Juergen Cox

Juergen Cox

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Juergen Cox

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Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research.

Methods Mol Biol 2018 ;1711:133-148

Computational Systems Biochemistry Group, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.

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http://dx.doi.org/10.1007/978-1-4939-7493-1_7DOI Listing
October 2018

EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification.

Nat Methods 2018 07 18;15(7):527-530. Epub 2018 Jun 18.

Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.

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http://dx.doi.org/10.1038/s41592-018-0037-8DOI Listing
July 2018

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes.

Nat Methods 2018 06 7;15(6):440-448. Epub 2018 May 7.

Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.

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http://www.nature.com/articles/s41592-018-0003-5
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http://dx.doi.org/10.1038/s41592-018-0003-5DOI Listing
June 2018

Guidelines for Genome-Scale Analysis of Biological Rhythms.

J Biol Rhythms 2017 Oct 3;32(5):380-393. Epub 2017 Nov 3.

27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.

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http://dx.doi.org/10.1177/0748730417728663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5692188PMC
October 2017

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.

Nat Protoc 2016 Dec 27;11(12):2301-2319. Epub 2016 Oct 27.

Computational Systems Biochemistry, Max-Planck Institute for Biochemistry, Martinsried, Germany.

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http://dx.doi.org/10.1038/nprot.2016.136DOI Listing
December 2016

Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome.

Genome Med 2016 Apr 21;8(1):44. Epub 2016 Apr 21.

Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.

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http://dx.doi.org/10.1186/s13073-016-0293-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4841045PMC
April 2016

Proteomic maps of breast cancer subtypes.

Nat Commun 2016 Jan 4;7:10259. Epub 2016 Jan 4.

Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.

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http://dx.doi.org/10.1038/ncomms10259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4725767PMC
January 2016

Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow.

J Proteome Res 2015 Nov 28;14(11):4885-95. Epub 2015 Oct 28.

Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany.

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http://dx.doi.org/10.1021/acs.jproteome.5b00720DOI Listing
November 2015

Visualization of LC-MS/MS proteomics data in MaxQuant.

Proteomics 2015 Apr 5;15(8):1453-6. Epub 2015 Mar 5.

Max-Planck-Institute of Biochemistry, Computational Systems Biochemistry, Martinsried, Germany.

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http://dx.doi.org/10.1002/pmic.201400449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024039PMC
April 2015

Cell-type-resolved quantitative proteomics of murine liver.

Cell Metab 2014 Dec;20(6):1076-87

Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2014.11.002DOI Listing
December 2014

N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.

Mol Cell Proteomics 2014 Jan 4;13(1):240-51. Epub 2013 Nov 4.

Proteomics and Signal Transduction Department, Max-Planck Institute of Biochemistry, D-82152 Martinsried, Germany;

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http://dx.doi.org/10.1074/mcp.M113.033977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879617PMC
January 2014

Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.

Mol Cell Proteomics 2013 Jun 22;12(6):1709-22. Epub 2013 Feb 22.

Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.

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http://dx.doi.org/10.1074/mcp.M112.024919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675825PMC
June 2013

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data.

BMC Bioinformatics 2012 5;13 Suppl 16:S12. Epub 2012 Nov 5.

Department for Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/1471-2105-13-S16-S12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489530PMC
May 2013

Proteomic portrait of human breast cancer progression identifies novel prognostic markers.

Cancer Res 2012 May 13;72(9):2428-39. Epub 2012 Mar 13.

Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.

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http://dx.doi.org/10.1158/0008-5472.CAN-11-3711DOI Listing
May 2012

System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap.

Mol Cell Proteomics 2012 Mar 20;11(3):M111.013722. Epub 2011 Oct 20.

Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.

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http://dx.doi.org/10.1074/mcp.M111.013722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316726PMC
March 2012

Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins.

Mol Cell Proteomics 2012 Mar 25;11(3):M111.014050. Epub 2012 Jan 25.

Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M111.014050
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http://dx.doi.org/10.1074/mcp.M111.014050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316730PMC
March 2012

Analysis of high accuracy, quantitative proteomics data in the MaxQB database.

Mol Cell Proteomics 2012 Mar 2;11(3):M111.014068. Epub 2012 Feb 2.

Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, D-82152 Martinsried, Germany.

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http://dx.doi.org/10.1074/mcp.M111.014068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316731PMC
March 2012

Deep proteome and transcriptome mapping of a human cancer cell line.

Mol Syst Biol 2011 Nov 8;7:548. Epub 2011 Nov 8.

Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.

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http://msb.embopress.org/cgi/doi/10.1038/msb.2011.81
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http://dx.doi.org/10.1038/msb.2011.81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261714PMC
November 2011

Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer.

Mol Cell Proteomics 2011 Sep 3;10(9):M111.011015. Epub 2011 Jun 3.

Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.

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http://dx.doi.org/10.1074/mcp.M111.011015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284220PMC
September 2011

Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation.

Mol Cell Proteomics 2011 Aug 17;10(8):M110.003699. Epub 2011 May 17.

Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

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http://dx.doi.org/10.1074/mcp.M110.003699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149084PMC
August 2011

More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.

J Proteome Res 2011 Apr 28;10(4):1785-93. Epub 2011 Feb 28.

Department for Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany.

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http://pubs.acs.org/doi/abs/10.1021/pr101060v
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http://dx.doi.org/10.1021/pr101060vDOI Listing
April 2011

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics.

Nat Protoc 2011 Feb;6(2):147-57

Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.

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http://www.nature.com/articles/nprot.2010.192
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http://dx.doi.org/10.1038/nprot.2010.192DOI Listing
February 2011

Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation.

J Proteome Res 2010 Dec 26;9(12):6786-94. Epub 2010 Oct 26.

Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, 82152 Martinsried, Germany.

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http://dx.doi.org/10.1021/pr100637qDOI Listing
December 2010

Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation.

Mol Cell Proteomics 2010 Oct 7;9(10):2252-61. Epub 2010 Jul 7.

Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.

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http://dx.doi.org/10.1074/mcp.M110.001537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953918PMC
October 2010

Proteomic changes resulting from gene copy number variations in cancer cells.

PLoS Genet 2010 Sep 2;6(9):e1001090. Epub 2010 Sep 2.

Department for Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Martinsried, Germany.

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http://dx.doi.org/10.1371/journal.pgen.1001090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932691PMC
September 2010

Super-SILAC mix for quantitative proteomics of human tumor tissue.

Nat Methods 2010 May 4;7(5):383-5. Epub 2010 Apr 4.

Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany.

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http://www.nature.com/articles/nmeth.1446
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http://dx.doi.org/10.1038/nmeth.1446DOI Listing
May 2010

PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites.

Genome Biol 2007 ;8(11):R250

Department for Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz, D-82152 Martinsried, Germany.

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http://dx.doi.org/10.1186/gb-2007-8-11-r250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258193PMC
August 2008