EW Robinson, AV Tolmachev, RM Heeren, and L Pasa-Tolic. 2011. "C60 Secondary Ion Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Analytical Chemistry 83(24):9552-9556.  doi:10.1021/ac2023348
  • Tolmachev AV, EW Robinson, S Wu, RD Smith, and L Pasa-Tolic. 2011. "Trapping radial electric field optimization in compensated FTICR Cells." Journal of the American Society for Mass Spectrometry 22(8):1334-1342.  doi:10.1007/s13361-011-0167-z
  • Wu S, N Tolic, Z Tian, EW Robinson, and L Pasa-Tolic. 2011. "An integrated top-down and bottom-up strategy for characterization protein isoforms and modifications." Chapter 18 in Bioinformatics for Comparative Proteomics: Methods in Molecular Biology, vol. 694, ed. CH Wu and C Chen, pp. 291-304.  Springer, New York, NY. 
  • Zhang H, F Yang, W Qian, RN Brown, Y Wang, ED Merkley, JH Park, ME Monroe, SO Purvine, RJ Moore, L Shi, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton. 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(19):7260-7268.  doi:10.1021/ac2000829

2010

  • Hixson KK, D Lopez-Ferrer, EW Robinson, and L Pasa-Tolic. 2010. "Proteomics." In Encyclopedia of Spectroscopy and Spectrometry, 2nd edition, ed. J Lindon, GE Trantor, D Koppenaal, pp. 2280-2288.  Academic Press, Amsterdam, Netherlands Antilles. 
  • Liu M, J Hou, L Huang, X Huang, TH Heibeck, R Zhao, L Pasa-Tolic, RD Smith, Y Li, K Fu, Z Zhang, S Hinrichs, and SJ Ding. 2010. "Site-Specific Proteomics Approach for Study Protein S-Nitrosylation." Analytical Chemistry 82(17):7160-7168.  doi:10.1021/ac100569d
  • Lourette NM, HS Smallwood, S Wu, EW Robinson, TC Squier, RD 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(6):930-939. 
  • Mercer R, SJ Callister, MS Lipton, L Pasa-Tolic, H Strnad, V Paces, JT Beatty, and AS Lang. 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(11):2701-2710.  doi:10.1128/JB.00160-10
  • Tian Z, R Zhao, N Tolic, RJ Moore, DL Stenoien, EW Robinson, RD Smith, and L Pasa-Tolic. 2010. "Two-dimensional liquid chromatography system for online top-down mass spectrometry." Proteomics 10(20):3610-3620.  doi:10.1002/pmic.201000367
  • Vomaske J, SM Varnum, R Melnychuk, P Smith, L Pasa-Tolic, JI Shutthanandan, and DN Streblow. 2010. "HCMV pUS28 initiates pro-migratory signaling via activation of Pyk2 kinase." Herpesviridae 1(1):Article No.: 2.  doi:10.1186/2042-4280-1-2
  • Zhang H, RN Brown, W Qian, ME Monroe, SO Purvine, RJ Moore, MA Gritsenko, L Shi, MF Romine, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton. 2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9(5):2160-2169. 

