Yufeng Shen

Summary

Affiliation: Pacific Northwest National Laboratory
Country: USA

Publications

  1. pmc Blood peptidome-degradome profile of breast cancer
    Yufeng Shen
    Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS ONE 5:e13133. 2010
  2. pmc Strategy for degradomic-peptidomic analysis of human blood plasma
    Yufeng Shen
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
    J Proteome Res 9:2339-46. 2010
  3. pmc De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins
    Yufeng Shen
    Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 80:7742-54. 2008
  4. pmc Mass spectrometry analysis of proteome-wide proteolytic post-translational degradation of proteins
    Yufeng Shen
    Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 80:5819-28. 2008
  5. pmc Identification of disulfide bonds in protein proteolytic degradation products using de novo-protein unique sequence tags approach
    Yufeng Shen
    Biological Sciences Division, and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
    J Proteome Res 9:4053-60. 2010
  6. ncbi request reprint Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics
    Yufeng Shen
    Biological Science Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99352, USA
    Expert Rev Proteomics 2:431-47. 2005
  7. pmc A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy
    Joshua N Adkins
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Proteomics 5:3454-66. 2005
  8. ncbi request reprint More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometry
    Quanzhou Luo
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    J Proteome Res 5:1091-7. 2006
  9. ncbi request reprint Characterization of the human blood plasma proteome
    Yufeng Shen
    Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Proteomics 5:4034-45. 2005
  10. ncbi request reprint High-efficiency on-line solid-phase extraction coupling to 15-150-microm-i.d. column liquid chromatography for proteomic analysis
    Yufeng Shen
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 75:3596-3605. 2003

