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Fundamental and Computational Sciences Directorate

Staff information

Yufeng Shen

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

PNNL Publications


  • 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
  • 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


  • 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. 


  • Liu X, Y Sirotkin, Y Shen, GA Anderson, YHS Tsai, YS Ting, DR Goodlett, RD Smith, V Bafna, and PA Pevzner. 2012. "Protein Identification Using Top-Down." Molecular & Cellular Proteomics. MCP 11(6):M111.008524.  doi:10.1074/mcp.M111.008524
  • Shen Y, N Tolic, SO Purvine, and RD 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(2):668-677. 
  • Xie F, RD Smith, and Y Shen. 2012. "Advanced proteomic liquid chromatography." Journal of Chromatography A 1261:78-90.  doi:10.1016/j.chroma.2012.06.098
  • Yang F, Y Shen, DG Camp, II, and RD Smith. 2012. "High pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis." Expert Review of Proteomics 9(2):129-134.  doi:10.1586/EPR.12.15


  • Shen Y, N Tolic, SO Purvine, and RD Smith. 2011. "Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information." Journal of Proteome Research doi:10.1021/pr200597j
  • Shen Y, N Tolic, F Xie, R Zhao, SO Purvine, AA Schepmoes, RJ Moore, GA Anderson, and RD Smith. 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(9):3929-3943.  doi:10.1021/pr200052c
  • Wang Y, F Yang, MA Gritsenko, Y Wang, TRW Clauss, T Liu, Y Shen, ME Monroe, D Lopez-Ferrer, T Reno, RJ Moore, RL Klemke, DG Camp, II, and RD Smith. 2011. "Reversed-Phase Chromatography with Multiple Fraction Concatenation Strategy for Proteome Profiling of Human MCF10A Cells." Proteomics 11(10):2019-2026.  doi:10.1002/pmic.201000722


  • Shen Y, N Tolic, SO Purvine, and RD Smith. 2010. "Identification of Disulfide Bonds in Protein Proteolytic Degradation Products Using de Novo-Protein Unique Sequence Tags Approach." Journal of Proteome Research 9(8):4053-4060. 
  • Shen Y, N Tolic, T Liu, R Zhao, BO Petritis, MA Gritsenko, DG Camp, II, RJ Moore, SO Purvine, FJ Esteva, and RD Smith. 2010. " Blood Peptidome-Degradome Profile of Breast Cancer." PLoS One 5(10):Article No.: e13133.  doi:10.1371/journal.pone.0013133
  • Shen Y, T Liu, N Tolic, BO Petritis, R Zhao, RJ Moore, SO Purvine, DG Camp, II, and RD Smith. 2010. "A strategy for degradomic-peptidomic analysis of the human blood plasma ." Journal of Proteome Research 9(5):2339-2346.  doi:10.1021/pr901083m


  • Zhao R, SJ Ding, Y Shen, DG Camp, II, EA Livesay, HR Udseth, and RD Smith. 2009. "Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput." Journal of Chromatography B 877(8-9):663-670. 
  • Shen Y, JS Page, and RD Smith. 2009. "Advanced Capillary Liquid Chromatography-Mass Spectrometry for Proteomics ." Chapter 2 in Advances in Chromatography, vol. 47, ed. E Grushka and N Grinberg, pp. 31-58.  CRC Press, Boca Raton, FL. 