2009

  • Ream TS, JR Haag, AT Wierzbicki, CD Nicora, AD Norbeck, JK Zhu, G Hagen, TJ Guilfoyle, L Pasa-Tolic, and CS Pikaard. 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(2):192-203.  doi:doi:10.1016/j.molcel.2008.12.015
  • Ream TS, JR Haag, AT Wierzbicki, CD Nicora, AD Norbeck, JK Zhu, G Hagen, TJ Guilfoyle, L Pasa-Tolic, and CS Pikaard. 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(2):192-203.  doi:10.1016/j.molcel.2008.12.015
  • Springer DL, JH Miller, SL Spinelli, L Pasa-Tolic, SO Purvine, DS Daly, RC Zangar, S Jin, N Blumberg, CW Francis, MB Taubman, AE Casey, SD Wittlin, and RP Phipps. 2009. "Platelet Proteome Changes Associated with Diabetes and During Platelet Storage for Transfusion." Journal of Proteome Research 8(5):2261-2272. 
  • Tolmachev AV, EW Robinson, S Wu, L Pasa-Tolic, and RD Smith. 2009. "FT-ICR MS optimization for the analysis of intact proteins." International Journal of Mass Spectrometry 287(1-3 SP ISS):32-38.  doi:10.1016/j.ijms.2008.10.010
  • Umar A, H Kang, AM Timmermans, MP Look, ME Meijer-van Gelder, MA den Bakker, N Jaitly, JW Martens, TM Luider, JA Foekens, and L Pasa-Tolic. 2009. "Identification of a putative protein profile associating with tamoxifen therapy resistance in breast cancer." Molecular & Cellular Proteomics. MCP 8(6):1278-1294.  doi:10.1074/mcp.M800493-MCP200
  • Wu S, F Yang, R Zhao, N Tolic, EW Robinson, DG Camp, II, RD Smith, and L Pasa-Tolic. 2009. "An integrated workflow for characterizing intact phosphoproteins from complex mixtures." Analytical Chemistry 81(11):4210-4219.  doi:10.1021/ac802487q
  • Wu S, NM Lourette, N Tolic, R Zhao, R Robinson, AV Tolmachev, RD Smith, and L Pasa-Tolic. 2009. "An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications." Journal of Proteome Research 8(3):1347-1357. 
  • Yang F, S Wu, DL Stenoien, R Zhao, ME Monroe, MA Gritsenko, SO Purvine, AD Polpitiya, N Tolic, Q Zhang, AD Norbeck, DJ Orton, RJ Moore, K Tang, GA Anderson, L Pasa-Tolic, DG Camp, II, and RD Smith. 2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ-labeled phosphopeptides." Analytical Chemistry 81(10):4137-4143.  doi:10.1021/ac802605m

2008

  • Lopez-Ferrer D, K Petritis, NM Lourette, BH Clowers, KK Hixson, TH Heibeck, DC Prior, L Pasa-Tolic, DG Camp, II, ME Belov, and RD Smith. 2008. "Fast On-Line Digestion System for Protein Characterization ." Analytical Chemistry 80(23):8930-8936.  doi:10.1021/ac800927v
  • Pasa-Tolic L, JM Jacobs, W Qian, and RD Smith. 2008. "Quantitative Proteomics using Nano-LC with High Accuracy Mass Spectrometry." Chapter 7 in Clinical Proteomics: From Diagnosis to Therapy, ed. JE Van Eyk and MJ Dunn, pp. 89-100.  Wiley-VCH, Weinheim, Germany. 
  • Brewer HM, AD Norbeck, JN Adkins, NP Manes, C Ansong, L Shi, Y Rikihisa, T Kikuchi, S Wong, RD Estep, F Heffron, L Pasa-Tolic, and RD Smith. 2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." Journal of Biomolecular Techniques:JBT 19(5):285-295. 
  • Shen Y, N Tolic, KK Hixson, SO Purvine, L Pasa-Tolic, W Qian, JN Adkins, RJ Moore, and RD Smith. 2008. "Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags." Analytical Chemistry 80(6):1871-82.  doi:10.1021/ac702328x
  • Tolmachev AV, EW Robinson, S Wu, H Kang, NM Lourette, L Pasa-Tolic, and RD Smith. 2008. " Trapped-ion cell with improved DC potential harmonicity for FT-ICR MS." Journal of the American Society for Mass Spectrometry 19(4):586 - 597.  doi:10.1016/j.jasms.2008.01.006
  • Umar A, M Jaremko, PC Burgers, TM Luider, JA 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(3):445-55. 

2007

  • Kang H, L Pasa-Tolic, and RD 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(7):1332-1343.  doi:doi:10.1016/j.jasms.2007.04.011
  • Sharma S, DC Simpson, N Tolic, N Jaitly, AM Mayampurath, RD 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(2):602-610.  doi:10.1021/pr060354a
  • Smallwood HS, NM Lourette, CB Boschek, DJ Bigelow, RD Smith, L Pasa-Tolic, and TC Squier. 2007. "Identification of a Denitrase Activity Against Calmodulin in Activated Macrophages Using High-Field Liquid Chromatography - FTICR Mass Spectrometry." Biochemistry 46(37):10498-10505. 
  • Umar A, TN Luider, JA Foekens, and L Pasa-Tolic. 2007. "NanoLC-FT-ICR MS improves proteome coverage attainable for ~3000 laser microdissected breast carcinoma cells." Proteomics 7(2):323-329.  doi:10.1002/pmic.200600293

