Publications by authors named "Steven P Gygi"

100Publications

The insulin receptor adaptor IRS2 is an APC/C substrate that promotes cell cycle protein expression and a robust spindle assembly checkpoint.

Mol Cell Proteomics 2020 Jun 18. Epub 2020 Jun 18.

Cell Biology, Harvard Medical School, United States

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http://dx.doi.org/10.1074/mcp.RA120.002069DOI Listing
June 2020

Homogeneous Oligomers of Pro-apoptotic BAX Reveal Structural Determinants of Mitochondrial Membrane Permeabilization.

Mol Cell 2020 Jul 12;79(1):68-83.e7. Epub 2020 Jun 12.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2020.05.029DOI Listing
July 2020

A conserved RNA degradation complex required for spreading and epigenetic inheritance of heterochromatin.

Elife 2020 06 3;9. Epub 2020 Jun 3.

Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, United States.

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http://dx.doi.org/10.7554/eLife.54341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7269676PMC
June 2020

Sample multiplexing for targeted pathway proteomics in aging mice.

Proc Natl Acad Sci U S A 2020 05 24;117(18):9723-9732. Epub 2020 Apr 24.

Department of Cell Biology, Harvard Medical School, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1919410117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211924PMC
May 2020

Selection of Heating Temperatures Improves the Sensitivity of the Proteome Integral Solubility Alteration Assay.

J Proteome Res 2020 May 13;19(5):2159-2166. Epub 2020 Apr 13.

Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/acs.jproteome.0c00063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7294736PMC
May 2020

A Triple Knockout Isobaric-Labeling Quality Control Platform with an Integrated Online Database Search.

J Am Soc Mass Spectrom 2020 Jul 27;31(7):1344-1349. Epub 2020 Mar 27.

Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/jasms.0c00029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7332369PMC
July 2020

A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging.

Cell 2020 03 27;180(5):968-983.e24. Epub 2020 Feb 27.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.02.012DOI Listing
March 2020

ELAC1 Repairs tRNAs Cleaved during Ribosome-Associated Quality Control.

Cell Rep 2020 Feb;30(7):2106-2114.e5

Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.01.082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7067598PMC
February 2020

Parallel Notched Gas-Phase Enrichment for Improved Proteome Identification and Quantification with Fast Spectral Acquisition Rates.

J Proteome Res 2020 Jul 17;19(7):2750-2757. Epub 2020 Feb 17.

Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/acs.jproteome.9b00715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334078PMC
July 2020

High-density chemical cross-linking for modeling protein interactions.

Proc Natl Acad Sci U S A 2020 01 17;117(1):93-102. Epub 2019 Dec 17.

Department of Cell Biology, Harvard Medical School, Boston, MA 02115

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http://dx.doi.org/10.1073/pnas.1902931116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6955236PMC
January 2020

Optimized Workflow for Multiplexed Phosphorylation Analysis of TMT-Labeled Peptides Using High-Field Asymmetric Waveform Ion Mobility Spectrometry.

J Proteome Res 2020 01 18;19(1):554-560. Epub 2019 Dec 18.

Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.9b00759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6996458PMC
January 2020

Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance.

Mol Cell 2020 01 26;77(1):51-66.e8. Epub 2019 Nov 26.

Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.10.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224636PMC
January 2020

Thiol-based direct threat sensing by the stress-activated protein kinase Hog1.

Sci Signal 2019 11 26;12(609). Epub 2019 Nov 26.

Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1126/scisignal.aaw4956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7263400PMC
November 2019

Multiplexed proteome profiling of carbon source perturbations in two yeast species with SL-SP3-TMT.

J Proteomics 2020 01 15;210:103531. Epub 2019 Oct 15.

Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.jprot.2019.103531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889822PMC
January 2020

The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.

Cell Stem Cell 2019 11 3;25(5):622-638.e13. Epub 2019 Oct 3.

Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2019.08.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7247364PMC
November 2019

Evaluating False Transfer Rates from the Match-between-Runs Algorithm with a Two-Proteome Model.

J Proteome Res 2019 11 2;18(11):4020-4026. Epub 2019 Oct 2.

Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.9b00492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7346880PMC
November 2019

Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation.

Cell Syst 2019 09 11;9(3):258-270.e6. Epub 2019 Sep 11.

Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Digestive Disease Center, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6816257PMC
September 2019

mTMT: An Alternative, Nonisobaric, Tandem Mass Tag Allowing for Precursor-Based Quantification.

Anal Chem 2019 10 20;91(19):12167-12172. Epub 2019 Sep 20.

Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.

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http://dx.doi.org/10.1021/acs.analchem.9b03162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7294932PMC
October 2019

PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression.

Mol Cell 2019 08 3;75(3):620-630.e9. Epub 2019 Jul 3.

Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765193040
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http://dx.doi.org/10.1016/j.molcel.2019.05.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688901PMC
August 2019

Epstein-Barr-Virus-Induced One-Carbon Metabolism Drives B Cell Transformation.

Cell Metab 2019 09 27;30(3):539-555.e11. Epub 2019 Jun 27.

Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2019.06.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6720460PMC
September 2019

Activation of PASK by mTORC1 is required for the onset of the terminal differentiation program.

Proc Natl Acad Sci U S A 2019 05 9;116(21):10382-10391. Epub 2019 May 9.

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132;

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http://dx.doi.org/10.1073/pnas.1804013116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6534978PMC
May 2019

Dual Sensing of Physiologic pH and Calcium by EFCAB9 Regulates Sperm Motility.

Cell 2019 05 2;177(6):1480-1494.e19. Epub 2019 May 2.

Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA; Department of Gynecology and Obstetrics, Yale School of Medicine, New Haven, CT 06510, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193034
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http://dx.doi.org/10.1016/j.cell.2019.03.047DOI Listing
May 2019

Targeted Degradation of Glucose Transporters Protects against Arsenic Toxicity.

Mol Cell Biol 2019 05 30;39(10). Epub 2019 Apr 30.

Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA

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http://dx.doi.org/10.1128/MCB.00559-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497993PMC
May 2019

Regulation of MicroRNA Machinery and Development by Interspecies S-Nitrosylation.

Cell 2019 02;176(5):1014-1025.e12

Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.01.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6559381PMC
February 2019

TomahaqCompanion: A Tool for the Creation and Analysis of Isobaric Label Based Multiplexed Targeted Assays.

J Proteome Res 2019 02 12;18(2):594-605. Epub 2018 Dec 12.

Department of Microchemistry, Proteomics and Lipidomics , Genentech , South San Francisco , California 94080 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315617PMC
February 2019

TKO6: A Peptide Standard To Assess Interference for Unit-Resolved Isobaric Labeling Platforms.

J Proteome Res 2019 01 6;18(1):565-570. Epub 2018 Dec 6.

Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00902
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http://dx.doi.org/10.1021/acs.jproteome.8b00902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465125PMC
January 2019

The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments.

Ann Appl Stat 2018 Dec 13;12(4):2075-2095. Epub 2018 Nov 13.

Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, CB 7420, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics University of North Carolina at Chapel Hill 120 Mason Farm Rd, Campus Box 7260 Chapel Hill, NC 27599 USA.

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https://projecteuclid.org/euclid.aoas/1542078037
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http://dx.doi.org/10.1214/18-AOAS1144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249692PMC
December 2018

Web-Based Search Tool for Visualizing Instrument Performance Using the Triple Knockout (TKO) Proteome Standard.

J Proteome Res 2019 02 27;18(2):687-693. Epub 2018 Nov 27.

Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6358484PMC
February 2019

Proteomic profiling of yeast heterochromatin connects direct physical and genetic interactions.

Curr Genet 2019 Apr 12;65(2):495-505. Epub 2018 Oct 12.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 E. 17th Ave, Aurora, CO, 80045, USA.

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http://dx.doi.org/10.1007/s00294-018-0889-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421107PMC
April 2019

The NAD Salvage Pathway Supports PHGDH-Driven Serine Biosynthesis.