Collaborators

Detail Information

Publications49

  1. pmc Blood peptidome-degradome profile of breast cancer
    Yufeng Shen
    Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS ONE 5:e13133. 2010
    ..Cancer invasion and metastasis are closely associated with activities within the degradome; however, little is known about whether these activities can be detected in the blood of cancer patients...
  2. pmc Strategy for degradomic-peptidomic analysis of human blood plasma
    Yufeng Shen
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
    J Proteome Res 9:2339-46. 2010
    ....
  3. pmc De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins
    Yufeng Shen
    Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 80:7742-54. 2008
    ..The combined de novo-UStag approach complements the UStag method previously reported by enabling the discovery of new protein modifications...
  4. pmc Mass spectrometry analysis of proteome-wide proteolytic post-translational degradation of proteins
    Yufeng Shen
    Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 80:5819-28. 2008
    ..This study shows that the intracellular peptides are informational targets for directly probing the protein degradation-involved molecular mechanisms and cell biology processes...
  5. pmc Identification of disulfide bonds in protein proteolytic degradation products using de novo-protein unique sequence tags approach
    Yufeng Shen
    Biological Sciences Division, and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
    J Proteome Res 9:4053-60. 2010
    ..Using this method, we identified the intermolecular and intramolecular disulfides in human blood plasma peptidome peptides that have molecular weights of up to approximately 10 kDa...
  6. ncbi request reprint Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics
    Yufeng Shen
    Biological Science Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99352, USA
    Expert Rev Proteomics 2:431-47. 2005
    ..The instrumental robustness required for automation and providing high-quality routine performance nanoscale proteomic analyses is also discussed...
  7. pmc A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy
    Joshua N Adkins
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Proteomics 5:3454-66. 2005
    ..The AMT tag strategy not only improved our sample throughput but also provided a basis for estimated quantitation...
  8. ncbi request reprint More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometry
    Quanzhou Luo
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    J Proteome Res 5:1091-7. 2006
    ..The improved sensitivity allowed LC-MS measurements of immunopurified protein phosphatase 5 that were in good agreement with quantitative Western blot analyses...
  9. ncbi request reprint Characterization of the human blood plasma proteome
    Yufeng Shen
    Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Proteomics 5:4034-45. 2005
    ....
  10. ncbi request reprint High-efficiency on-line solid-phase extraction coupling to 15-150-microm-i.d. column liquid chromatography for proteomic analysis
    Yufeng Shen
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 75:3596-3605. 2003
    ..The SPE-capillary LC implementation also facilitates automation and enables use of both disposable SPE columns and electrospray emitters, providing a robust basis for automated proteomic analyses...
  11. ncbi request reprint Increased proteome coverage for quantitative peptide abundance measurements based upon high performance separations and DREAMS FTICR mass spectrometry
    Ljiljana Pasa-Tolic
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    J Am Soc Mass Spectrom 13:954-63. 2002
    ..We show that implementation of the DREAMS approach allows assignment of approximately 80% more peptide pairs, thus providing quantitative information for approximately 18,000 peptide pairs in a single analysis...
  12. ncbi request reprint Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurements
    Yufeng Shen
    Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 77:7763-73. 2005
    ..For <120-s proteomic analysis, TOF MS analyses were more effective, while FTICR MS was more effective for the >150-s analysis due to the improved mass accuracies attained using longer spectrum acquisition times...
  13. pmc Phosphopeptide elution times in reversed-phase liquid chromatography
    Jeongkwon Kim
    Environmental Molecular Science Laboratory, MSIN K8 98, Pacific Northwest National Laboratory, P O Box 999, Richland, WA 99352, USA
    J Chromatogr A 1172:9-18. 2007
    ..28 and +0.59 min). The predictive capability for the observed RPLC elution time change due to phosphorylation has been suggested, which will aid in assigning confident phosphopeptide identifications and their subsequent confirmation...
  14. ncbi request reprint Ultrasensitive proteomics using high-efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MS
    Yufeng Shen
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 76:144-54. 2004
    ..Compared with single-stage FTICR measurements, ion trap MS/MS provided a much lower proteome measurement coverage and dynamic range for a given analysis time and sample quantity...
  15. ncbi request reprint High-performance separations and mass spectrometric methods for high-throughput proteomics using accurate mass tags
    Richard D Smith
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Adv Protein Chem 65:85-131. 2003
  16. ncbi request reprint Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics
    Yufeng Shen
    Biological Science Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 77:3090-100. 2005
    ..A single run of the 20 kpsi RPLC-accurate mass MS detected >5000 different compounds from a metabolomics sample...
  17. pmc Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags
    Yufeng Shen
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 80:1871-82. 2008
    ....
  18. pmc Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach
    Wei Jun Qian
    Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Mol Cell Proteomics 4:700-9. 2005
    ....
  19. ncbi request reprint Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry
    Eric F Strittmatter
    Biological Sciences Division and Environmental and Molecular Sciences Laboratory, Richland, Washington 99352, USA
    J Proteome Res 3:760-9. 2004
    ..Further improvements from the use of elution time information can be expected as both the experimental control of elution time reproducibility and the predictive capability are improved...
  20. pmc Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods
    Yufeng Shen
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
    J Proteome Res 10:3929-43. 2011
    ..These results also suggest that the decoy strategy may inaccurately estimate identification FDRs...
  21. pmc Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses
    Eric A Livesay
    Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
    Anal Chem 80:294-302. 2008
    ..The high reproducibility of this system is demonstrated using consecutive analyses of global tryptic digest of the microbe Shewanella oneidensis...
  22. ncbi request reprint Preparation of 20-microm-i.d. silica-based monolithic columns and their performance for proteomics analyses
    Quanzhou Luo
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 77:5028-35. 2005
    ..The number of identified peptides increased from 32 to 390 as the injection amount was increased from 0.5 to 100 ng. Both the run-to-run and column-to-column reproducibility for proteomic analyses were also evaluated...
  23. ncbi request reprint An accurate mass tag strategy for quantitative and high-throughput proteome measurements
    Richard D Smith
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Proteomics 2:513-23. 2002
    ..Using this strategy, in our first application we have been able to identify AMTs for >60% of the potentially expressed proteins in the organism Deinococcus radiodurans...
  24. ncbi request reprint High-throughput global peptide proteomic analysis by combining stable isotope amino acid labeling and data-dependent multiplexed-MS/MS
    Scott J Berger
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 74:4994-5000. 2002
    ..We also describe the utility of peptide composition and fragment information to support peptide identifications and examine the potential application of lysine labeling for differential quantitative protein analysis...