2006

  • Lipton MS, MF Romine, ME Monroe, DA Elias, L Pasa-Tolic, GA Anderson, DJ Anderson, JK Fredrickson, KK Hixson, CD Masselon, HM Mottaz, N Tolic, and RD Smith. 2006. "AMT Tag Approach to Proteomic Characterization of Deinococcus Radiodurans and Shewanella Oneidensis ." In Microbial Proteomics, Methods of Biochemical Analysis, vol. 49, ed. I. Humphery-Smith and M. Hecker, pp. 113-134.  John Wiley & Sons, Inc., Hoboken, NJ. 
  • Simpson DC, S Ahn, L Pasa-Tolic, B Bogdanov, HM Mottaz, AN Vilkov, GA Anderson, MS Lipton, and RD Smith. 2006. "Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling." Electrophoresis 27(13):2722-2733.  doi:10.1002/elps.200600037
  • Simson DC, S Ahn, L Pasa-Tolic, B Bogdanov, HM Brewer, AN Vilkov, GA Anderson, MS Lipton, and RD Smith. 2006. "Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling ." Electrophoresis 27(13):2722-2733.  doi:10.1002/elps.200600037
  • Zhang Y, Y Song, F Yin, E Broderick, K Siegel, A Goddard, E Nieves, L Pasa-Tolic, Y Tanaka, H Wang, CT Morita, and E Oldfield. 2006. "Structural Studies of V?2Vd2 T Cell Phosphoantigens." Chemistry & Biology 13(9):985-992.  doi:10.1016/j.chembiol.2006.08.007

2005

  • Yang F, B Bogdanov, EF Strittmatter, AN Vilkov, MA Gritsenko, L Shi, DA Elias, S Ni, MF Romine, L Pasa-Tolic, MS Lipton, and RD Smith. 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(3):846-854.  doi:10.1021/pr0497475
  • Huang Y, JM Triscari, GC Tseng, L Pasa-Tolic, MS Lipton, RD Smith, and VH Wysocki. 2005. "Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns." Analytical Chemistry 77(18):5800-5813. 
  • Kolker E, AF Picone, MY Galperin, MF Romine, R Higdon, KS Makarova, N Kolker, GA Anderson, X Qiu, KJ Auberry, G Babnigg, AS Beliaev, P Edlefsen, DA Elias, YA Gorby, T Holzman, J Klappenbach, K Konstantinidis, ML Land, MS Lipton, LA McCue, ME Monroe, L Pasa-Tolic, GE Pinchuk, SO Purvine, M Serres, S Tsapin, BA Zakrajsek, W Zhu, J Zhou, F Larimer, C Lawrence, M Riley, FR Collart, JR Yates, III, RD Smith, CS Giometti, K Nealson, JK Fredrickson, and JM Tiedje. 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(6):2099-2104. 
  • Masselon CD, L Pasa-Tolic, N Tolic, GA Anderson, B Bogdanov, AN Vilkov, Y Shen, R Zhao, W Qian, MS Lipton, DG Camp, II, and RD Smith. 2005. "Targeted Comparative Proteomics by Liquid Chromatography - Tandem Fourier ion cyclotron resonance Mass Spectrometry." Analytical Chemistry 77(2):400-406. 

2004

  • Pasa-Tolic L, CD Masselon, RC Barry, Y Shen, and RD Smith. 2004. "Proteomic Analyses using an Accurate Mass and Time Tag Strategy." BioTechniques 37(4):621-636. 
  • Tolmachev AV, AN Vilkov, B Bogdanov, L Pasa-Tolic, CD Masselon, and RD Smith. 2004. "Collisional Activation of Ions in RF Ion Traps and Ion Guides: The Effective Ion Temperature Treatment." Journal of the American Society for Mass Spectrometry 15(11):1616-1628. 
  • Gorshkov MV, CD Masselon, EN Nikolaev, HR Udseth, L Pasa-Tolic, and RD Smith. 2004. "Consideration for Electron Capture Dissociation Efficiency in FTICR Mass Spectrometry." International Journal of Mass Spectrometry 234(1-3):131-136. 
  • Huang Y, JM Triscari, L Pasa-Tolic, GA Anderson, MS Lipton, RD Smith, and VH 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(10):3034-3035. 
  • Martinovic S, L Pasa-Tolic, and RD Smith. 2004. "Capillary Isoelectric Focusing-Mass Spectrometry of Proteins and Protein Complexes." Chapter 14 in Capillary Electrophoresis of Proteins and Peptides: Methods in Molecular Biology, vol. 276, ed. MA Strege and AL Lagu, pp. 291-304.  Human Press, Totowa, NJ. 
  • Shen Y, N Tolic, CD Masselon, L Pasa-Tolic, DG Camp, II, GA Anderson, RD Smith, and MS Lipton. 2004. "Nanoscale Proteomics." Analytical and Bioanalytical Chemistry 378(4):1037-1045. 
  • Shen Y, N Tolic, CD Masselon, L Pasa-Tolic, DG Camp, II, KK Hixson, R Zhao, GA Anderson, and RD Smith. 2004. "Ultrasensitive Proteomics using High-Efficiency on-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS." Analytical Chemistry 76(1):144-154. 
  • Varnum SM, DN Streblow, ME Monroe, P Smith, KJ Auberry, L Pasa-Tolic, D Wang, DG Camp, II, KD Rodland, HS Wiley, W Britt, T Shenk, RD Smith, and J Nelson. 2004. "Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome ." Journal of Virology 78(20):10960-10966. 
  • Vilkov AN, B Bogdanov, L Pasa-Tolic, DC Prior, GA Anderson, CD Masselon, RJ Moore, and RD Smith. 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(22):2682-2690. 

