Xiao Jun Li

Summary

Affiliation: Institute for Systems Biology
Country: USA

Publications

  1. ncbi request reprint A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry
    Xiao Jun Li
    Institute for Systems Biology, Seattle, Washington 98103 8904, USA
    Mol Cell Proteomics 4:1328-40. 2005
  2. ncbi request reprint A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry
    Xiao Jun Li
    The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
    Anal Chem 76:3856-60. 2004
  3. ncbi request reprint The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of s
    Priska D von Haller
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Mol Cell Proteomics 2:428-42. 2003
  4. ncbi request reprint The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and t
    Priska D von Haller
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Mol Cell Proteomics 2:426-7. 2003
  5. ncbi request reprint High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry
    Hui Zhang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Cell Proteomics 4:144-55. 2005
  6. ncbi request reprint Improving mass and liquid chromatography based identification of proteins using bayesian scoring
    Sharon S Chen
    University of Washington, Department of Bioengineering, Seattle, Washington 98105, USA
    J Proteome Res 4:2174-84. 2005
  7. ncbi request reprint Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme
    Eugene C Yi
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proteomics 5:380-7. 2005
  8. pmc System-based proteomic analysis of the interferon response in human liver cells
    Wei Yan
    Institute for Systems Biology, Seattle, WA 98103, USA
    Genome Biol 5:R54. 2004
  9. ncbi request reprint Abundance ratio-dependent proteomic analysis by mass spectrometry
    Timothy J Griffin
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    Anal Chem 75:867-74. 2003
  10. ncbi request reprint Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry
    Hui Zhang
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103 8904, USA
    Nat Biotechnol 21:660-6. 2003

Detail Information

Publications18

  1. ncbi request reprint A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry
    Xiao Jun Li
    Institute for Systems Biology, Seattle, Washington 98103 8904, USA
    Mol Cell Proteomics 4:1328-40. 2005
    ..We demonstrate through these two study cases that the SpecArray software suite can serve as an effective software platform in the LC-MS approach for quantitative proteomics...
  2. ncbi request reprint A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry
    Xiao Jun Li
    The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
    Anal Chem 76:3856-60. 2004
    ..Local patterns of the image can also be used to identify chemical contaminants and specific peptide features. Therefore, this software tool may have broad application in MS-based proteomics...
  3. ncbi request reprint The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of s
    Priska D von Haller
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Mol Cell Proteomics 2:428-42. 2003
    ..Finally, by repeating the experiment, information relating to the general reproducibility and validity of this approach to large-scale proteomic analyses was also obtained...
  4. ncbi request reprint The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and t
    Priska D von Haller
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Mol Cell Proteomics 2:426-7. 2003
    ..In total, these data sets contained 7667 individual peptide identifications, which represented 2669 unique peptide sequences, corresponding to 685 proteins and related protein groups...
  5. ncbi request reprint High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry
    Hui Zhang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Cell Proteomics 4:144-55. 2005
    ..We further identify, by tandem mass spectrometry, some of the peptides that were consistently elevated in cancer mice compared with their control littermates...
  6. ncbi request reprint Improving mass and liquid chromatography based identification of proteins using bayesian scoring
    Sharon S Chen
    University of Washington, Department of Bioengineering, Seattle, Washington 98105, USA
    J Proteome Res 4:2174-84. 2005
    ..This method resulted in 6 times more peptide sequence identifications from a single LC-MS analysis of yeast than from shotgun peptide sequencing using LC-MS/MS...
  7. ncbi request reprint Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme
    Eugene C Yi
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proteomics 5:380-7. 2005
    ....
  8. pmc System-based proteomic analysis of the interferon response in human liver cells
    Wei Yan
    Institute for Systems Biology, Seattle, WA 98103, USA
    Genome Biol 5:R54. 2004
    ....
  9. ncbi request reprint Abundance ratio-dependent proteomic analysis by mass spectrometry
    Timothy J Griffin
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    Anal Chem 75:867-74. 2003
    ..cerevisiae...
  10. ncbi request reprint Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry
    Hui Zhang
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103 8904, USA
    Nat Biotechnol 21:660-6. 2003
    ..The recovered peptides are then identified and quantified by MS/MS. We applied the approach to the analysis of plasma membrane proteins and proteins contained in human blood serum...
  11. ncbi request reprint Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry
    Xiao Jun Li
    The Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    Anal Chem 75:6648-57. 2003
    ....
  12. ncbi request reprint ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer
    Ning Zhang
    The Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Proteomics 5:4096-106. 2005
    ..The results using MALDI-TOF-TOF MS/MS data demonstrate that multiple peptides can be effectively identified simultaneously with high confidence using ProbIDtree...
  13. ncbi request reprint Lipid raft proteins and their identification in T lymphocytes
    Bernd Wollscheid
    Institute for Systems Biology, Seattle, WA 98103, USA
    Subcell Biochem 37:121-52. 2004
    ..Similar approaches, applied to other model cell systems, will provide valuable new insights into both cellular signal transduction and lipid raft biology...
  14. ncbi request reprint Identification of TFB5, a new component of general transcription and DNA repair factor IIH
    Jeffrey A Ranish
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    Nat Genet 36:707-13. 2004
    ..The identification of a new, evolutionarily conserved, core TFIIH subunit is essential for our understanding of TFIIH function in transcription, DNA repair and human disease...
  15. pmc A uniform proteomics MS/MS analysis platform utilizing open XML file formats
    Andrew Keller
    Institute for Systems Biology, Seattle, WA, USA
    Mol Syst Biol 1:2005.0017. 2005
    ..We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, and Waters Q-TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET...
  16. ncbi request reprint Engagement of membrane immunoglobulin enhances Id3 promoter activity in WEHI-231 B lymphoma cells
    Xiao Jun Li
    Department of Medical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, 210002, China
    Acta Pharmacol Sin 26:486-91. 2005
    ..In the present study, we examined whether engagement of mIg will affect promoter activity of the Id3 gene in WEHI-231 cells...
  17. ncbi request reprint Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry
    W Andy Tao
    The Bindley Bioscience Center and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
    Nat Methods 2:591-8. 2005
    ..The dynamic changes in phosphorylation were quantified in these proteins...
  18. pmc Overexpression of ribosomal protein L15 is associated with cell proliferation in gastric cancer
    Hui Wang
    Department of Vascular and Endocrine Surgery, Xijing Hospital, The Fourth Military Medical University, 17 Changle Western Road, Xi an 710032, China
    BMC Cancer 6:91. 2006
    ..In our previous study of microarray, ribosomal protein L15 (RPL15) was identified as an upregulated gene in gastric cancer...