Research Topics
| Jimmy K EngSummaryAffiliation: University of Washington Country: USA Publications
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Detail Information
Publications
A face in the crowd: recognizing peptides through database searchJimmy K Eng
University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA
Mol Cell Proteomics 10:R111.009522. 2011..This review revisits the mechanism of sequence database searching and discusses how various parameter settings impact the underlying search...- A fast SEQUEST cross correlation algorithmJimmy K Eng
Department of Genome Sciences, University of Washington, Seattle, Washington, USA
J Proteome Res 7:4598-602. 2008.... - A guided tour of the Trans-Proteomic PipelineEric W Deutsch
Institute for Systems Biology, Seattle, WA, USA
Proteomics 10:1150-9. 2010.... - Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancerJeffrey R Whiteaker
Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
J Proteome Res 6:3962-75. 2007..Furthermore, the approach can be extended to find biomarkers relevant to human disease... - Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data setsEric W Deutsch
Institute for Systems Biology, Seattle, WA 98103, USA
Proteomics 10:1190-5. 2010.... - 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.... - MaRiMba: a software application for spectral library-based MRM transition list assemblyCarly A Sherwood
Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
J Proteome Res 8:4396-405. 2009..To illustrate the use of MaRiMba, we used the tool to design and execute an MRM-MS experiment in which we targeted the proteins of a well-defined and previously published standard mixture... - Quantification of the compositional information provided by immonium ions on a quadrupole-time-of-flight mass spectrometerLaura J Hohmann
Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
Anal Chem 80:5596-606. 2008..This compositional information provided by the immonium ion peaks could substantially improve algorithms used for spectral assignment in mass spectrometry analysis using QTOF platforms... - Proteomic analyses using Grifola frondosa metalloendoprotease Lys-NLaura Hohmann
Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, USA
J Proteome Res 8:1415-22. 2009..Finally, immonium ion peaks produced from Lys-N digested peptides originate from the carboxy terminus in contrast to tryptic peptides where immonium ions originate from the amino terminus... - Installation and use of the Computational Proteomics Analysis System (CPAS)Tamra Myers
Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
Curr Protoc Bioinformatics . 2007..All components of the CPAS toolkit are freely available at http://cpas.fhcrc.org... - Building consensus spectral libraries for peptide identification in proteomicsHenry Lam
Institute for Systems Biology, Seattle, Washington 98103, USA
Nat Methods 5:873-5. 2008..It allows individual researchers to condense raw data into spectral libraries, summarizing information about observed proteomes into a concise and retrievable format for future data analyses... - Head-to-head comparison of serum fractionation techniquesJeffrey R Whiteaker
Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109 1024, USA
J Proteome Res 6:828-36. 2007..The reported dataset is publicly available and provides a standard against which emergent technologies can be compared and evaluated for their contribution to serum-based biomarker discovery... - Precursor charge state prediction for electron transfer dissociation tandem mass spectraVagisha Sharma
Department of Biochemistry, University of Washington, Seattle, Washington, USA
J Proteome Res 9:5438-44. 2010..The tool is freely available, open source, cross platform compatible, and demonstrated to perform well when compared with an existing charge state prediction tool. The program is available from http://code.google.com/p/etdz/... - Fast parallel tandem mass spectral library searching using GPU hardware accelerationLydia Ashleigh Baumgardner
Institute for Systems Biology, Seattle, Washington, USA
J Proteome Res 10:2882-8. 2011..Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment... - Development and validation of a spectral library searching method for peptide identification from MS/MSHenry Lam
Institute for Systems Biology, Seattle, WA, USA
Proteomics 7:655-67. 2007..This method of spectral library searching is especially suited for targeted proteomics applications, offering superior performance to traditional sequence searching... - The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software toolsJohn Klimek
Institute for Systems Biology, Seattle, Washington 98103, USA
J Proteome Res 7:96-103. 2008..All data, including the native raw instrument and mzXML formats and the PeptideProphet validated peptide assignments, are available at http://regis-web.systemsbiology.net/PublicDatasets/... - Installation and use of LabKey Server for proteomicsJoshua Eckels
LabKey Software, Seattle, Washington, USA
Curr Protoc Bioinformatics . 2011..Supported builds of LabKey Server are freely available at http://www.labkey.com/. Documentation and source code are available under the Apache License 2.0 at http://www.labkey.org... - 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... - Proteomics data repositoriesMichael Riffle
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Proteomics 9:4653-63. 2009..Resources are described in terms of their intended purpose and the features and functionality provided to users... - Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profilesBrian D Piening
Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, Washington, 98109, USA
J Proteome Res 5:1527-34. 2006..This work is done on complex LC-MS profiles of Saccharomyces cerevisiae which present a significant challenge to peptide feature detection algorithms... - 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... - Sites of ubiquitin attachment in Saccharomyces cerevisiaeLea M Starita
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
Proteomics 12:236-40. 2012..However, such peptides with GG shifts have been difficult to discover. We identify 870 unique sites of ubiquitin attachment on 438 different proteins of the yeast Saccharomyces cerevisiae... - General framework for developing and evaluating database scoring algorithms using the TANDEM search engineBrendan Maclean
Fred Hutchinson Cancer Research Center Seattle, USA
Bioinformatics 22:2830-2. 2006..The pluggable scores and the X! suite of applications are all written in C++. AVAILABILITY: Source code for the scoring functions is available from http://proteomics.fhcrc.org.. - Protein identification using TurboSEQUESTDeborah H Lundgren
University of Connecticut Health Center, Farmington, Connecticut, USA
Curr Protoc Bioinformatics . 2005..It also provides an overview of the SEQUEST algorithm and a discussion of data filtering methods, critical issues in data interpretation, and available resources that can facilitate proper interpretation of SEQUEST results... - An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysisEugene A Kapp
Joint ProteomicS Laboratory, Ludwig Institute for Cancer Research (Melbourne Branch)/Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
Proteomics 5:3475-90. 2005..e., the use of multiple (at least two) search algorithms to reduce the number of FPs. complement... - An alternative sampling algorithm for use in liquid chromatography/tandem mass spectrometry experimentsBernhard M Kohli
Division of Psychiatry Research, August Forel Strasse 1, 8008 Zurich, Switzerland
Rapid Commun Mass Spectrom 19:589-96. 2005..Further validation of the algorithm will require its incorporation by equipment manufacturers into the instrument control programs... - 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...