Eric W Deutsch

Summary

Affiliation: Institute for Systems Biology
Country: USA

Publications

  1. pmc Development of data representation standards by the human proteome organization proteomics standards initiative
    Eric W Deutsch
    Institute for Systems Biology, Seattle, USA
    J Am Med Inform Assoc 22:495-506. 2015
  2. pmc File formats commonly used in mass spectrometry proteomics
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA 98109, USA
    Mol Cell Proteomics 11:1612-21. 2012
  3. pmc A guided tour of the Trans-Proteomic Pipeline
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Proteomics 10:1150-9. 2010
  4. 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
  5. pmc A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas
    Terry Farrah
    Institute for Systems Biology, Seattle, WA 98109, USA
    Mol Cell Proteomics 10:M110.006353. 2011
  6. pmc PASSEL: the PeptideAtlas SRMexperiment library
    Terry Farrah
    Institute for Systems Biology, Seattle, WA 98109, USA
    Proteomics 12:1170-5. 2012
  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. doi request reprint Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
    Eric W Deutsch
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Physiol Genomics 33:18-25. 2008
  9. pmc Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
    Eric W Deutsch
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Biotechnol 26:305-12. 2008
  10. pmc Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proteomics 10:1190-5. 2010

Detail Information

Publications43

  1. pmc Development of data representation standards by the human proteome organization proteomics standards initiative
    Eric W Deutsch
    Institute for Systems Biology, Seattle, USA
    J Am Med Inform Assoc 22:495-506. 2015
    ....
  2. pmc File formats commonly used in mass spectrometry proteomics
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA 98109, USA
    Mol Cell Proteomics 11:1612-21. 2012
    ..A brief overview of the most common file formats in use today is presented here, along with a discussion of related topics...
  3. pmc A guided tour of the Trans-Proteomic Pipeline
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Proteomics 10:1150-9. 2010
    ....
  4. 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
    ....
  5. pmc A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas
    Terry Farrah
    Institute for Systems Biology, Seattle, WA 98109, USA
    Mol Cell Proteomics 10:M110.006353. 2011
    ..We have made this resource available via PeptideAtlas, a large, multiorganism, publicly accessible compendium of peptides identified in tandem MS experiments conducted by laboratories around the world...
  6. pmc PASSEL: the PeptideAtlas SRMexperiment library
    Terry Farrah
    Institute for Systems Biology, Seattle, WA 98109, USA
    Proteomics 12:1170-5. 2012
    ..Further, PASSELwill help in the assessment of proteotypic peptide performance in a wide array of samples containing the same peptide, as well as across multiple experimental protocols...
  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. doi request reprint Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
    Eric W Deutsch
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Physiol Genomics 33:18-25. 2008
    ..In this review, we provide an overview of the general analysis approaches, software tools, and repositories that are enabling successful proteomics research via tandem mass spectrometry...
  9. pmc Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
    Eric W Deutsch
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Biotechnol 26:305-12. 2008
    ..This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal...
  10. pmc Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proteomics 10:1190-5. 2010
    ....
  11. pmc Interfaces to PeptideAtlas: a case study of standard data access systems
    Sarah Killcoyne
    Institute for Systems Biology, Seattle, WA 98109, USA
    Brief Bioinform 13:615-26. 2012
    ..g. security versus speed). This means that an understanding of specific requirements and tradeoffs is necessary before selecting the access technology...
  12. pmc Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
    Steven Lewis
    Institute for Systems Biology, Seattle, WA, USA
    BMC Bioinformatics 13:324. 2012
    ..Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed...
  13. ncbi request reprint Development and validation of a spectral library searching method for peptide identification from MS/MS
    Henry 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...
  14. 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...
  15. pmc Prevalence of transcription promoters within archaeal operons and coding sequences
    Tie Koide
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Syst Biol 5:285. 2009
    ..Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements...
  16. pmc State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet
    Eric W Deutsch
    Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
    J Proteome Res 14:3461-73. 2015
    ..We present the methodology and results for maintaining rigorous quality along with a discussion of the implications of the remaining sources of errors in the build...
  17. pmc Building consensus spectral libraries for peptide identification in proteomics
    Henry 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...
  18. pmc MaRiMba: a software application for spectral library-based MRM transition list assembly
    Carly 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...
  19. 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...
  20. pmc SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology
    Bruz Marzolf
    Institute for Systems Biology, 1441 N, 34th Street, Seattle, Washington, USA
    BMC Bioinformatics 7:286. 2006
    ..The automation of this information extraction requires high throughput management and analysis of genomic expression data, and integration of these data with other data types...
  21. pmc PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
    Eric W Deutsch
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    EMBO Rep 9:429-34. 2008
    ..Here, we describe the PeptideAtlas Project, its contents and components, and show how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics...
  22. pmc Combining results of multiple search engines in proteomics
    David Shteynberg
    Institute for Systems Biology, Seattle, Washington 98109, USA
    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. ..
  23. 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...
  24. pmc Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea
    Nitin S Baliga
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 14:2221-34. 2004
    ..Finally, as expected from the larger genome, H. marismortui encodes many more functions and seems to have fewer nutritional requirements for survival than does Halobacterium sp. NRC-1...
  25. pmc The state of the human proteome in 2012 as viewed through PeptideAtlas
    Terry Farrah
    Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
    J Proteome Res 12:162-71. 2013
    ..We characterize these "PA-unseen" proteins in terms of tissue localization, transcript abundance, and Gene Ontology enrichment, and propose reasons for their absence from PeptideAtlas and strategies for detecting them in the future...
  26. pmc mspecLINE: bridging knowledge of human disease with the proteome
    Jeremy Handcock
    Institute for Systems Biology, 1441 N 34th St, Seattle, WA 98103, USA
    BMC Med Genomics 3:7. 2010
    ..We used an established semantic distance measure that is based on the co-occurrence of disease and protein terms in the MEDLINE bibliographic database...
  27. pmc reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra
    David Shteynberg
    Institute for Systems Biology, Seattle, WA, USA
    J Am Soc Mass Spectrom 26:1837-47. 2015
    ..The reSpect tool is free and open source, provided within the TPP and available at the TPP website. Graphical Abstract ᅟ. ..
  28. pmc Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Proteomics Clin Appl 9:745-54. 2015
    ..We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of MS/MS datasets, as well as some major upcoming features. ..
  29. pmc TraML--a standard format for exchange of selected reaction monitoring transition lists
    Eric W Deutsch
    Institute for Systems Biology, Seattle, Washington 98109, USA
    Mol Cell Proteomics 11:R111.015040. 2012
    ....
  30. pmc Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics
    Ulrike Kusebauch
    Institute for Systems Biology, Seattle, Washington
    Curr Protoc Bioinformatics 46:13.25.1-28. 2014
    ..PeptideAtlas, SRMAtlas, and PASSEL are publicly available freely via the Web site http://www.peptideatlas.org. In this protocol, we describe the use of these resources, we highlight how to submit, search, collate and download data...
  31. pmc Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage
    Phu T Van
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    J Proteome Res 7:3755-64. 2008
    ..Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics...
  32. pmc The PeptideAtlas Project
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Methods Mol Biol 604:285-96. 2010
    ..The PeptideAtlas resource is useful for experiment planning, improving genome annotation, and other data mining projects. PeptideAtlas has become especially useful for planning targeted proteomics experiments...
  33. doi request reprint Using the Human Plasma PeptideAtlas to study human plasma proteins
    Terry Farrah
    Institute for Systems Biology, Seattle, WA, USA
    Methods Mol Biol 728:349-74. 2011
    ..Herein, the reader is instructed in the use of the Human Plasma PeptideAtlas through an illustrated exploration of cytokine receptors in plasma...
  34. pmc ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry
    Mi Youn K Brusniak
    Institute for Systems Biology, Seattle, WA, USA
    BMC Bioinformatics 12:78. 2011
    ....
  35. pmc Mining PeptideAtlas for biomarkers and therapeutics in human disease
    Sarah Killcoyne
    Institute for Systems Biology, 401 Terry Ave North, Seattle, WA 98109, USA
    Curr Pharm Des 18:748-54. 2012
    ..Here we describe PeptideAtlas and associated methods for mining the data, as well as the software tools necessary to support large-scale integration and mining...
  36. ncbi request reprint A common open representation of mass spectrometry data and its application to proteomics research
    Patrick G A Pedrioli
    Institute for Systems Biology, 1441 North 34 Street, Seattle, Washington 98103 8904, USA
    Nat Biotechnol 22:1459-66. 2004
    ..We have also developed an accompanying suite of supporting programs. We expect that this format will facilitate data management, interpretation and dissemination in proteomics research...
  37. pmc Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline
    Joseph Slagel
    From the Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109
    Mol Cell Proteomics 14:399-404. 2015
    ....
  38. pmc Mass spectrometer output file format mzML
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Methods Mol Biol 604:319-31. 2010
    ..At the time of release, there already existed several implementations of the format and vendors have committed to supporting the format in their products...
  39. pmc A mouse plasma peptide atlas as a resource for disease proteomics
    Qing Zhang
    Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Biol 9:R93. 2008
    ..A major finding from this study is the identification of novel isoforms and transcript variants not previously predicted from genome analysis...
  40. doi request reprint Tandem mass spectrometry spectral libraries and library searching
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Methods Mol Biol 696:225-32. 2011
    ..In this chapter, an overview of spectral library searching and the libraries currently available are presented...
  41. ncbi request reprint A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry
    Wei Yan
    The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Mol Cell Proteomics 3:1039-41. 2004
    ..An increase of the threshold to p > or = 0.9 (corresponding to an error rate of less than 1%) resulted in 2,159 unique protein identifications (1,146, 1,235, and 1,318 for the Huh7, HFH, and HH4 cells, respectively)...
  42. pmc Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
    Richard Bonneau
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Genome Biol 5:R52. 2004
    ..The work reported here demonstrates that de novo structure prediction is now a viable option for providing general function information for many proteins of unknown function...
  43. ncbi request reprint Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)
    Eric W Deutsch
    Institute for Systems Biology, Seattle, Washington 98103, USA
    OMICS 10:205-8. 2006
    ..The full specification will soon be published as a version 1.0 proposal to the community, upon which a more full discussion must take place so that the final specification may be achieved with the involvement of the whole community...