  25. pmc Targeted comparative proteomics by liquid chromatography-tandem Fourier ion cyclotron resonance mass spectrometry
    Christophe Masselon
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MSIN K8 98, Richland, Washington 99352, USA
    Anal Chem 77:400-6. 2005
    ..We also demonstrate the application of this method to the identification of Shewanella oneidensis peptides/proteins exhibiting differential abundance in suboxic versus aerobic cell cultures...
  26. ncbi request reprint Proteomic analyses using an accurate mass and time tag strategy
    Ljiljana Pasa-Tolic
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Biotechniques 37:621-4, 626-33, 636 passim. 2004
    ..The AMT tag approach is poised to become a new standard technique for the in-depth and high-throughput analysis of complex organisms and clinical samples, with the potential to extend the analysis to a single mammalian cell...
  27. pmc Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells
    Yuexi Wang
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Proteomics 11:2019-26. 2011
    ..The results demonstrate that the concatenated high pH reversed-phased strategy is an attractive alternative to strong cation exchange for two-dimensional shotgun proteomic analysis...
  28. ncbi request reprint Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses
    Konstantinos Petritis
    Biological Sciences Division and Environmental and Molecular Laboratory, Pacific Northwest National Laboratory, P O Box 999, Richland, Washington 99352, USA
    Anal Chem 75:1039-48. 2003
    ..Thus, integration of ANN peptide elution time prediction in the proteomic research will increase both the number of protein identifications and their confidence...
  29. ncbi request reprint Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach
    Ruihua Fang
    Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland Washington 99352, USA
    Mol Cell Proteomics 5:714-25. 2006
    ..Numerous proteins involved in anaerobic energy metabolism exhibited up to a 10-fold increase in relative abundance when S. oneidensis was transitioned from aerobic to suboxic conditions...
  30. ncbi request reprint High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics
    Yufeng Shen
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 74:4235-49. 2002
    ....
  31. ncbi request reprint Utilizing human blood plasma for proteomic biomarker discovery
    Jon M Jacobs
    Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99352, USA
    J Proteome Res 4:1073-85. 2005
    ..Continued development of depletion and enrichment techniques, coupled with improved pre-MS separations (both at the protein and peptide level) holds promise in extending the dynamic range of proteomic analysis...
  32. ncbi request reprint Gene expression profiling using advanced mass spectrometric approaches
    Ljiljana Pasa-Tolic
    Environmental Molecular Sciences Laboratory, MSIN K8 98, Pacific Northwest National Laboratory, PO Box 999, Richland, Washington 99352, USA
    J Mass Spectrom 37:1185-98. 2002
    ....
  33. pmc Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR
    Sang Won Lee
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P O Box 999, Richland, WA 99352, USA
    Proc Natl Acad Sci U S A 99:5942-7. 2002
    ....
  34. pmc High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis
    Feng Yang
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Expert Rev Proteomics 9:129-34. 2012
    ....
  35. pmc 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
    Yufeng Shen
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
    J Proteome Res 11:668-77. 2012
    ..g., 0.6%), providing an improved basis for investigating potential disease-related peptidome components...
  36. ncbi request reprint Ultrahigh-throughput proteomics using fast RPLC separations with ESI-MS/MS
    Yufeng Shen
    Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 77:6692-701. 2005
    ..The results confirm that such analyses using very fast (minutes) RPLC separations based on columns packed with microsized porous particles are primarily limited by the MS/MS analysis speed...
  37. ncbi request reprint Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome
    Yufeng Shen
    Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Anal Chem 76:1134-44. 2004
    ..The analyses identified relatively low-level (approximately pg/mL) proteins (e.g., cytokines) coexisting with high-abundance proteins (e.g., mg/mL-level serum albumin)...
  38. pmc Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput
    Rui Zhao
    Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, P O Box 999, Richland, WA 99352, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 877:663-70. 2009
    ....
  39. ncbi request reprint The use of accurate mass tags for high-throughput microbial proteomics
    Richard D Smith
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    OMICS 6:61-90. 2002
    ..Additional developments, including the use of multiplexed-MS/MS capabilities and methods for dynamic range expansion of proteome measurements that promise to further extend the quality of proteomics measurements, are also described...
  40. pmc Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags
    Mary S Lipton
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P O Box 999, MSIN K8 98, Richland, WA 99352, USA
    Proc Natl Acad Sci U S A 99:11049-54. 2002
    ..This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical...
  41. pmc Advanced proteomic liquid chromatography
    Fang Xie
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    J Chromatogr A 1261:78-90. 2012
    ..This review provides an overview of advanced capillary liquid chromatography techniques and methodologies that greatly improve separation resolving power and proteomics analysis coverage, sensitivity, and throughput...
  42. ncbi request reprint Proteomics based on high-efficiency capillary separations
    Yufeng Shen
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Electrophoresis 23:3106-24. 2002
    ..We emphasize developments at our laboratory and illustrate technical advances that attempt to review the role of separations within the broader context of a state-of-the-art integrated proteomics effort...
  43. ncbi request reprint Ultra-sensitive and quantitative characterization of proteomes
    Richard D Smith
    Biological Sciences Division, Pacific Northwest National Laboratory, P O Box 999, MS K8 98, Richland, WA 99352, USA
    Mol Biosyst 2:221-30. 2006
    ....
  44. ncbi request reprint Ultrasensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes
    Richard D Smith
    Pacific Northwest National Laboratory, P O Box 999, Richland, WA 99352, USA
    Acc Chem Res 37:269-78. 2004
    ..The increased dynamic range of measurements and low zeptomole regime detection limits obtainable open new avenues for biological research...
  45. ncbi request reprint Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metabolic profiling
    Jie Ding
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Anal Chem 79:6081-93. 2007
    ..ATCC 51142 metabolite extracts. In addition, 12 compounds were tentatively identified, based on accurate mass, isotopic distribution, and MS/MS information...
  46. ncbi request reprint Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation
    Jinzhi Chen
    Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
    Electrophoresis 23:3143-8. 2002
    ..The results of our preliminary studies display significant differences in the separation profiles of peptide samples obtained from salivary glands of animals staged at the 6 and 12 h following puparium formation...
  47. pmc A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery
    Xiaohu Wang
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
    Nucleic Acids Res 36:4863-71. 2008
    ....
  48. pmc Conformational pathways in the gating of Escherichia coli mechanosensitive channel
    Yifei Kong
    Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, BCM 125, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 99:5999-6004. 2002
    ..Moreover, the intermediate open states of mechanosensitive channels are not symmetric, i.e., the opening does not follow iris-like motion, which sharply contrasts to the potassium channel KcsA...
  49. pmc The genome of the sea urchin Strongylocentrotus purpuratus
    Erica Sodergren
    Science 314:941-52. 2006
    ..This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes...