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Fundamental and Computational Sciences Directorate

Staff information

Feng Yang

Omic Biological Applications
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352
509/371-6347

PNNL Publications

2012

  • Alfaro JF, CX Gong, ME Monroe, JT Aldrich, TRW Clauss, SO Purvine, Z Wang, DG Camp, II, J Shabanowitz, P Stanley, GW Hart, DF Hunt, F Yang, and RD Smith. 2012. "Tandem Mass Spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets." Proceedings of the National Academy of Sciences of the United States of America 109(19):7280-7285.  doi:10.1073/pnas.1200425109
  • Chauvin T, F Xie, T Liu, CD Nicora, F Yang, DG Camp, II, RD Smith, and KP Roberts. 2012. "A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome." Biology of Reproduction 87(6):Article No. 141.  doi:10.1095/biolreprod.112.104208
  • 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
  • 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
  • Yang F, KM Waters, BJM Webb-Robertson, MB Sowa, CH Freiin von Neubeck, JT Aldrich, LM Markillie, RM Wirgau, MA Gristenko, R Zhao, DG Camp, II, RD Smith, and DL Stenoien. 2012. "Quantitative Phosphoproteomics Identifies Filaggrin and other Targets of Ionizing Radiation in a Human Skin Model." Experimental Dermatology 21(5):352-357.  doi:10.1111/j.1600-0625.2012.01470.x

2011

  • 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
  • Wang Y, F Yang, Y Fu, X Huang, W Wang, X Jiang, MA Gritsenko, R Zhao, ME Monroe, OC Pertz, SO Purvine, DJ Orton, JM Jacobs, DG Camp, II, RD Smith, and RL Klemke. 2011. "Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction." Journal of Biological Chemistry 286(20):18190-18201. 
  • 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 IMAC Resin Enrichment and Higher-Energy Collisional Dissociation." Analytical Chemistry 83(19):7260-7268.  doi:10.1021/ac2000829

2010

  • Ham BM, H Jayachandran, F Yang, N Jaitly, AD Polpitiya, ME Monroe, L Wang, R Zhao, SO Purvine, EA Livesay, DG Camp, II, SS Rossie, and RD Smith. 2010. "Novel Ser/Thr Protein Phosphatase 5 (PP5) Regulated Targets during DNA Damage Identified by Proteomics Analysis." Journal of Proteome Research 9(2):945-953.  doi:10.1021/pr9008207
  • Yang F, KM Waters, JH Miller, MA Gritsenko, R Zhao, X Du, EA Livesay, SO Purvine, ME Monroe, Y Wang, DG Camp, II, RD Smith, and DL Stenoien. 2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5(11):e14152.  doi:10.1371/journal.pone.0014152
  • Zhang X, ME Monroe, B Chen, MH Chin, TH Heibeck, AA Schepmoes, F Yang, BO Petritis, DG Camp, II, JG Pounds, JM Jacobs, DJ Smith, DJ Bigelow, RD Smith, and W Qian. 2010. "Endogenous 3, 4- Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical." Molecular & Cellular Proteomics. MCP 9(6):1199-1208. 

2009

  • Heibeck TH, SJ Ding, LK Opresko, R Zhao, AA Schepmoes, F Yang, AV Tolmachev, ME Monroe, DG Camp, II, RD Smith, HS Wiley, and W Qian. 2009. "An Extensive Survey of Tyrosine Phosphorylation Revealing New Sites in Human Mammary Epithelial Cells." Journal of Proteome Research 8(8):3852-3861. 
  • 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
  • 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

