Alexey I Nesvizhskii

Summary

Affiliation: Institute for Systems Biology
Country: USA

Publications

  1. pmc Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
    Frank Desiere
    Nestle Research Center, 1000 Lausanne 26, Switzerland
    Genome Biol 6:R9. 2005
  2. ncbi request reprint Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS
    Alexey I Nesvizhskii
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    Drug Discov Today 9:173-81. 2004
  3. ncbi request reprint Interpretation of shotgun proteomic data: the protein inference problem
    Alexey I Nesvizhskii
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 4:1419-40. 2005
  4. ncbi request reprint A statistical model for identifying proteins by tandem mass spectrometry
    Alexey I Nesvizhskii
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    Anal Chem 75:4646-58. 2003
  5. 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
  6. pmc iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
    David Shteynberg
    Institute for Systems Biology, Seattle, WA, USA
    Mol Cell Proteomics 10:M111.007690. 2011
  7. pmc Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas
    Nichole L King
    Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
    Genome Biol 7:R106. 2006
  8. 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
  9. pmc The PeptideAtlas project
    Frank Desiere
    Institute for Systems Biology, Seattle, WA, USA
    Nucleic Acids Res 34:D655-8. 2006
  10. 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

Collaborators

Detail Information

Publications34

  1. pmc Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
    Frank Desiere
    Nestle Research Center, 1000 Lausanne 26, Switzerland
    Genome Biol 6:R9. 2005
    ..This resource could serve as an expandable repository for MS-derived proteome information...
  2. ncbi request reprint Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS
    Alexey I Nesvizhskii
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    Drug Discov Today 9:173-81. 2004
    ..Here, we review currently available computational tools and discuss the need for statistical criteria in the analysis of large proteomics datasets...
  3. ncbi request reprint Interpretation of shotgun proteomic data: the protein inference problem
    Alexey I Nesvizhskii
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 4:1419-40. 2005
    ....
  4. ncbi request reprint A statistical model for identifying proteins by tandem mass spectrometry
    Alexey I Nesvizhskii
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    Anal Chem 75:4646-58. 2003
    ..Fast, consistent, and transparent, it provides a standard for publishing large-scale protein identification data sets in the literature and for comparing the results obtained from different experiments...
  5. 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...
  6. pmc iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
    David Shteynberg
    Institute for Systems Biology, Seattle, WA, USA
    Mol Cell Proteomics 10:M111.007690. 2011
    ....
  7. pmc Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas
    Nichole L King
    Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
    Genome Biol 7:R106. 2006
    ..We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development...
  8. 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...
  9. pmc The PeptideAtlas project
    Frank Desiere
    Institute for Systems Biology, Seattle, WA, USA
    Nucleic Acids Res 34:D655-8. 2006
    ..Here we present a summary of our process and details about the Human, Drosophila and Yeast PeptideAtlas builds...
  10. 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...
  11. ncbi request reprint Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    Andrew Keller
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Anal Chem 74:5383-92. 2002
    ..This analysis makes it possible to filter large volumes of MS/MS database search results with predictable false identification error rates and can serve as a common standard by which the results of different research groups are compared...
  12. pmc A guided tour of the Trans-Proteomic Pipeline
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Proteomics 10:1150-9. 2010
    ....
  13. ncbi request reprint Human Plasma PeptideAtlas
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proteomics 5:3497-500. 2005
    ..The resulting compendium of peptides and their associated samples, proteins, and genes is made publicly available as a reference for future research on human plasma...
  14. pmc Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction
    Ramsey A Saleem
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 9:2076-88. 2010
    ..These properties are consistent with a scale-free topology, demonstrating that scale-free properties are conserved in condition-specific networks...
  15. pmc Investigation of neutral loss during collision-induced dissociation of peptide ions
    Daniel B Martin
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Anal Chem 77:4870-82. 2005
    ..Clarification of the rules that govern neutral loss, when incorporated into analysis software, will improve our ability to correctly assign spectra to peptide sequences...
  16. doi request reprint Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes
    Marcello Marelli
    Homestead Clinical Corporation, Seattle, WA, USA
    Methods Mol Biol 432:357-71. 2008
    ..The methods for the analyses of the yeast peroxisome are described in detail; however, these concepts are generally applicable to the study of other organelles...
  17. pmc The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes
    Bong Kim
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 104:16068-73. 2007
    ..The results demonstrate that TFIIS is a PIC component that is required for efficient formation and/or stability of the complex...
  18. pmc Combining results of multiple search engines in proteomics
    David Shteynberg
    Institute for Systems Biology, Seattle, Washington 98109
    Mol Cell Proteomics 12:2383-93. 2013
    ..Here we review the techniques and available software for combining the results of multiple search engines and briefly compare the relative performance of these techniques. ..
  19. pmc Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane
    Marcello Marelli
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Biol 167:1099-112. 2004
    ..Rho1p regulates the assembly state of actin on the peroxisome membrane, thereby controlling peroxisome membrane dynamics and biogenesis...
  20. ncbi request reprint Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides
    Alexey I Nesvizhskii
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 5:652-70. 2006
    ....
  21. ncbi request reprint Experimental protein mixture for validating tandem mass spectral analysis
    Andrew Keller
    Institute for Systems Biology, Seattle, Washington 98103, USA
    OMICS 6:207-12. 2002
    ..We show how the sensitivity and error rate are affected by the use of various filtering criteria based upon SEQUEST scores and the number of tryptic termini of assigned peptides...
  22. pmc Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
    Eugene Kolker
    BIATECH, Bothell, Washington 98011, USA
    J Bacteriol 185:4593-602. 2003
    ..The direct proteomics approach to studying protein expression in vivo reported here is a powerful method that is applicable to proteome analysis of any (micro)organism...
  23. ncbi request reprint Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
    Lennart Martens
    Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
    Proteomics 5:3501-5. 2005
    ..Finally, some suggestions are made for both immediate and future storage of MS data in public repositories...
  24. pmc Improved sequence tag generation method for peptide identification in tandem mass spectrometry
    Xia Cao
    Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Proteome Res 7:4422-34. 2008
    ..The overall superior performance of the sequence tag-based peptide identification method is demonstrated by comparison with a commonly used SEQUEST/PeptideProphet approach...
  25. doi request reprint Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies
    Brian C Searle
    Proteome Software Inc, 1340 S W Bertha Boulevard, Suite 201, Portland, Oregon 97219 2039, USA
    J Proteome Res 7:245-53. 2008
    ..The increased rate of peptide assignments also translates into a substantially larger number of protein identifications in LC/MS/MS studies compared to a typical analysis using a single database-search tool...
  26. ncbi request reprint Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics
    Hyungwon Choi
    Department of Pathology and Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Proteome Res 7:254-65. 2008
    ....
  27. ncbi request reprint Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling
    Hyungwon Choi
    Department of Pathology and Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
    J Proteome Res 7:286-92. 2008
    ..The statistical approaches presented here require that the data set contain a sufficient number of decoy (known to be incorrect) peptide identifications, which can be obtained using the target-decoy database search strategy...
  28. ncbi request reprint False discovery rates and related statistical concepts in mass spectrometry-based proteomics
    Hyungwon Choi
    Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Proteome Res 7:47-50. 2008
    ..In this work, we provide a background on statistical significance analysis in the field of mass spectrometry-based proteomics, and present our perspective on the current and future developments in this area...
  29. ncbi request reprint Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis
    Johan Malmstrom
    Institute for Molecular Systems Molecular Biology, Swiss Federal Institute for Technology Zürich ETH, Hoenggerberg 8093 Zürich, Switzerland
    J Proteome Res 5:2241-9. 2006
    ....
  30. ncbi request reprint Analysis and validation of proteomic data generated by tandem mass spectrometry
    Alexey I Nesvizhskii
    University of Michigan, Department of Pathology and Center for Computational Medicine and Biology, Ann Arbor, Michigan 48105, USA
    Nat Methods 4:787-97. 2007
    ..We place special emphasis on the elaboration of results that are supported by sound statistical arguments...
  31. ncbi request reprint Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence
    Peter J Ulintz
    Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48103, USA
    Mol Cell Proteomics 7:71-87. 2008
    ..This work also addresses the overall value of generating MS(3) data as compared with an MS(2)-only approach with a focus on the analysis of phosphopeptide data...
  32. pmc Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS
    Chul Yoo
    Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
    J Mass Spectrom 42:312-34. 2007
    ..It was also observed that the comparison to intact MW and other MS information was particularly useful for analyzing proteins whose identifications were suggested by one sequenced peptide from fraction digest analysis...
  33. ncbi request reprint Protein identification by tandem mass spectrometry and sequence database searching
    Alexey I Nesvizhskii
    Department of Pathology, University of Michigan, Ann Arbor, USA
    Methods Mol Biol 367:87-119. 2007
    ....
  34. ncbi request reprint Humoral response profiling reveals pathways to prostate cancer progression
    Barry S Taylor
    Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Mol Cell Proteomics 7:600-11. 2008
    ..Thus, in addition to functioning as markers in prostate cancer detection, humoral response profiles can serve as powerful tools revealing pathway dysregulation that might otherwise be suppressed by the complexity of the cancer proteome...