Research Topics
| Alexey I NesvizhskiiSummaryAffiliation: Institute for Systems Biology Country: USA Publications
| Collaborators
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Detail Information
Publications
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometryFrank 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...
Interpretation of shotgun proteomic data: the protein inference problemAlexey I Nesvizhskii
Institute for Systems Biology, Seattle, Washington 98103, USA
Mol Cell Proteomics 4:1419-40. 2005....- Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MSAlexey 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... - A statistical model for identifying proteins by tandem mass spectrometryAlexey 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... - 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 sPriska 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... - iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimatesDavid Shteynberg
Institute for Systems Biology, Seattle, WA, USA
Mol Cell Proteomics 10:M111.007690. 2011.... - Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlasNichole 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... - Lipid raft proteins and their identification in T lymphocytesBernd 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... - 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 tPriska 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... - The PeptideAtlas projectFrank 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... - Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database searchAndrew 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... - A guided tour of the Trans-Proteomic PipelineEric W Deutsch
Institute for Systems Biology, Seattle, WA, USA
Proteomics 10:1150-9. 2010.... - Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome inductionRamsey 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... - Human Plasma PeptideAtlasEric 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... - Investigation of neutral loss during collision-induced dissociation of peptide ionsDaniel 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... 
Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomesMarcello 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...- The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexesBong 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... - Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptidesAlexey I Nesvizhskii
Institute for Systems Biology, Seattle, Washington 98103, USA
Mol Cell Proteomics 5:652-70. 2006.... - Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membraneMarcello 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... - Experimental protein mixture for validating tandem mass spectral analysisAndrew 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... - Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MSChul 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... - Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20Eugene 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... - Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositoriesLennart 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... - Improved sequence tag generation method for peptide identification in tandem mass spectrometryXia 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... - Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologiesBrian 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... - Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomicsHyungwon Choi
Department of Pathology and Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
J Proteome Res 7:254-65. 2008.... - Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modelingHyungwon 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... - False discovery rates and related statistical concepts in mass spectrometry-based proteomicsHyungwon 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... - Protein identification by tandem mass spectrometry and sequence database searchingAlexey I Nesvizhskii
Department of Pathology, University of Michigan, Ann Arbor, USA
Methods Mol Biol 367:87-119. 2007.... - Analysis and validation of proteomic data generated by tandem mass spectrometryAlexey 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... - Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidencePeter 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... - Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresisJohan 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.... - Humoral response profiling reveals pathways to prostate cancer progressionBarry 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...