Staff information

PNNL Publications

2024

• Anderson C.G., M.M. Tfaily, R.K. Chu, N. Tolic, P.M. Fox, P.S. Nico, and S. Fendorf, et al. 2024. "Seasonal controls on microbial depolymerization and oxidation of organic matter in floodplain soils." Environmental Science & Technology 58, no. 38:16815 - 16823. PNNL-SA-201526. doi:10.1021/acs.est.4c05109
• DiDonato N., A. Rivas Ubach, W.R. Kew, N. Sokol, C.S. Clendinen, J.E. Kyle, and C. Martinez, et al. 2024. "Improved characterization of soil organic matter by integrating FT-ICR MS, liquid chromatography tandem mass spectrometry and molecular networking: a case study of root litter decay under drought conditions." Analytical Chemistry 96, no. 29:11699-11706. PNNL-SA-199596. doi:10.1021/acs.analchem.4c00184

2023

• Chen H., H. Uzun, N. Tolic, R.K. Chu, T. Karanfil, and A.T. Chow. 2023. "Molecular Transformation of Dissolved Organic Matter During the Processes of Wildfire, Alum Coagulation, and Disinfection Using ESI(-) and ESI(+) FT-ICR MS." ACS ES&T Water 3, no. 8:2571-2580. PNNL-SA-187331. doi:10.1021/acsestwater.3c00135
• Naasko K.I., D.T. Naylor, E.B. Graham, S.P. Couvillion, R.E. Danczak, N. Tolic, and C.D. Nicora, et al. 2023. "Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry." mBio 14, no. 5:Art. No. e01758-23. PNNL-SA-187582. doi:10.1128/mbio.01758-23
• Yang J., L. Huang, W. She, G. Wu, Y. Wan, H. Dong, and R.K. Chu, et al. 2023. "Compositional changes of dissolved organic molecules along water flow and their influencing factors in the Three Gorges Reservoir." Chemical Geology 639. PNNL-SA-154608. doi:10.1016/j.chemgeo.2023.121741

2021

• Chroumpi T., M. Peng, L. Markillie, H.D. Mitchell, C.D. Nicora, C.M. Hutchinson, and V.L. Paurus, et al. 2021. "Re-routing of sugar catabolism provides a better insight into fungal flexibility in using plant biomass-derived monomers as substrates." Frontiers in Bioengineering and Biotechnology 9. PNNL-SA-158642. doi:10.3389/fbioe.2021.644216
• Danczak R.E., A.E. Goldman, R.K. Chu, J.G. Toyoda, V.A. Garayburu-Caruso, N. Tolic, and E.B. Graham, et al. 2021. "Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties." Science of the Total Environment 788. PNNL-SA-156110. doi:10.1016/j.scitotenv.2021.147409

2020

• Hawkes J., J. D'Andrilli, J.N. Agar, M. Barrow, S. Berg, N. Catalan, and H. Chen, et al. 2020. "An international laboratory comparison of dissolved organic matter composition by high resolution mass spectrometry: Are we getting the same answer?." Limnology and Oceanography Methods 18, no. 6:235-258. PNNL-SA-147033. doi:10.1002/lom3.10364
• Morrison E., M. Shields, T.S. Bianchi, Y. Liu, S. Newman, N. Tolic, and R.K. Chu. 2020. "Multiple biomarkers highlight the importance of water column processes in treatment wetland organic matter cycling." Water Research 168. PNNL-SA-146989. doi:10.1016/j.watres.2019.115153
• Samarah L.Z., R. Khattar, T.H. Tran, S.A. Stopka, C.A. Brantner, P. Parlanti, and D. Velickovic, et al. 2020. "Single-Cell Metabolic Profiling: Metabolite Formulas from Isotopic Fine Structures in Heterogeneous Plant Cell Populations." Analytical Chemistry 92, no. 10:7289-7298. PNNL-SA-152789. doi:10.1021/acs.analchem.0c00936

2019

• Fudyma J.D., J.E. Lyon, R. Aminitabrizi, H. Gieschen, R.K. Chu, D.W. Hoyt, and J.E. Kyle, et al. 2019. "Untargeted metabolomic profiling of Sphagnum fallax reveals novel antimicrobial metabolites." Plant Direct 3, no. 11:Article No. e00179. PNNL-SA-146621. doi:10.1002/pld3.179
• Nunez J., S.M. Colby, D.G. Thomas, M. Tfaily, N. Tolic, E. Ulrich, and J.R. Sobus, et al. 2019. "Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples." Journal of Chemical Information and Modeling 59, no. 9:4052-4060. PNNL-SA-148332. doi:10.1021/acs.jcim.9b00444
• Shen Y., R. Zhao, N. Tolic, M. Tfaily, E.W. Robinson, R.M. Boiteau, and L. Pasa Tolic, et al. 2019. "Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter." Faraday Discussions 218. PNNL-SA-141115. doi:10.1039/C9FD00011A
• Zhou Z., T. Yu, H. Dong, L. Huang, R.K. Chu, N. Tolic, and X. Wang, et al. 2019. "Chemical oxygen demand (COD) removal from bio-treated coking wastewater by hydroxyl radicals produced from a reduced clay mineral." Applied Clay Science 180, no. 2019:105199. PNNL-SA-161778. doi:10.1016/j.clay.2019.105199

2018

• Chen H., Z. Yang, R.K. Chu, N. Tolic, L. Liang, D.E. Graham, and S.D. Wullschleger, et al. 2018. "Molecular Insights into Arctic Soil Organic Matter Degradation under Warming." Environmental Science & Technology 52, no. 8:4555-4564. PNNL-SA-136151. doi:10.1021/acs.est.7b05469
• Park J., P.D. Piehowski, C.S. Wilkins, M. Zhou, J.A. Mendoza, G.M. Fujimoto, and B.C. Gibbons, et al. 2018. "Author Correction: Informed-Proteomics: open-source software package for top-down proteomics." Nature Methods 15. PNNL-SA-162101. doi:10.1038/s41592-018-0040-0
• Rivas-Ubach A., Y. Liu, T.S. Bianchi, N. Tolic, G.C. Jansson, and L. Pasa Tolic. 2018. "Moving beyond the van Krevelen diagram: A new stoichiometric approach for compound classification in organisms." Analytical Chemistry 90, no. 10:6152-6160. PNNL-SA-134250. doi:10.1021/acs.analchem.8b00529

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
• Chen H., R.C. Johnston, B.F. Mann, R.K. Chu, N. Tolic, J.M. Parks, and B. Gu. 2017. "Identification of Mercury and Dissolved Organic Matter Complexes Using Ultrahigh Resolution Mass Spectrometry." Environmental Science & Technology Letters 4, no. 2:59-65. PNNL-SA-125213. doi:10.1021/acs.estlett.6b00460
• Cook R.D., Y. Lin, Z. Peng, E.J. Boone, R.K. Chu, J.E. Dukett, and M.J. Gunsch, et al. 2017. "Biogenic, urban, and wildfire influences on the molecular composition of dissolved organic compounds in cloud water." Atmospheric Chemistry and Physics 17, no. 24:15167-15180. PNNL-SA-130575. doi:10.5194/acp-17-15167-2017
• 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
• 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
• 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
• 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

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
• Kaplan D.I., C. Xu, S. Huang, Y. Lin, N. Tolic, K.M. Roscioli, and P.H. Santschi, et al. 2016. "Unique Organic Matter and Microbial Properties in the Rhizosphere of a Wetland Soil." Environmental Science & Technology 50, no. 8:4169-4177. PNNL-SA-117429. doi:10.1021/acs.est.5b05165
• 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., 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
• Sun J., T. Dutta, R. Parthasarathi, K. Kim, N. Tolic, R.K. Chu, and N.G. Isern, et al. 2016. "Rapid room temperature solubilization and depolymerization of polymeric lignin at high loadings." Green Chemistry 18, no. 22:6012-6020. PNNL-SA-120307. doi:10.1039/C6GC02258H
• 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
• 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

2015

• Mann B.F., H. Chen, E.M. Herndon, R.K. Chu, N. Tolic, E. Portier, and T.R. Chowdhury, et al. 2015. "Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry." PLoS One 10, no. 6:Article No. e0130557. PNNL-SA-111173. doi:10.1371/journal.pone.0130557
• 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
• Xu Z., C. Wu, F. Xie, G.W. Slysz, N. Tolic, M.E. Monroe, and V.A. Petyuk, et al. 2015. "Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes." Journal of Proteome Research 14, no. 1:422-433. PNNL-SA-103951. doi:10.1021/pr500840w

2014

• 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
• 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
• 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

• 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
• 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

• Shen Y., N. Tolic, S.O. Purvine, and R.D. Smith. 2012. "Improving Collision Induced Dissociation (CID), High Energy Collision Dissociation (HCD), and Electron Transfer Dissociation (ETD) Fourier Transform MS/MS Degradome-Peptidome Identifications Using High Accuracy Mass Information." Journal of Proteome Research 11, no. 2:668-677. PNNL-SA-79420.
• 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

2011

• Ansong C., N. Tolic, S.O. Purvine, S. Porwollik, M.B. Jones, H. Yoon, and S.H. Payne, et al. 2011. "Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium." BMC Genomics 12. PNNL-SA-77195. doi:10.1186/1471-2164-12-433
• 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
• Shen Y., N. Tolic, F. Xie, R. Zhao, S.O. Purvine, A.A. Schepmoes, and R.J. Moore, et al. 2011. "Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods." Journal of Proteome Research 10, no. 9:3929-3943. PNNL-SA-75441. doi:10.1021/pr200052c
• Shen Y., N. Tolic, S.O. Purvine, and R.D. Smith. 2011. "Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information." Journal of Proteome Research. PNNL-SA-81060. doi:10.1021/pr200597j
• 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.

2010

• Jung H., S.O. Purvine, H. Kim, V.A. Petyuk, S. Hyung, M.E. Monroe, and D. Mun, et al. 2010. "Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data." Analytical Chemistry 82, no. 20:8510-8518. PNNL-SA-74157. doi:10.1021/ac101388b
• Shen Y., N. Tolic, S.O. Purvine, and R.D. Smith. 2010. "Identification of Disulfide Bonds in Protein Proteolytic Degradation Products Using de Novo-Protein Unique Sequence Tags Approach." Journal of Proteome Research 9, no. 8:4053-4060. PNNL-SA-73098.
• Shen Y., N. Tolic, T. Liu, R. Zhao, B.O. Petritis, M.A. Gritsenko, and D.G. Camp, et al. 2010. "Blood Peptidome-Degradome Profile of Breast Cancer." PLoS One 5, no. 10:Article No.: e13133. PNNL-SA-70095. doi:10.1371/journal.pone.0013133
• Shen Y., T. Liu, N. Tolic, B.O. Petritis, R. Zhao, R.J. Moore, and S.O. Purvine, et al. 2010. "A strategy for degradomic-peptidomic analysis of the human blood plasma." Journal of Proteome Research 9, no. 5:2339-2346. PNNL-SA-71375. doi:10.1021/pr901083m
• 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

2009

• Chowdhury S.M., X. Du, N. Tolic, S. Wu, R.J. Moore, M.U. Mayer, and R.D. Smith, et al. 2009. "Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry." Analytical Chemistry 81, no. 13:5524-5532. PNNL-SA-61747. doi:10.1021/ac900853k
• 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
• Zhang H., X. Tang, G.R. Munske, N. Tolic, G.A. Anderson, and J.E. Bruce. 2009. "Identification of Protein-Protein Interactions and Topologies in Living Cells with Chemical Cross-linking and Mass Spectrometry." Molecular & Cellular Proteomics. MCP 8, no. 3:409-420. PNNL-SA-60535.