2003

  • Tolmachev AV, AN Vilkov, L Pasa-Tolic, HR Udseth, and RD Smith. 2003. "Suppression of the Lower Charge State Ions in the External Accumulation RF Multipole with a Reduced Trapping DC Potential." Journal of the American Society for Mass Spectrometry 14(11):1229-1235. 
  • 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(1):85-99. 
  • Masselon CD, L Pasa-Tolic, SW Lee, L Li, GA Anderson, R Harkewicz, and RD Smith. 2003. "Identification of Tryptic Peptides from Large Databases using Multiplexed Tandem Mass Spectrometry: Simulations and Experimental Results." Proteomics 3(7):1279-1286. 
  • Mohan D, L Pasa-Tolic, CD Masselon, N Tolic, B Bogdanov, KK Hixson, RD Smith, and CS Lee. 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(17):4432-4440. 
  • Petritis K, LJ Kangas, PL Ferguson, GA Anderson, L Pasa-Tolic, MS Lipton, KJ Auberry, EF Strittmatter, Y Shen, R Zhao, and RD Smith. 2003. "Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses." Analytical Chemistry 75(5):1039-1048. 
  • Shen Y, RJ Moore, R Zhao, J Blonder, DL Auberry, CD Masselon, L Pasa-Tolic, KK Hixson, KJ Auberry, and RD Smith. 2003. "High-Efficiency On-Line Solid-Phase Extraction Coupling to 15-150 um I.D. Column Liquid Chromatography for Proteomic Analysis." Analytical Chemistry 75(14):3596-3605. 

2002

  • Berger SJ, SW Lee, GA Anderson, L Pasa-Tolic, N Tolic, Y Shen, R Zhao, and RD Smith. 2002. "High-Throughput Global Peptide Proteomic Analysis by Combining Stable Isotope Amino Acid Labeling and Data-Dependent Multiplexed-MS/MS." Analytical Chemistry 74(19):4994-5000. 
  • Blonder J, MB Goshe, RJ Moore, L Pasa-Tolic, CD Masselon, MS Lipton, and RD Smith. 2002. "Enrichment of Integral Membrane Proteins for Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry." Journal of Proteome Research 1(4):351-360. 
  • Harkewicz R, ME Belov, GA Anderson, L Pasa-Tolic, CD Masselon, DC Prior, HR Udseth, and RD Smith. 2002. "ESI-FTICR Mass Spectrometry Employing Data-Dependent External Ion Selection and Accumulation." Journal of the American Society for Mass Spectrometry 13(2):144-154. 
  • Lee SW, SJ Berger, S Martinovic, L Pasa-Tolic, GA Anderson, Y Shen, R Zhao, and RD Smith. 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(9):5942-5947. 
  • Lipton MS, L Pasa-Tolic, GA Anderson, DJ Anderson, DL Auberry, JR Battista, MJ Daly, JK Fredrickson, KK Hixson, HM Kostandarithes, CD Masselon, LM Markillie, RJ Moore, MF Romine, Y Shen, EF Strittmatter, N Tolic, HR Udseth, A Venkateswaran, KK Wong, R Zhao, and RD Smith. 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(17):11049-11054. 
  • Martinovic S, TD Veenstra, GA Anderson, L Pasa-Tolic, and RD Smith. 2002. "Selective Incorporation Acids for Identification Proteome-wide Level." Journal of Mass Spectrometry 37(1):99-107. 
  • Pasa-Tolic L, MS Lipton, CD Masselon, GA Anderson, Y Shen, N Tolic, and RD Smith. 2002. "Gene expression profiling using advanced mass spectrometric approaches." Journal of Mass Spectrometry 37(12):1185-1198. 
  • Pasa-Tolic L, R Harkewicz, GA Anderson, N Tolic, Y Shen, R Zhao, BD Thrall, CD Masselon, and RD Smith. 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(8):954-963. 
  • Smith RD, GA Anderson, MS Lipton, L Pasa-Tolic, Y Shen, TP Conrads, TD Veenstra, and HR Udseth. 2002. "An Accurate Mass Tag Strategy for Quantitative and High-Throughput Proteome Measurements." Proteomics 2:513-523. 
  • Smith RD, GA Anderson, MS Lipton, CD Masselon, L Pasa-Tolic, Y Shen, and HR Udseth. 2002. "The Use of Accurate Mass Tags for High-Throughput Microbial Proteomics." OMICS. A Journal of Integrative Biology 6(1):61-90. 
  • Smith RD, GA Anderson, TP Conrads, CD Masselon, MS Lipton, L Pasa-Tolic, and TD Veenstra. 2002. "Advanced Mass Spectrometric Approaches for Rapid and Quantitative Proteomics." Chapter 8 in Applied Electrospray Mass Spectrometry, ed. BN Pramanik,, AK Ganguly & ML Gross, pp. 307-360.  Marcel Dekker, New York, NY. 