  • Livesay EA, K Tang, BK Taylor, MA Buschbach, DF Hopkins, BL Lamarche, R Zhao, Y Shen, DJ Orton, RJ Moore, RT Kelly, HR Udseth, and RD Smith. 2008. "Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses." Analytical Chemistry 80(1):294-302.  doi:10.1021/ac701727r
  • Metz TO, JS Page, ES Baker, K Tang, J Ding, Y Shen, and RD Smith. 2008. "High Resolution Separations and Improved Ion Production and Transmission in Metabolomics." Trends in Analytical Chemistry. TrAC 27(3):205-214.  doi:10.1016/j.trac.2007.11.003
  • Shen Y, N Tolic, KK Hixson, SO Purvine, GA Anderson, and RD Smith. 2008. "De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins ." Analytical Chemistry 80(20):7742-7754.  doi:10.1021/ac801123p
  • 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
  • Shen Y, KK Hixson, N Tolic, DG Camp, II, SO Purvine, RJ Moore, and RD Smith. 2008. "Mass Spectrometry Analysis of Proteome-wide Proteolytic Post-translational Degradation of Proteins." Analytical Chemistry 80(15):5819-5828.  doi:10.1021/ac800077w


  • Ding J, CM Sorensen, Q Zhang, H Jiang, N Jaitly, EA Livesay, Y Shen, RD Smith, and TO Metz. 2007. "Capillary LC Coupled with High-Mass Measurement Accuracy Mass Spectrometry for Metabolic Profiling." Analytical Chemistry 79(16):6081-6093.  doi:10.1021/ac070064t
  • Kim J, K Petritis, Y Shen, DG Camp, II, RJ Moore, and RD Smith. 2007. "Phosphopeptide elution times in reversed-phase liquid chromatography." Journal of Chromatography A 1172(1):9-18.  doi:doi:10.1016/j.chroma.2007.09.032
  • Metz TO, Q Zhang, JS Page, Y Shen, SJ Callister, JM Jacobs, and RD Smith. 2007. "The future of liquid chromatography-mass spectrometry in metabolic profiling and metabolomic studies for biomarker discovery." Biomarkers in Medicine 1(1):159-185. 


  • Fang R, DA Elias, ME Monroe, Y Shen, M McIntosh, P Wang, CD Goddard, SJ Callister, RJ Moore, YA Gorby, JN Adkins, JK Fredrickson, MS Lipton, and RD Smith. 2006. "Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 5(4):714-725.  doi:10.1074/mcp.M500301-MCP200
  • Luo Q, K Tang, F Yang, A Elias, Y Shen, RJ Moore, R Zhao, KK Hixson, SS Rossie, and RD Smith. 2006. "More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometry ." Journal of Proteome Research 5(5):1091-1097. 
  • Smith RD, K Tang, and Y Shen. 2006. "Ultra-sensitive and quantitative characterization of proteomes." Molecular Biosystems 2(5):221-230.  doi:10.1039/b601468b


  • Adkins JN, ME Monroe, KJ Auberry, Y Shen, JM Jacobs, DG Camp, II, F Vitzthum, KD Rodland, RC Zangar, RD Smith, and JG Pounds. 2005. "A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy." Proteomics 5(13):3454-3466.  doi:10.1002/pmic.200401333
  • Jacobs JM, JN Adkins, W Qian, T Liu, Y Shen, DG Camp, II, and RD Smith. 2005. "Utilizing human blood plasma for proteomic biomarker discovery." Journal of Proteome Research 4(4):1073-1085.  doi:10.1021/pr0500657
  • Jacobs JM, ME Monroe, W Qian, Y Shen, GA Anderson, and RD Smith. 2005. "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements." International Journal of Mass Spectrometry 240(3):195-212. 
  • Luo Q, Y Shen, KK Hixson, R Zhao, F Yang, RJ Moore, HM Mottaz, and RD Smith. 2005. "Preparation of 20-µm-i.d. Silica-based Monolithic Columns and Application for Proteomic Analysis." Analytical Chemistry 77(15):5028-5035. 
  • 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. 
  • Qian W, ME Monroe, T Liu, JM Jacobs, GA Anderson, Y Shen, RJ Moore, DJ Anderson, R Zhang, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, DG Camp, II, and RD Smith. 2005. "Quantitative Proteome Analysis of Human Plasma Following in vivo Lipopolysaccharide Administration using O-16/O-18 Labeling and the Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 4(5):700-709. 
  • Shen Y, and RD Smith. 2005. "Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics." Expert Review of Proteomics 2(3):431-447. 
  • Shen Y, EF Strittmatter, R Zhang, TO Metz, RJ Moore, F Li, HR Udseth, RD Smith, KK Unger, D Kumar, and D Lubda. 2005. "Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurments." Analytical Chemistry 77(23):7763-7773.  doi: 10.1021/ac051257o
  • Shen Y, J Kim, EF Strittmatter, JM Jacobs, DG Camp, II, R Fang, N Tolic, RJ Moore, and RD Smith. 2005. "Characterization of the human blood plasma proteome." Proteomics 5(15):4034-4045. 
  • Shen Y, R Zhang, RJ Moore, J Kim, TO Metz, KK Hixson, R Zhao, EA Livesay, HR Udseth, and RD Smith. 2005. "Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics ." Analytical Chemistry 77(10):3090-3100. 
  • Shen Y, RC Smith, KK Unger, D Kumar, and D Lubda. 2005. "Ultrahigh-Throughput Proteomics Using Fast RPLC Separations with ESI-MS/MS." Analytical Chemistry 77(20):6692-6701. 