Cell Rep 2018 08;24(9):2381-2391.e5

Department of Pathology, Dalhousie University, Halifax, NS, Canada; Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada; Centre for Innovative and Collaborative Health Services Research, IWK Health Centre, Halifax, NS, Canada; Department of Biology, Dalhousie University, Halifax, NS, Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183121
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http://dx.doi.org/10.1016/j.celrep.2018.07.086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402325PMC
August 2018

ACP Acylation Is an Acetyl-CoA-Dependent Modification Required for Electron Transport Chain Assembly.

Mol Cell 2018 08;71(4):567-580.e4

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765183051
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http://dx.doi.org/10.1016/j.molcel.2018.06.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104058PMC
August 2018

Role of Selenof as a Gatekeeper of Secreted Disulfide-Rich Glycoproteins.

Cell Rep 2018 05;23(5):1387-1398

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.04.009DOI Listing
May 2018

Characterization of Plasmodium falciparum Atypical Kinase PfPK7 Dependent Phosphoproteome.

J Proteome Res 2018 06 30;17(6):2112-2123. Epub 2018 Apr 30.

Division of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences , University of Central Florida , Orlando , Florida 32826 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00062DOI Listing
June 2018

An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies.

J Am Soc Mass Spectrom 2018 07 18;29(7):1505-1511. Epub 2018 Apr 18.

Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.

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http://dx.doi.org/10.1007/s13361-018-1946-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6004253PMC
July 2018

Isobaric Tag-Based Protein Profiling of a Nicotine-Treated Alpha7 Nicotinic Receptor-Null Human Haploid Cell Line.

Proteomics 2018 06 15;18(11):e1700475. Epub 2018 May 15.

Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1002/pmic.201700475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990481PMC
June 2018

Proteome-Wide Evaluation of Two Common Protein Quantification Methods.

J Proteome Res 2018 05 19;17(5):1934-1942. Epub 2018 Apr 19.

Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984592PMC
May 2018

Filter-Based Protein Digestion (FPD): A Detergent-Free and Scaffold-Based Strategy for TMT Workflows.

J Proteome Res 2018 03 13;17(3):1227-1234. Epub 2018 Feb 13.

Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/acs.jproteome.7b00840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984590PMC
March 2018

OTUD4 Is a Phospho-Activated K63 Deubiquitinase that Regulates MyD88-Dependent Signaling.

Mol Cell 2018 02;69(3):505-516.e5

Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6819006PMC
February 2018

Loss of the deubiquitinase USP36 destabilizes the RNA helicase DHX33 and causes preimplantation lethality in mice.

J Biol Chem 2018 02 22;293(6):2183-2194. Epub 2017 Dec 22.

From the Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006-Oviedo, Spain,

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http://www.jbc.org/lookup/doi/10.1074/jbc.M117.788430
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http://dx.doi.org/10.1074/jbc.M117.788430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808777PMC
February 2018

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling.

Cell 2018 01 14;172(1-2):106-120.e21. Epub 2017 Dec 14.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.11.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766360PMC
January 2018

Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags.

J Proteome Res 2018 01 15;17(1):590-599. Epub 2017 Dec 15.

Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/acs.jproteome.7b00699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5806995PMC
January 2018

Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the egg.

Proc Natl Acad Sci U S A 2017 12 28;114(50):E10838-E10847. Epub 2017 Nov 28.

Department of Systems Biology, Harvard Medical School, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1709207114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5740657PMC
December 2017

The skeletal phenotype of achondrogenesis type 1A is caused exclusively by cartilage defects.

Development 2018 01 8;145(1). Epub 2018 Jan 8.

Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA 02115, USA

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http://dev.biologists.org/lookup/doi/10.1242/dev.156588
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http://dx.doi.org/10.1242/dev.156588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5825869PMC
January 2018

SAMTOR is an -adenosylmethionine sensor for the mTORC1 pathway.

Science 2017 11;358(6364):813-818

Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1126/science.aao3265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5747364PMC
November 2017

BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data.

J Proteome Res 2018 01 31;17(1):722-726. Epub 2017 Oct 31.

Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/acs.jproteome.7b00572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7029486PMC
January 2018

Improved Method for Determining Absolute Phosphorylation Stoichiometry Using Bayesian Statistics and Isobaric Labeling.

J Proteome Res 2017 11;16(11):4217-4226

Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/acs.jproteome.7b00571DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301010PMC
November 2017