Karl R Clauser

Karl R Clauser

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Karl R Clauser

Karl R Clauser

Publications by authors named "Karl R Clauser"

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MatrisomeDB: the ECM-protein knowledge database.

Nucleic Acids Res 2019 Oct 5. Epub 2019 Oct 5.

Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA.

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http://dx.doi.org/10.1093/nar/gkz849DOI Listing
October 2019

Proteomic analyses of ECM during pancreatic ductal adenocarcinoma progression reveal different contributions by tumor and stromal cells.

Proc Natl Acad Sci U S A 2019 Sep 4;116(39):19609-19618. Epub 2019 Sep 4.

Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139;

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http://dx.doi.org/10.1073/pnas.1908626116DOI Listing
September 2019

TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach.

Mol Cell Proteomics 2019 Jul 9;18(7):1468-1478. Epub 2019 Apr 9.

From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany;

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http://www.mcponline.org/lookup/doi/10.1074/mcp.TIR119.00138
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http://dx.doi.org/10.1074/mcp.TIR119.001385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6601210PMC
July 2019

Site-specific identification and quantitation of endogenous SUMO modifications under native conditions.

Nat Commun 2017 10 27;8(1):1171. Epub 2017 Oct 27.

Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0378, USA.

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http://dx.doi.org/10.1038/s41467-017-01271-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5660086PMC
October 2017

Methods, Tools and Current Perspectives in Proteogenomics.

Mol Cell Proteomics 2017 06 29;16(6):959-981. Epub 2017 Apr 29.

§The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;

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http://dx.doi.org/10.1074/mcp.MR117.000024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5461547PMC
June 2017

Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast.

Mol Cell Proteomics 2017 04 25;16(4):512-523. Epub 2017 Jan 25.

From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.

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http://dx.doi.org/10.1074/mcp.M116.063818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383775PMC
April 2017

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction.

Immunity 2017 02;46(2):315-326

Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA; Harvard Medical School, Boston, MA, 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2017.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405381PMC
February 2017

Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression.

Sci Rep 2017 01 10;7:40495. Epub 2017 Jan 10.

David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, U.S.A.

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http://dx.doi.org/10.1038/srep40495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223159PMC
January 2017

The extracellular matrix: Tools and insights for the "omics" era.

Matrix Biol 2016 Jan 8;49:10-24. Epub 2015 Jul 8.

David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0945053X150012
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http://dx.doi.org/10.1016/j.matbio.2015.06.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013529PMC
January 2016

MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins.

Nucleic Acids Res 2016 Jan 7;44(D1):D1251-7. Epub 2015 Oct 7.

Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA Broad Institute, Cambridge, MA 02141, USA Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA

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http://dx.doi.org/10.1093/nar/gkv1003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702768PMC
January 2016

Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis.

J Vis Exp 2015 Jul 23(101):e53057. Epub 2015 Jul 23.

Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology.

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http://dx.doi.org/10.3791/53057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4545199PMC
July 2015

A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages.

Nat Cell Biol 2014 Nov 28;16(11):1105-17. Epub 2014 Sep 28.

1] Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA [2] MIT Ludwig Center for Molecular Oncology, Cambridge, Massachusetts 02139, USA [3] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/ncb3041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296514PMC
November 2014

Clawing through evolution: toxin diversification and convergence in the ancient lineage Chilopoda (centipedes).

Mol Biol Evol 2014 Aug 20;31(8):2124-48. Epub 2014 May 20.

Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, AustraliaVenom Evolution Laboratory, School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Australia

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http://dx.doi.org/10.1093/molbev/msu162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104317PMC
August 2014

Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver.

BMC Cancer 2014 Jul 18;14:518. Epub 2014 Jul 18.

David H, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://bmccancer.biomedcentral.com/articles/10.1186/1471-240
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http://dx.doi.org/10.1186/1471-2407-14-518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223627PMC
July 2014

Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters.

Elife 2014 Mar 11;3:e01308. Epub 2014 Mar 11.

David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944437PMC
http://dx.doi.org/10.7554/eLife.01308DOI Listing
March 2014

Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides.

J Proteome Res 2013 Jun 30;12(6):2846-57. Epub 2013 May 30.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.

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http://dx.doi.org/10.1021/pr400173dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4591044PMC
June 2013

Shotgun protein sequencing with meta-contig assembly.

Mol Cell Proteomics 2012 Oct 13;11(10):1084-96. Epub 2012 Jul 13.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1074/mcp.M111.015768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494147PMC
October 2012

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.

Mol Cell Proteomics 2012 Jun 30;11(6):M111.014423. Epub 2011 Dec 30.

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1074/mcp.M111.014423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433912PMC
June 2012

Modification site localization scoring: strategies and performance.

Mol Cell Proteomics 2012 May 11;11(5):3-14. Epub 2012 Feb 11.

University of California San Francisco, 600 16th Street, Genentech Hall N-474A, San Francisco, California 94158, USA.

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http://dx.doi.org/10.1074/mcp.R111.015305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418845PMC
May 2012

Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.

Mol Cell Proteomics 2012 May 14;11(5):148-59. Epub 2012 Apr 14.

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1074/mcp.M111.016857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418844PMC
May 2012

The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.

Mol Cell Proteomics 2012 Apr 9;11(4):M111.014647. Epub 2011 Dec 9.

Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1074/mcp.M111.014647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322572PMC
April 2012

Cdk5 is required for memory function and hippocampal plasticity via the cAMP signaling pathway.

PLoS One 2011 30;6(9):e25735. Epub 2011 Sep 30.

Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025735PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184170PMC
March 2012

A face in the crowd: recognizing peptides through database search.

Mol Cell Proteomics 2011 Nov 29;10(11):R111.009522. Epub 2011 Aug 29.

University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1074/mcp.R111.009522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3226415PMC
November 2011

Optimizing performance of glycopeptide capture for plasma proteomics.

J Proteome Res 2010 Apr;9(4):1706-15

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1021/pr900845mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855884PMC
April 2010

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

Mol Cell Proteomics 2007 Jul 19;6(7):1123-34. Epub 2007 Apr 19.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1074/mcp.M700001-MCP200DOI Listing
July 2007

Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate.

EMBO J 2007 May 19;26(9):2262-73. Epub 2007 Apr 19.

Department of Biology, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1038/sj.emboj.7601683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1864981PMC
May 2007