  • Zhang Q, VA Petyuk, AA Schepmoes, DJ Orton, ME Monroe, F Yang, RD Smith, and TO Metz. 2008. "Analysis of Non-Enzymatically Glycated Peptides: Neutral-Loss Triggered MS3 Versus Multi-Stage Activation Tandem Mass Spectrometry." Rapid Communications in Mass Spectrometry 22(19):3027-3034.  doi:10.1002/rcm.3703
  • Ding SJ, Y Wang, JM Jacobs, W Qian, F Yang, AV Tolmachev, X Du, W Wang, RJ Moore, ME Monroe, SO Purvine, KM Waters, TH Heibeck, JN Adkins, DG Camp, II, RL Klemke, and RD Smith. 2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step 18O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7(10):4215-24.  doi:10.1021/pr7007785
  • Du X, F Yang, NP Manes, DL Stenoien, ME Monroe, JN Adkins, DJ States, SO Purvine, DG Camp, II, and RD Smith. 2008. "Linear Discriminant Analysis - Based Estimation of the False Discovery Rate for Phosphopeptide Identifications ." Journal of Proteome Research 7(6):2195-2203.  doi:10.1021/pr070510t
  • Ham BM, F Yang, H Jayachandran, N Jaitly, ME Monroe, MA Gritsenko, EA Livesay, R Zhao, SO Purvine, DJ Orton, JN Adkins, DG Camp, II, SS Rossie, and RD Smith. 2008. "The Influence of Sample Preparation and Replicate Analyses on HeLa Cell Phosphoproteome Coverage." Journal of Proteome Research 7(6):2215-2221. 
  • Pertz OC, Y Wang, F Yang, W Wang, J gay, MA Gritsenko, TRW Clauss, DJ Anderson, T Liu, KJ Auberry, DG Camp, II, RD Smith, and RL Klemke. 2008. ""Spatial Mapping of the Neurite and Soma Proteomes Reveals a Functional Cdc42/Rac Regulatory Network"." Proceedings of the National Academy of Sciences of the United States of America 105(6):1931-1936.  doi:10.1073/pnas.0706545105

2007

  • Elias DA, F Yang, HM Mottaz, AS Beliaev, and MS Lipton. 2007. "Enrichment of Functional Redox Reactive Proteins and Identification by Mass Spectrometry Results in Several Terminal Fe(III)-reducing Candidate Proteins in Shewanella oneidensis MR-1." Journal of Microbiological Methods 68(2):367-375. 
  • Wang Y, SJ Ding, W Wang, F Yang, JM Jacobs, DG Camp, II, RD Smith, and RL Klemke. 2007. "Methods for Pseudopodia Purification and Proteomic Analysis." Sciences STKE Signal Transduction Knowledge Environment 2007(400):p14. 
  • Wang Y, SJ Ding, W Wang, JM Jacobs, W Qian, RJ Moore, F Yang, DG Camp, II, RD Smith, and RL Klemke. 2007. "Profiling Signaling Polarity in Chemotactic Cells." Proceedings of the National Academy of Sciences of the United States of America 104(20):8328-8333.  doi:10.1073/pnas.0701103104
  • Yang F, DG Camp, II, MA Gritsenko, Q Luo, RT Kelly, TRW Clauss, WR Brinkley, RD Smith, and DL Stenoien. 2007. " Identification of a novel mitotic phosphorylation motif associated with protein localization to the mitotic apparatus." Journal of Cell Science 120(22):4060-70.  doi:10.1242/jcs.014795
  • Yang F, N Jaitly, H Jayachandran, Q Lou, ME Monroe, X Du, MA Gritsenko, R Zhang, DJ Anderson, SO Purvine, JN Adkins, RJ Moore, HM Mottaz, SJ Ding, MS Lipton, DG Camp, II, HR Udseth, RD Smith, and SS Rossie. 2007. "Applying a Targeted Label-free Approach using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition." Journal of Proteome Research 6(11):4489-4497.  doi:10.1021/pr070068e

2006

  • 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. 
  • Yang F, DL Stenoien, EF Strittmatter, JH Wang, L Ding, MS Lipton, ME Monroe, CD Nicora, MA Gritsenko, K Tang, R Fang, JN Adkins, DG Camp, II, DJ Chen, and RD Smith. 2006. "Phosphoproteome Profiling of Human Skin Fibroplast Cells in Response to Low- and High-Dose Irradiation ." Journal of Proteome Research 5(5):1252-1260. 

2005

  • 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. 
  • 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

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