  • 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. 
  • 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, JM Jacobs, DG Camp, II, R Fang, RJ Moore, RD Smith, W Xiao, RW Davis, and RG Tompkins. 2004. "Ultra-High-Efficiency Strong Cation Exchange LC/RPLC/MS/MS for High Dynamic Range Characterization of the Human Plasma Proteome." Analytical Chemistry 76(4):1134-1144. 
  • 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. 
  • Smith RD, Y Shen, and K Tang. 2004. "Ultra-sensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes." Accounts of Chemical Research 37(4):269-278. 
  • Strittmatter EF, LJ Kangas, K Petritis, HM Mottaz, GA Anderson, Y Shen, JM Jacobs, DG Camp, II, and RD Smith. 2004. "Application of Peptide LC Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry." Journal of Proteome Research 3(4):760-769. 


  • 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. 


  • 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. 
  • Chen J, CS Lee, Y Shen, RD Smith, and EH Baehrecke. 2002. "Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation." Electrophoresis 23:3143-3148. 
  • 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. 
  • 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. 
  • Shen Y, R Zhao, SJ Berger, GA Anderson, N Rodriguez, and RD Smith. 2002. "High-Efficiency Nanoscale Liquid Chromatography Coupled On-Line with Mass Spectrometry using Nanoelectrospray Ionization for Proteomics." Analytical Chemistry 74:4235-4249. 
  • Shen Y, and RD Smith. 2002. "Proteomics Based on High-Efficiency Capillary Separations." Electrophoresis 23:3106-3124. 
  • 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. 


  • Belov ME, GA Anderson, NH Angell, Y Shen, N Tolic, HR Udseth, and RD 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(21):5052-5060. 
  • 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. 
  • Shen Y, SJ Berger, and RD Smith. 2001. "High-Efficiency Capillary Isoelectric Focusing of Protein Complexes from Escherichia coli Cytosolic Extracts." Journal of Chromatography A 914(1-2):257-264. 
  • 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. 


  • 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. 
  • Shen Y, and RD Smith. 2000. "High-Resolution Capillary Isoelectric Focusing of Proteins Using Highly Hydrophilic-Substituted Cellulose-Coated Capillaries." Journal of Microcolumn Separations 12(3):135-141. 
  • Shen Y, SJ Berger, GA Anderson, and RD Smith. 2000. "High-Efficiency Capillary Isoelectric Focusing of Peptides." Analytical Chemistry 72(9):2154-2159. 


  • Shen Y, F Xiang, TD Veenstra, NK Fung, and RD Smith. 1999. "High-Resolution Capillary Isoelectric Focusing of Complex Protein Mixtures from Lysates of Microogranisms." Analytical Chemistry 71:5348-5353. 

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