Publications by authors named "Eric W Deutsch"

100Publications

mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements.

J Proteome Res 2020 Oct 29. Epub 2020 Oct 29.

Department of Population Health Sciences and Bristol Veterinary School, University of Bristol, Bristol BS8 2BN, United Kingdom.

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http://dx.doi.org/10.1021/acs.jproteome.0c00192DOI Listing
October 2020

BioHackathon 2015: Semantics of data for life sciences and reproducible research.

F1000Res 2020 24;9:136. Epub 2020 Feb 24.

National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan.

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http://dx.doi.org/10.12688/f1000research.18236.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141167PMC
February 2020

Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.

Proteomics 2020 Nov 2;20(21-22):e1900362. Epub 2020 Apr 2.

Institute for Systems Biology, Seattle, WA, 98109, USA.

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http://dx.doi.org/10.1002/pmic.201900362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7483226PMC
November 2020

Advances in Identifying and Characterizing the Human Proteome.

J Proteome Res 2019 12;18(12):4079-4084

Institute for Systems Biology, Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics & School of Public Health , University of Michigan.

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http://dx.doi.org/10.1021/acs.jproteome.9b00745DOI Listing
December 2019

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data.

J Proteome Res 2019 12 11;18(12):4085-4097. Epub 2019 Oct 11.

Affinity Proteomics, SciLifeLab , KTH Royal Institute of Technology , 171 65 Stockholm , Sweden.

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http://dx.doi.org/10.1021/acs.jproteome.9b00503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6898750PMC
December 2019

Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods.

J Proteome Res 2018 12;17(12):4023-4030

Institute for Systems Biology, Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics & School of Public Health, University of Michigan.

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http://dx.doi.org/10.1021/acs.jproteome.8b00885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288998PMC
December 2018

Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper.

J Proteome Res 2018 12 28;17(12):4337-4344. Epub 2018 Sep 28.

Institute for Systems Biology , 401 Terry Ave North , Seattle , Washington 98109 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438762PMC
December 2018

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.

Genome Biol 2018 01 31;19(1):12. Epub 2018 Jan 31.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s13059-017-1377-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793360PMC
January 2018

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

J Proteome Res 2017 12 9;16(12):4281-4287. Epub 2017 Oct 9.

Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States.

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http://dx.doi.org/10.1021/acs.jproteome.7b00375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5872831PMC
December 2017

The PeptideAtlas of the Domestic Laying Hen.

J Proteome Res 2017 03 14;16(3):1352-1363. Epub 2017 Feb 14.

W.M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States.

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http://dx.doi.org/10.1021/acs.jproteome.6b00952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5877420PMC
March 2017

Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV.

J Proteome Res 2016 11;15(11):3945-3950

Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan.

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http://dx.doi.org/10.1021/acs.jproteome.6b00803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129621PMC
November 2016

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

J Proteome Res 2016 11 12;15(11):4091-4100. Epub 2016 Sep 12.

Institute for Systems Biology , Seattle, Washington 98109, United States.

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http://dx.doi.org/10.1021/acs.jproteome.6b00445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5096980PMC
November 2016

Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.

J Proteome Res 2016 11 20;15(11):3979-3987. Epub 2016 Sep 20.

Center for Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1021/acs.jproteome.6b00444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129618PMC
November 2016

Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications.

J Proteome Res 2016 11 20;15(11):3951-3960. Epub 2016 Sep 20.

Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States.

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http://dx.doi.org/10.1021/acs.jproteome.6b00511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129622PMC
November 2016

An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results.

J Am Soc Mass Spectrom 2016 11 28;27(11):1728-1734. Epub 2016 Jul 28.

Institute for Systems Biology, Seattle, Washington, 98109, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5061604PMC
http://dx.doi.org/10.1007/s13361-016-1435-8DOI Listing
November 2016

A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage.

J Proteomics 2016 Jan 19;131:122-130. Epub 2015 Oct 19.

Departamento de Microbiología II, Universidad Complutense Madrid (UCM), Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Corresponding author at: Departamento de Microbiología II, Universidad Complutense Madrid (UCM), Facultad de Farmacia, Plaza Ramón y Cajal s/n, 28040, Madrid, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2015.10.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670622PMC
January 2016

Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light.

J Proteome Res 2015 Sep;14(9):3409-14

Department of Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.

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http://pubs.acs.org/doi/10.1021/acs.jproteome.5b00785
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http://dx.doi.org/10.1021/acs.jproteome.5b00785DOI Listing
September 2015

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

J Proteome Res 2015 Sep 30;14(9):3452-60. Epub 2015 Jul 30.

Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755311PMC
September 2015

Development of data representation standards by the human proteome organization proteomics standards initiative.

J Am Med Inform Assoc 2015 May 28;22(3):495-506. Epub 2015 Feb 28.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/jamia/ocv001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457114PMC
May 2015

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

Mol Cell Proteomics 2015 Feb 23;14(2):399-404. Epub 2014 Nov 23.

From the ‡Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109.

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http://dx.doi.org/10.1074/mcp.O114.043380DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350034PMC
February 2015

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.

Proteomics 2014 Nov 9;14(21-22):2363-8. Epub 2014 Oct 9.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201470164DOI Listing
November 2014

Numerical compression schemes for proteomics mass spectrometry data.

Mol Cell Proteomics 2014 Jun 27;13(6):1537-42. Epub 2014 Mar 27.

From the ‡Department of Immunotechnology, Lund University, Medicon Village building 406, 223 81 Lund Sweden; ‖‖Bioinformatics Infrastructure for Life Sciences, Lund University, Sweden.

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http://dx.doi.org/10.1074/mcp.O114.037879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4047472PMC
June 2014

The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research.

Proteomics 2014 Mar 16;14(6):763-73. Epub 2014 Feb 16.

Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1002/pmic.201300398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340707PMC
March 2014

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins.

J Proteome Res 2014 Jan 23;13(1):15-20. Epub 2013 Dec 23.

SIB-Swiss Institute of Bioinformatics , CMU - Rue Michel-Servet 1, 1211 Geneva, Switzerland.

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http://dx.doi.org/10.1021/pr401144xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928647PMC
January 2014

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.

Proteomics 2013 Oct;13(20):2931-7

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201370166DOI Listing
October 2013

A Candida albicans PeptideAtlas.

J Proteomics 2014 Jan 26;97:62-8. Epub 2013 Jun 26.

Dept. Microbiología II, Universidad Complutense de Madrid, Madrid, Spain; IRYCIS: Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2013.06.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951211PMC
January 2014

Combining results of multiple search engines in proteomics.

Mol Cell Proteomics 2013 Sep 29;12(9):2383-93. Epub 2013 May 29.

Institute for Systems Biology, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1074/mcp.R113.027797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769318PMC
September 2013

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.

Mol Cell Proteomics 2013 Aug 18;12(8):2332-40. Epub 2013 Apr 18.

Quantitative Biology Center and Department of Computer Science, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.

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http://dx.doi.org/10.1074/mcp.O113.028506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734589PMC
August 2013

The state of the human proteome in 2012 as viewed through PeptideAtlas.

J Proteome Res 2013 Jan 5;12(1):162-71. Epub 2012 Dec 5.

Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.

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http://dx.doi.org/10.1021/pr301012jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928036PMC
January 2013

File formats commonly used in mass spectrometry proteomics.

Authors:
Eric W Deutsch

Mol Cell Proteomics 2012 Dec 6;11(12):1612-21. Epub 2012 Sep 6.

Institute for Systems Biology, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1074/mcp.R112.019695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518119PMC
December 2012

Interfaces to PeptideAtlas: a case study of standard data access systems.

Brief Bioinform 2012 Sep 22;13(5):615-26. Epub 2011 Nov 22.

Institute for Systems Biology, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1093/bib/bbr067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431717PMC
September 2012

A Bovine PeptideAtlas of milk and mammary gland proteomes.

Proteomics 2012 Sep;12(18):2895-9

Department of Animal Science and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1002/pmic.201200057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4771623PMC
September 2012

Mining PeptideAtlas for biomarkers and therapeutics in human disease.

Curr Pharm Des 2012 ;18(6):748-54

Institute for Systems Biology, 401 Terry Ave. North, Seattle, WA 98109, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361040PMC
http://dx.doi.org/10.2174/138161212799277833DOI Listing
July 2012

A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues.

BMC Genomics 2011 Jun 3;12:290. Epub 2011 Jun 3.

Centre for High-Throughput Biology and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada.

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http://dx.doi.org/10.1186/1471-2164-12-290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213019PMC
June 2011

Using the Human Plasma PeptideAtlas to study human plasma proteins.

Methods Mol Biol 2011 ;728:349-74

Institute for Systems Biology, Seattle, WA, USA.

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http://dx.doi.org/10.1007/978-1-61779-068-3_23DOI Listing
July 2011

Tandem mass spectrometry spectral libraries and library searching.

Authors:
Eric W Deutsch

Methods Mol Biol 2011 ;696:225-32

Institute for Systems Biology, Seattle, WA, USA.

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http://dx.doi.org/10.1007/978-1-60761-987-1_13DOI Listing
February 2011