2001

  • Conrads TP, K Alving, TD Veenstra, ME Belov, GA Anderson, DJ Anderson, MS Lipton, L Pasa-Tolic, HR Udseth, WB Chrisler, BD Thrall, and RD Smith. 2001. "Quantitative Analysis of Bacterial and Mammalian Proteomes using a Combination of Cysteine Affinity Tags and 15N-Metabolic Labeling." Analytical Chemistry 73(9):2132-2139. 
  • Kane RS, PT Glink, RG Chapman, JC Mcdonald, PK Jensen, H Gao, L Pasa-Tolic, RD Smith, and GM Whitesides. 2001. "Basicity of the Amino Groups of the Aminoglycoside Amikacin Using Capillary Electrophoresis and coupled CE-MS-MS techniques." Analytical Chemistry 73(16):4028-4036. 
  • Li L, CD Masselon, GA Anderson, L Pasa-Tolic, SW Lee, Y Shen, R Zhao, MS Lipton, TP Conrads, N Tolic, and RD Smith. 2001. "High-Throughput Peptide Identification from Protein Digests Using Data-Dependent Multiplexed Tandem FTICR Mass Spectrometry Coupled with Capillary Liquid Chromatography." Analytical Chemistry 73(14):3312-3322. 
  • Shen Y, R Zhao, ME Belov, TP Conrads, GA Anderson, K Tang, L Pasa-Tolic, TD Veenstra, MS Lipton, HR Udseth, and RD Smith. 2001. "Packed Capillary Reversed-Phase Liquid Chromatography with High Performance Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Proteomics ." Analytical Chemistry 73(8):1766-1775. 
  • Shen Y, N Tolic, R Zhao, L Pasa-Tolic, L Li, SJ Berger, R Harkewicz, GA Anderson, ME Belov, and RD Smith. 2001. "High-Throughput Proteomics Using High Efficiency Multiple-Capillary Liquid Chromatography With On-Line High-Performance ESI FTICR Mass Spectrometry." Analytical Chemistry 73(13):3011-3021. 
  • Smith RD, L Pasa-Tolic, MS Lipton, PK Jensen, GA Anderson, Y Shen, TP Conrads, HR Udseth, R Harkewicz, ME Belov, CD Masselon, and TD Veenstra. 2001. "Rapid quantitative measurements of proteomes by Fourier transform ion cyclotron resonance mass spectrometry." Electrophoresis 22:1652-1668. 

