Publications by authors named "Michael MacCoss"

100Publications

Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment.

Anal Chem 2020 09 12;92(17):11809-11817. Epub 2020 Aug 12.

Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States.

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http://dx.doi.org/10.1021/acs.analchem.0c02075DOI Listing
September 2020

RNA aptamer capture of macromolecular complexes for mass spectrometry analysis.

Nucleic Acids Res 2020 09;48(15):e90

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.

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http://dx.doi.org/10.1093/nar/gkaa542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7470977PMC
September 2020

Audit logs to enforce document integrity in Skyline and Panorama.

Bioinformatics 2020 Aug;36(15):4366-4368

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

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http://dx.doi.org/10.1093/bioinformatics/btaa547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7520049PMC
August 2020

Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries.

Mol Cell Proteomics 2020 07 20;19(7):1088-1103. Epub 2020 Apr 20.

Institute for Systems Biology, Seattle, Washington, USA

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http://dx.doi.org/10.1074/mcp.P119.001913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338082PMC
July 2020

Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins.

Cell Rep 2020 02;30(8):2463-2471.e5

Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA; University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.01.096DOI Listing
February 2020

Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics.

J Proteome Res 2020 03 24;19(3):1147-1153. Epub 2020 Feb 24.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.

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http://dx.doi.org/10.1021/acs.jproteome.9b00666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7175947PMC
March 2020

Peptidomics Approaches for the Identification of Bioactive Molecules from .

J Proteome Res 2020 04 2;19(4):1392-1408. Epub 2020 Mar 2.

Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.

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http://dx.doi.org/10.1021/acs.jproteome.9b00509DOI Listing
April 2020

Assessing Protein Sequence Database Suitability Using Sequencing.

Mol Cell Proteomics 2020 01 15;19(1):198-208. Epub 2019 Nov 15.

Department of Genome Sciences, University of Washington, Seattle, Washington.

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http://dx.doi.org/10.1074/mcp.TIR119.001752DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944239PMC
January 2020

Kinetochore-associated Stu2 promotes chromosome biorientation in vivo.

PLoS Genet 2019 10 4;15(10):e1008423. Epub 2019 Oct 4.

Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6795502PMC
October 2019

Thesaurus: quantifying phosphopeptide positional isomers.

Nat Methods 2019 08 29;16(8):703-706. Epub 2019 Jul 29.

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

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http://dx.doi.org/10.1038/s41592-019-0498-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012383PMC
August 2019

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.

Anal Chem 2019 06 22;91(11):6953-6961. Epub 2019 May 22.

Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany.

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http://dx.doi.org/10.1021/acs.analchem.9b00658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6625963PMC
June 2019

Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.

J Am Soc Mass Spectrom 2019 Apr 22;30(4):669-684. Epub 2019 Jan 22.

Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA, USA.

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http://dx.doi.org/10.1007/s13361-018-2122-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445824PMC
April 2019

The Interaction Dynamics of Two Potato Leafroll Virus Movement Proteins Affects Their Localization to the Outer Membranes of Mitochondria and Plastids.

Viruses 2018 10 26;10(11). Epub 2018 Oct 26.

United States Department of Agriculture, Biological Integrated Pest Management Research Unit, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, USA.

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http://www.mdpi.com/1999-4915/10/11/585
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http://dx.doi.org/10.3390/v10110585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265731PMC
October 2018

Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles.

PLoS Genet 2018 09 26;14(9):e1007694. Epub 2018 Sep 26.

Department of Genome Sciences, University of Washington, Seattle, WA, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175534PMC
September 2018

Candidatus Liberibacter asiaticus Minimally Alters Expression of Immunity and Metabolism Proteins in Hemolymph of Diaphorina citri, the Insect Vector of Huanglongbing.

J Proteome Res 2018 09 27;17(9):2995-3011. Epub 2018 Aug 27.

Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Sciences, Cornell University , Ithaca , New York 14853 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00183DOI Listing
September 2018

Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions.

J Am Soc Mass Spectrom 2018 Nov 25;29(11):2182-2188. Epub 2018 Jul 25.

Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd. MSIN K8-98, P.O. Box 999, Richland, WA, 99352, USA.

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http://dx.doi.org/10.1007/s13361-018-2028-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191345PMC
November 2018

Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems.

BMC Genomics 2018 Jun 22;19(1):488. Epub 2018 Jun 22.

Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA.