2008

• Shen Y., K.K. Hixson, N. Tolic, D.G. Camp, S.O. Purvine, R.J. Moore, and R.D. Smith. 2008. "Mass Spectrometry Analysis of Proteome-wide Proteolytic Post-translational Degradation of Proteins." Analytical Chemistry 80, no. 15:5819-5828. PNNL-SA-58041. doi:10.1021/ac800077w
• Shen Y., N. Tolic, K.K. Hixson, S.O. Purvine, G.A. Anderson, and R.D. Smith. 2008. "De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins." Analytical Chemistry 80, no. 20:7742-7754. PNNL-SA-60782. doi:10.1021/ac801123p
• 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
• Zhang H., X. Tang, G.R. Munske, N. Tolic, G.A. Anderson, and J.E. Bruce. 2008. "Identification of protein-protein interaction and topologies in living cells by chemical cross-linking and mass spectrometry." Molecular & Cellular Proteomics. MCP 8, no. 3:409-420. PNNL-SA-54794. doi:10.1074/mcp.M800232-MCP200
• Zhang H., X. Tang, G.R. Munske, N.L. Zakharova, L. Yang, C. Zheng, and M.A. Wolff, et al. 2008. "In Vivo Identification of the Outer Membrane Protein OmcA-MtrC Interaction Network in Shewanella oneidensis MR-1 Cells Using Novel Hydrophobic Chemical Cross-Linkers." Journal of Proteome Research 7, no. 4:1712-1720. PNNL-SA-59029. doi:10.1021/pr7007658

2007

• Anderson G.A., N. Tolic, X. Tang, C. Zheng, and J.E. Bruce. 2007. "Informatics Strategies for Large-Scale Novel Cross-linking Analysis." Journal of Proteome Research 6, no. 9:3412-3421. PNNL-SA-54795. doi:10.1021/pr070035z
• Anderson G.A., N. Tolic, X. Tang, C. Zheng, and J.E. Bruce. 2007. "Informatics Strategies for Large-Scale Novel Cross-linking Analysis." Journal of Proteome Research 6, no. 9:3412-3421. PNNL-SA-56252. doi:10.1021/pr070035z
• Monroe M.E., N. Tolic, N. Jaitly, J.L. Shaw, J.N. Adkins, and R.D. Smith. 2007. "VIPER: an advanced software package to support high-throughput LC-MS peptide identification." Bioinformatics 23, no. 15- August 2007:2021-2023. PNNL-SA-52622. doi:10.1093/bioinformatics/btm281
• 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

2006

• Elshafey A., N. Tolic, M.M. Young, K.L. Sale, R.D. Smith, and V. Kery. 2006. "“Zero-length” Cross-linking in Solid State as an Approach for Analysis of Protein -Protein Interactions." Protein Science 15, no. 3:429-440. PNNL-SA-46071.
• Kiebel G.R., K.J. Auberry, N. Jaitly, D. Clark, M.E. Monroe, E.S. Peterson, and N. Tolic, et al. 2006. "PRISM: A Data Management System for High-Throughput Proteomics." Proteomics 6, no. 6:1783-1790. PNNL-SA-45753. doi:10.1002/pmic.200500500
• 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.

2005

• 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.
• Shen Y., J. Kim, E.F. Strittmatter, J.M. Jacobs, D.G. Camp, R. Fang, and N. Tolic, et al. 2005. "Characterization of the human blood plasma proteome." Proteomics 5, no. 15:4034-4045. PNWD-SA-6708.

2004

• 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.

2003

• 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.

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.
• 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.
• 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.

2001

• Belov M.E., G.A. Anderson, N.H. Angell, Y. Shen, N. Tolic, H.R. Udseth, and R.D. Smith. 2001. "Dynamic Range Expansion Applied to Mass Spectrometry (DREAMS) Based on Data-Dependent Selective Ion Ejection in Capillary Liquid Chromatography Fourier Transform Ion Cyclotron Resonance for Enhanced Proteome Characterization." Analytical Chemistry 73, no. 21:5052-5060. PNNL-SA-35028.
• 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.

2000

• 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.

1999

• 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.