2000

  • Bruce JE, GA Anderson, MD Brands, L Pasa-Tolic, and RD 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(5):416-421. 
  • Conrads TP, GA Anderson, TD Veenstra, L Pasa-Tolic, and RD Smith. 2000. "Utility of Accurate Mass Tags for Proteome-Wide Protein Identification." Analytical Chemistry 72(14):3349-3354. 
  • Gao H, Y Shen, TD Veenstra, R Harkewicz, GA Anderson, JE Bruce, L Pasa-Tolic, and RD Smith. 2000. "Two Dimensional Electrophoretic/Chromatographic Separations Combined with Electrospray Ionization FTICR Mass Spectrometry for High Throughput Proteome Analysis." Journal of Microcolumn Separations 12(7):383-390. 
  • Goodlet DR, JE Bruce, GA Anderson, B Rist, L Pasa-Tolic, ON Fiehn, RD Smith, and R Aebersold. 2000. "Protein Identification with a Single Accurate Mass of a Cysteine-Containing Peptide and Constrained Database Searching." Analytical Chemistry 72(6):1112-1118. 
  • Jensen PK, L Pasa-Tolic, KK Peden, S Martinovic, MS Lipton, GA Anderson, N Tolic, KK Wong, and RD Smith. 2000. "Mass Spectrometric Detection for Capillary Isoelectric Focusing Separations of Complex Protein Mixtures." Electrophoresis 21(7):1372-1380. 
  • Maier C, X Yan, ME Harder, MI Schimerlik, L Pasa-Tolic, and RD 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(3):237-243. 
  • Martinovic S, L Pasa-Tolic, CD Masselon, PK Jensen, CL Stone, and RD Smith. 2000. "Characterization of Human Alcohol Dehydrogenase Isoenzymes by Capillary Isoelectric Focusing-Mass Spectrometry." Electrophoresis 21(12):2368-2375. 
  • Martinovic S, SJ Berger, L Pasa-Tolic, and RD Smith. 2000. "Separation and Detection of Intact Noncovalent Protein Complexes from Mixtures by On-Line Capillary Isoelectric Focusing-Mass Spectrometry." Analytical Chemistry 72(21):5356-5360. 
  • Masselon CD, GA Anderson, R Harkewicz, JE Bruce, L Pasa-Tolic, and RD Smith. 2000. "Accurate Mass Multiplexed Tandem Mass Spectrometry for High-Throughput Polypeptide Identification from Mixtures." Analytical Chemistry 72(8):1918-1924. 
  • Veenstra TD, S Martinovic, GA Anderson, L Pasa-Tolic, and RD Smith. 2000. "Proteome Analysis using Selective Incorporation of Isotopically Labeled Amino Acids." Journal of the American Society for Mass Spectrometry 11(1):78-82. 
  • Wunschel DS, L Pasa-Tolic, B Feng, and RD 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(4):333-337. 
  • Zhang CX, F Xiang, L Pasa-Tolic, GA Anderson, TD Veenstra, and RD Smith. 2000. "Stepwise Mobilization of Focused Proteins in Capillary Isoelectric Focusing Mass Spectrometry." Analytical Chemistry 72(7):1462-1468. 

1999

  • Feng B, DS Wunschel, CD Masselon, L Pasa-Tolic, and RD Smith. 1999. "Retrieval of DNA using Soft-Landing after Mass Analysis by ESI-FTICR for Enzymatic Manipulation." Journal of the American Chemical Society 121(38):8961-8962. 
  • Gorshkov MV, L Pasa-Tolic, and RD 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 10:15-18. 
  • Jensen PK, L Pasa-Tolic, GA Anderson, JA Horner, MS Lipton, JE Bruce, and RD Smith. 1999. "Probing Proteomes Using Capillary Isoelectric Focusing-Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Analytical Chemistry 71(11):2076-2084. 
  • Li L, RW Garden, PD Floyd, TP Moroz, JM Gleeson, JV Sweedler, L Pasa-Tolic, and RD Smith. 1999. "Egg-Laying Hormone Peptides in the Aplysiidae Family." Journal of Experimental Biology 202:2961-2973. 
  • Pasa-Tolic L, PK Jensen, GA Anderson, MS Lipton, KK Peden, S Martinovic, N Tolic, JE Bruce, and RD Smith. 1999. "High Throughput Proteome-Wide Precision Measurements of Protein Expression using Mass Spectrometry." Journal of the American Chemical Society 121(34):7949-7950. 
  • Xu N, L Pasa-Tolic, RD Smith, S Ni, and BD Thrall. 1999. "Electrospray Ionization-Mass Spectrometry Study of the Interaction of Cisplatin-Adducted Oligonucleotides with Human XPA Minimal Binding Domain Protein." Analytical Biochemistry 272(1):26-33. 

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