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http://dx.doi.org/10.1186/s12864-018-4872-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6014011PMC
June 2018

Novel phosphorylation states of the yeast spindle pole body.

Biol Open 2018 Oct 8;7(10). Epub 2018 Oct 8.

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA

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http://dx.doi.org/10.1242/bio.033647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6215409PMC
October 2018

Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore-microtubule attachments.

Proc Natl Acad Sci U S A 2018 03 27;115(11):2740-2745. Epub 2018 Feb 27.

Department of Biochemistry, University of Washington, Seattle, WA 98195;

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http://dx.doi.org/10.1073/pnas.1718553115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5856539PMC
March 2018

Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.

Mol Cell Proteomics 2018 06 27;17(6):1239-1244. Epub 2018 Feb 27.

From the ‡University of Washington, Seattle, Washington 98195;

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http://dx.doi.org/10.1074/mcp.RA117.000543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986241PMC
June 2018

Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex.

Proc Natl Acad Sci U S A 2018 02 31;115(7):E1409-E1418. Epub 2018 Jan 31.

Institute of Molecular Biology, University of Oregon, Eugene, OR 97403;

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http://dx.doi.org/10.1073/pnas.1716622115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5816175PMC
February 2018

Evaluation of a Bead-Free Coimmunoprecipitation Technique for Identification of Virus-Host Protein Interactions Using High-Resolution Mass Spectrometry.

J Biomol Tech 2017 Sep 24;28(3):111-121. Epub 2017 Jul 24.

U.S. Department of Agriculture, Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.7171/jbt.17-2803-002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524270PMC
September 2017

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data.

Nat Methods 2017 Sep 7;14(9):903-908. Epub 2017 Aug 7.

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

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http://dx.doi.org/10.1038/nmeth.4390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578911PMC
September 2017

A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brain.

J Proteomics 2017 08 17;166:127-137. Epub 2017 Jul 17.

Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.

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http://dx.doi.org/10.1016/j.jprot.2017.07.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5722633PMC
August 2017

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.

Mass Spectrom Rev 2020 05 9;39(3):229-244. Epub 2017 Jul 9.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington.

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http://dx.doi.org/10.1002/mas.21540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799042PMC
May 2020

Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein.

J Comp Neurol 2017 Oct 24;525(15):3341-3359. Epub 2017 Jul 24.

Department of Biomedical Sciences, Florida State University, Tallahassee, Florida.

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http://dx.doi.org/10.1002/cne.24281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5564178PMC
October 2017

Proteomics Analysis Identifies Orthologs of Human Chitinase-Like Proteins as Inducers of Tube Morphogenesis Defects in .

Genetics 2017 06 12;206(2):973-984. Epub 2017 Apr 12.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065

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http://dx.doi.org/10.1534/genetics.116.199323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499198PMC
June 2017

Automated Trapping Column Exchanger for High-Throughput Nanoflow Liquid Chromatography.

Anal Chem 2017 02 30;89(4):2383-2389. Epub 2017 Jan 30.

Department of Genome Sciences, University of Washington School of Medicine , Box 355065, Seattle, Washington 98195-5065, United States.

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http://dx.doi.org/10.1021/acs.analchem.6b04227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798597PMC
February 2017

The Ndc80 complex bridges two Dam1 complex rings.

Elife 2017 02 13;6. Epub 2017 Feb 13.

Department of Biochemistry, University of Washington, Seattle, United States.

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http://dx.doi.org/10.7554/eLife.21069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5354518PMC
February 2017

Model System-Guided Protein Interaction Mapping for Virus Isolated from Phloem Tissue.

J Proteome Res 2016 12 16;15(12):4601-4611. Epub 2016 Nov 16.

Agricultural Research Service, USDA , Ithaca, New York 14853, United States.

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http://dx.doi.org/10.1021/acs.jproteome.6b00715DOI Listing
December 2016

An Automated Pipeline to Monitor System Performance in Liquid Chromatography-Tandem Mass Spectrometry Proteomic Experiments.

J Proteome Res 2016 12 4;15(12):4763-4769. Epub 2016 Oct 4.

Department of Genome Sciences, University of Washington , Seattle, Washington 98195, United States.

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http://dx.doi.org/10.1021/acs.jproteome.6b00744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5406750PMC
December 2016

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0.

J Am Soc Mass Spectrom 2016 11 29;27(11):1719-1727. Epub 2016 Aug 29.

Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Box 1031, 17121, Solna, Sweden.

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http://dx.doi.org/10.1007/s13361-016-1460-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5059416PMC
November 2016

Staphylococcus aureus Protein A Mediates Interspecies Interactions at the Cell Surface of Pseudomonas aeruginosa.

mBio 2016 05 24;7(3). Epub 2016 May 24.

Department of Microbiology, University of Washington, Seattle, Washington, USA Department of Pediatrics, University of Washington, Seattle, Washington, USA

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http://dx.doi.org/10.1128/mBio.00538-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895107PMC
May 2016

The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles.

PLoS Genet 2016 05 18;12(5):e1006074. Epub 2016 May 18.

Department of Biochemistry, University of Washington, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1006074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4871572PMC
May 2016

Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure.

J Struct Biol 2016 06 8;194(3):303-10. Epub 2016 Mar 8.

Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2016.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866596PMC
June 2016

Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards.

Methods Mol Biol 2016 ;1410:207-21

Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA.

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http://dx.doi.org/10.1007/978-1-4939-3524-6_12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5614897PMC
December 2016

A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva.

Proteomics 2016 Jan 15;16(1):159-73. Epub 2015 Dec 15.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.

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http://dx.doi.org/10.1002/pmic.201500224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703492PMC
January 2016

A deeper look into Comet--implementation and features.

J Am Soc Mass Spectrom 2015 Nov 27;26(11):1865-74. Epub 2015 Jun 27.

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

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http://dx.doi.org/10.1007/s13361-015-1179-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4607604PMC
November 2015

Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments.

Mol Cell Proteomics 2015 Sep 22;14(9):2331-40. Epub 2015 Jun 22.

From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington 98195;

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http://dx.doi.org/10.1074/mcp.M115.051300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4563719PMC
September 2015

Multiplexed peptide analysis using data-independent acquisition and Skyline.

Nat Protoc 2015 Jun 21;10(6):887-903. Epub 2015 May 21.

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

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http://dx.doi.org/10.1038/nprot.2015.055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127711PMC
June 2015

MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments.

Mol Cell Proteomics 2015 Sep 17;14(9):2405-19. Epub 2015 May 17.

From the ‡Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, California 94945; **Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143

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http://dx.doi.org/10.1074/mcp.O115.048181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4563724PMC
September 2015

Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments.

FASEB J 2015 Aug 14;29(8):3582-92. Epub 2015 May 14.

*Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA

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http://dx.doi.org/10.1096/fj.15-272666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511201PMC
August 2015

Kojak: efficient analysis of chemically cross-linked protein complexes.

J Proteome Res 2015 May 15;14(5):2190-8. Epub 2015 Apr 15.

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

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http://dx.doi.org/10.1021/pr501321hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428575PMC
May 2015

Insights into the polerovirus-plant interactome revealed by coimmunoprecipitation and mass spectrometry.

Mol Plant Microbe Interact 2015 Apr;28(4):467-81

1 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A.;

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http://dx.doi.org/10.1094/MPMI-11-14-0363-RDOI Listing
April 2015

Human valacyclovir hydrolase/biphenyl hydrolase-like protein is a highly efficient homocysteine thiolactonase.

PLoS One 2014 15;9(10):e110054. Epub 2014 Oct 15.

Department of Medicine (Division of Medical Genetics), University of Washington, Seattle, Washington, United States; Department of Genome Sciences, University of Washington, Seattle, Washington, United States.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110054PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198189PMC
June 2015

Substrate trapping proteomics reveals targets of the βTrCP2/FBXW11 ubiquitin ligase.

Mol Cell Biol 2015 Jan 20;35(1):167-81. Epub 2014 Oct 20.

Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

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http://dx.doi.org/10.1128/MCB.00857-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295375PMC
January 2015

Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics.

J Am Soc Mass Spectrom 2014 Dec 27;25(12):2048-59. Epub 2014 Sep 27.

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

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http://dx.doi.org/10.1007/s13361-014-0981-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417682PMC
December 2014

Crux: rapid open source protein tandem mass spectrometry analysis.

J Proteome Res 2014 Oct 9;13(10):4488-91. Epub 2014 Sep 9.

Great Lakes Bioenergy Research Center, University of Wisconsin-Madison , 1552 University Avenue, Madison, Wisconsin 53726, United States.

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http://dx.doi.org/10.1021/pr500741yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184452PMC
October 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014