Research Topics
| Yufeng ShenSummaryAffiliation: Pacific Northwest National Laboratory Country: USA Publications
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Detail Information
Publications
Blood peptidome-degradome profile of breast cancerYufeng 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...- Strategy for degradomic-peptidomic analysis of human blood plasmaYufeng Shen
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
J Proteome Res 9:2339-46. 2010.... - De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteinsYufeng 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... - Mass spectrometry analysis of proteome-wide proteolytic post-translational degradation of proteinsYufeng 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... - Identification of disulfide bonds in protein proteolytic degradation products using de novo-protein unique sequence tags approachYufeng 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... 
Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomicsYufeng 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...- More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometryQuanzhou 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... - A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategyJoshua 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... - Characterization of the human blood plasma proteomeYufeng Shen
Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Proteomics 5:4034-45. 2005.... - Increased proteome coverage for quantitative peptide abundance measurements based upon high performance separations and DREAMS FTICR mass spectrometryLjiljana 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... - Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurementsYufeng 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... - Phosphopeptide elution times in reversed-phase liquid chromatographyJeongkwon 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... - Ultrasensitive proteomics using high-efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MSYufeng 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... - High-performance separations and mass spectrometric methods for high-throughput proteomics using accurate mass tagsRichard D Smith
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Adv Protein Chem 65:85-131. 2003 - High-efficiency on-line solid-phase extraction coupling to 15-150-microm-i.d. column liquid chromatography for proteomic analysisYufeng 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... - Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomicsYufeng 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... - Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tagsYufeng Shen
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Anal Chem 80:1871-82. 2008.... - Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approachWei-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.... - Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometryEric 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... - Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methodsYufeng 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... - Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analysesEric 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... - Preparation of 20-microm-i.d. silica-based monolithic columns and their performance for proteomics analysesQuanzhou 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... - Proteomic analyses using an accurate mass and time tag strategyLjiljana 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... - Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approachRuihua 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... - High-throughput global peptide proteomic analysis by combining stable isotope amino acid labeling and data-dependent multiplexed-MS/MSScott 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... - An accurate mass tag strategy for quantitative and high-throughput proteome measurementsRichard 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... - Targeted comparative proteomics by liquid chromatography-tandem Fourier ion cyclotron resonance mass spectrometryChristophe 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... - Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cellsYuexi 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... - Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analysesKonstantinos 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... - Utilizing human blood plasma for proteomic biomarker discoveryJon 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... - High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomicsYufeng Shen
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Anal Chem 74:4235-49. 2002.... - Gene expression profiling using advanced mass spectrometric approachesLjiljana 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.... - Global analysis of the Deinococcus radiodurans proteome by using accurate mass tagsMary 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... - 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 informationYufeng 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... - High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysisFeng Yang
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Expert Rev Proteomics 9:129-34. 2012.... - Ultrahigh-throughput proteomics using fast RPLC separations with ESI-MS/MSYufeng 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... - Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteomeYufeng 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)... - The use of accurate mass tags for high-throughput microbial proteomicsRichard 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... - Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughputRui 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.... - Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICRSang-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.... - Advanced proteomic liquid chromatographyFang 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... - Proteomics based on high-efficiency capillary separationsYufeng 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... - Ultra-sensitive and quantitative characterization of proteomesRichard 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.... - Ultrasensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomesRichard 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... - Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metabolic profilingJie 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... - Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separationJinzhi 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... - A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discoveryXiaohu Wang
Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
Nucleic Acids Res 36:4863-71. 2008.... - Conformational pathways in the gating of Escherichia coli mechanosensitive channelYifei 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... - The genome of the sea urchin Strongylocentrotus purpuratusErica Sodergren
Science 314:941-52. 2006..This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes...