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Nicholas M. Riley - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
Mass spectrometry, glycoproteomics, proteomics, PTMs, chemical biology, glycobiology
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64 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Analytical Chemistry. 96: 7976-8010. PMID 38738990 DOI: 10.1021/acs.analchem.3c04497  0.412
2024 Goyette MA, Stevens LE, DePinho CR, Seehawer M, Nishida J, Li Z, Wilde CM, Li R, Qiu X, Pyke AL, Zhao S, Lim K, Tender GS, Northey JJ, Riley NM, et al. Cancer-stromal cell interactions in breast cancer brain metastases induce glycocalyx-mediated resistance to HER2-targeting therapies. Proceedings of the National Academy of Sciences of the United States of America. 121: e2322688121. PMID 38709925 DOI: 10.1073/pnas.2322688121  0.373
2023 Stewart N, Daly J, Drummond-Guy O, Krishnamoorthy V, Stark JC, Riley NM, Williams KC, Bertozzi CR, Wisnovsky S. The glyco-immune checkpoint receptor Siglec-7 interacts with T-cell ligands and regulates T-cell activation. The Journal of Biological Chemistry. 105579. PMID 38141764 DOI: 10.1016/j.jbc.2023.105579  0.406
2023 Delaveris CS, Wang CL, Riley NM, Li S, Kulkarni RU, Bertozzi CR. Microglia Mediate Contact-Independent Neuronal Network Remodeling via Secreted Neuraminidase-3 Associated with Extracellular Vesicles. Acs Central Science. 9: 2108-2114. PMID 38033791 DOI: 10.1021/acscentsci.3c01066  0.329
2023 Ahn G, Riley NM, Kamber RA, Wisnovsky S, Moncayo von Hase S, Bassik MC, Banik SM, Bertozzi CR. Elucidating the cellular determinants of targeted membrane protein degradation by lysosome-targeting chimeras. Science (New York, N.Y.). 382: eadf6249. PMID 37856615 DOI: 10.1126/science.adf6249  0.745
2023 Peltan EL, Riley NM, Flynn RA, Roberts DS, Bertozzi CR. Galectin-3 does not interact with RNA directly. Glycobiology. PMID 37815932 DOI: 10.1093/glycob/cwad076  0.376
2023 Delaveris CS, Wang CL, Riley NM, Li S, Kulkarni RU, Bertozzi CR. Microglia mediate contact-independent neuronal pruning via secreted Neuraminidase-3 associated with extracellular vesicles. Biorxiv : the Preprint Server For Biology. PMID 37662421 DOI: 10.1101/2023.08.21.554214  0.326
2023 Tharp K, Park S, Timblin G, Richards A, Twells N, Riley N, Peltan E, Shon J, Stevenson E, Tsui K, Palomba F, Lefebvre A, Soens R, Ayad N, Hoeve-Scott JT, et al. The microenvironment dictates glycocalyx construction and immune surveillance. Research Square. PMID 37645943 DOI: 10.21203/rs.3.rs-3164966/v1  0.699
2023 Pedram K, Shon DJ, Tender GS, Mantuano NR, Northey JJ, Metcalf KJ, Wisnovsky SP, Riley NM, Forcina GC, Malaker SA, Kuo A, George BM, Miller CL, Casey KM, Vilches-Moure JG, et al. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins. Nature Biotechnology. PMID 37537499 DOI: 10.1038/s41587-023-01840-6  0.715
2023 Wei W, Riley NM, Lyu X, Shen X, Guo J, Raun SH, Zhao M, Moya-Garzon MD, Basu H, Sheng-Hwa Tung A, Li VL, Huang W, Wiggenhorn AL, Svensson KJ, Snyder MP, et al. Organism-wide, cell-type-specific secretome mapping of exercise training in mice. Cell Metabolism. PMID 37141889 DOI: 10.1016/j.cmet.2023.04.011  0.355
2023 Hollander MJ, Malaker SA, Riley NM, Perez I, Abney NM, Gray MA, Maxson JE, Cochran JR, Bertozzi CR. Mutational screens highlight glycosylation as a modulator of colony-stimulating factor 3 receptor (CSF3R) activity. The Journal of Biological Chemistry. 104755. PMID 37116708 DOI: 10.1016/j.jbc.2023.104755  0.688
2023 Smith BAH, Deutzmann A, Correa KM, Delaveris CS, Dhanasekaran R, Dove CG, Sullivan DK, Wisnovsky S, Stark JC, Pluvinage JV, Swaminathan S, Riley NM, Rajan A, Majeti R, Felsher DW, et al. MYC-driven synthesis of Siglec ligands is a glycoimmune checkpoint. Proceedings of the National Academy of Sciences of the United States of America. 120: e2215376120. PMID 36897988 DOI: 10.1073/pnas.2215376120  0.393
2023 Boyce M, Malaker SA, Riley NM, Kohler JJ. The 2022 Nobel prize in chemistry - sweet! Glycobiology. PMID 36892406 DOI: 10.1093/glycob/cwad016  0.678
2022 Riley NM, Wen RM, Bertozzi CR, Brooks JD, Pitteri SJ. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Advances in Cancer Research. 157: 83-121. PMID 36725114 DOI: 10.1016/bs.acr.2022.09.001  0.426
2022 Riley NM, Bertozzi CR. Deciphering -glycoprotease substrate preferences with O-Pair Search. Molecular Omics. 18: 908-922. PMID 36373229 DOI: 10.1039/d2mo00244b  0.452
2022 Pedram K, Laqtom NN, Shon DJ, Di Spiezio A, Riley NM, Saftig P, Abu-Remaileh M, Bertozzi CR. Lysosomal cathepsin D mediates endogenous mucin glycodomain catabolism in mammals. Proceedings of the National Academy of Sciences of the United States of America. 119: e2117105119. PMID 36122205 DOI: 10.1073/pnas.2117105119  0.398
2022 Richards CM, Jabs S, Qiao W, Varanese LD, Schweizer M, Mosen PR, Riley NM, Klüssendorf M, Zengel JR, Flynn RA, Rustagi A, Widen JC, Peters CE, Ooi YS, Xie X, et al. The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection. Science (New York, N.Y.). eabn5648. PMID 36074821 DOI: 10.1126/science.abn5648  0.378
2022 Malaker SA, Riley NM, Shon DJ, Pedram K, Krishnan V, Dorigo O, Bertozzi CR. Revealing the human mucinome. Nature Communications. 13: 3542. PMID 35725833 DOI: 10.1038/s41467-022-31062-4  0.685
2022 Shon DJ, Fernandez D, Riley NM, Ferracane MJ, Bertozzi CR. Structure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences. The Journal of Biological Chemistry. 101917. PMID 35405095 DOI: 10.1016/j.jbc.2022.101917  0.41
2022 Daly J, Sarkar S, Natoni A, Stark JC, Riley NM, Bertozzi CR, Carlsten M, O'Dwyer ME. Targeting hypersialylation in multiple myeloma represents a novel approach to enhance NK cell-mediated tumor responses. Blood Advances. PMID 35294519 DOI: 10.1182/bloodadvances.2021006805  0.377
2021 Wei W, Riley NM, Lyu X, Bertozzi CR, Long JZ. Protocol for cell type-specific labeling, enrichment, and proteomic profiling of plasma proteins in mice. Star Protocols. 2: 101014. PMID 34950890 DOI: 10.1016/j.xpro.2021.101014  0.433
2021 Peters-Clarke TM, Riley NM, Westphall MS, Coon JJ. Practical Effects of Intramolecular Hydrogen Rearrangement in Electron Transfer Dissociation-Based Proteomics. Journal of the American Society For Mass Spectrometry. PMID 34874726 DOI: 10.1021/jasms.1c00284  0.466
2021 Bouchard G, Garcia-Marques FJ, Karacosta LG, Zhang W, Bermudez A, Riley NM, Varma S, Mehl LC, Benson JA, Shrager JB, Bertozzi CR, Pitteri SJ, Giaccia AJ, Plevritis SK. Multi-omics analysis of spatially distinct stromal cells reveals tumor-induced O-glycosylation of the CDK4-pRB axis in fibroblasts at the invasive tumor edge. Cancer Research. PMID 34853070 DOI: 10.1158/0008-5472.CAN-21-1705  0.377
2021 Pluvinage JV, Sun J, Claes C, Flynn RA, Haney MS, Iram T, Meng X, Lindemann R, Riley NM, Danhash E, Chadarevian JP, Tapp E, Gate D, Kondapavulur S, Cobos I, et al. The CD22-IGF2R interaction is a therapeutic target for microglial lysosome dysfunction in Niemann-Pick type C. Science Translational Medicine. 13: eabg2919. PMID 34851695 DOI: 10.1126/scitranslmed.abg2919  0.348
2021 Delaveris CS, Wilk AJ, Riley NM, Stark JC, Yang SS, Rogers AJ, Ranganath T, Nadeau KC, Blish CA, Bertozzi CR. Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19. Acs Central Science. 7: 650-657. PMID 34056095 DOI: 10.1021/acscentsci.0c01669  0.378
2021 Ahn G, Banik SM, Miller CL, Riley NM, Cochran JR, Bertozzi CR. LYTACs that engage the asialoglycoprotein receptor for targeted protein degradation. Nature Chemical Biology. PMID 33767387 DOI: 10.1038/s41589-021-00770-1  0.755
2021 Wisnovsky S, Möckl L, Malaker SA, Pedram K, Hess GT, Riley NM, Gray MA, Smith BAH, Bassik MC, Moerner WE, Bertozzi CR. Genome-wide CRISPR screens reveal a specific ligand for the glycan-binding immune checkpoint receptor Siglec-7. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33495350 DOI: 10.1073/pnas.2015024118  0.695
2021 Delaveris CS, Chiu SH, Riley NM, Bertozzi CR. Modulation of immune cell reactivity with -binding Siglec agonists. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33431669 DOI: 10.1073/pnas.2012408118  0.413
2020 Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Molecular & Cellular Proteomics : McP. 20: 100029. PMID 33583771 DOI: 10.1074/mcp.R120.002277  0.431
2020 Delaveris C, Wilk A, Riley N, Stark J, Yang S, Rogers A, Ranganath T, Nadeau K, Blish C, Bertozzi C. Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19. Chemrxiv : the Preprint Server For Chemistry. PMID 33469569 DOI: 10.26434/chemrxiv.13378148.v1  0.378
2020 Wei W, Riley NM, Yang AC, Kim JT, Terrell SM, Li VL, Garcia-Contreras M, Bertozzi CR, Long JZ. Cell type-selective secretome profiling in vivo. Nature Chemical Biology. PMID 33199915 DOI: 10.1038/s41589-020-00698-y  0.436
2020 Riley NM, Malaker SA, Bertozzi CR. Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis. Analytical Chemistry. PMID 33125225 DOI: 10.1021/acs.analchem.0c02950  0.684
2020 Lu L, Riley NM, Shortreed MR, Bertozzi CR, Smith LM. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nature Methods. PMID 33106676 DOI: 10.1038/s41592-020-00985-5  0.353
2020 Peters-Clarke TM, Schauer KL, Riley NM, Lodge JM, Westphall MS, Coon JJ. Optical Fiber-Enabled Photoactivation of Peptides and Proteins. Analytical Chemistry. PMID 32786458 DOI: 10.1021/Acs.Analchem.0C02087  0.438
2020 Banik SM, Pedram K, Wisnovsky S, Ahn G, Riley NM, Bertozzi CR. Lysosome-targeting chimaeras for degradation of extracellular proteins. Nature. PMID 32728216 DOI: 10.1038/S41586-020-2545-9  0.757
2020 Lodge JM, Schauer KL, Brademan DR, Riley NM, Shishkova E, Westphall MS, Coon JJ. Top-Down Characterization of an Intact Monoclonal Antibody using Activated Ion-Electron Transfer Dissociation. Analytical Chemistry. PMID 32608969 DOI: 10.1021/Acs.Analchem.0C00705  0.506
2020 Riley NM, Malaker SA, Driessen MD, Bertozzi CR. Optimal Dissociation Methods Differ for - and -Glycopeptides. Journal of Proteome Research. PMID 32500713 DOI: 10.1021/Acs.Jproteome.0C00218  0.704
2020 Leung KK, Wilson GM, Kirkemo LL, Riley NM, Coon JJ, Wells JA. Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogenes. Proceedings of the National Academy of Sciences of the United States of America. PMID 32205440 DOI: 10.1073/Pnas.1917947117  0.494
2019 Wagner ER, Myers KS, Riley NM, Coon JJ, Gasch AP. PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production. Plos One. 14: e0212389. PMID 31112537 DOI: 10.1371/Journal.Pone.0212389  0.398
2019 Brademan DR, Riley NM, Kwiecien NW, Coon JJ. Interactive Peptide Spectral Annotator: A Versatile Web-Based Tool for Proteomic Applications. Molecular & Cellular Proteomics : McP. PMID 31088857 DOI: 10.1074/Mcp.Tir118.001209  0.473
2019 Riley NM, Hebert AS, Westphall MS, Coon JJ. Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis. Nature Communications. 10: 1311. PMID 30899004 DOI: 10.1038/S41467-019-09222-W  0.669
2019 Myers KS, Riley NM, MacGilvray ME, Sato TK, McGee M, Heilberger J, Coon JJ, Gasch AP. Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. Plos Genetics. 15: e1008037. PMID 30856163 DOI: 10.1371/Journal.Pgen.1008037  0.406
2018 Rush MJP, Riley NM, Westphall MS, Coon JJ. Top-Down Characterization of Proteins with Intact Disulfide Bonds Using Activated-Ion Electron Transfer Dissociation. Analytical Chemistry. PMID 29949341 DOI: 10.1021/Acs.Analchem.8B01113  0.493
2018 Riley NM, Sikora JW, Seckler HS, Greer JB, Fellers RT, LeDuc RD, Westphall MS, Thomas PM, Kelleher NL, Coon JJ. The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins. Analytical Chemistry. PMID 29924586 DOI: 10.1021/Acs.Analchem.8B01638  0.547
2017 Hebert AS, Thoeing C, Riley NM, Kwiecien NW, Shiskova E, Huguet R, Cardasis HL, Kuehn A, Eliuk S, Zabrouskov V, Westphall MS, McAlister GC, Coon JJ. Improved Precursor Characterization for Data-Dependent Mass Spectrometry. Analytical Chemistry. PMID 29272103 DOI: 10.1021/Acs.Analchem.7B04808  0.766
2017 Riley NM, Coon JJ. The Role of Electron Transfer Dissociation in Modern Proteomics. Analytical Chemistry. PMID 29172454 DOI: 10.1021/Acs.Analchem.7B04810  0.501
2017 Riley NM, Westphall MS, Coon JJ. Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation. Journal of the American Society For Mass Spectrometry. PMID 29027149 DOI: 10.1007/S13361-017-1808-7  0.527
2017 Riley NM, Westphall MS, Coon JJ. Activated Ion Electron Transfer Dissociation Enables Comprehen-sive Top-Down Protein Fragmentation. Journal of Proteome Research. PMID 28608681 DOI: 10.1021/Acs.Jproteome.7B00249  0.496
2017 Leach FE, Riley NM, Westphall MS, Coon JJ, Amster IJ. Negative Electron Transfer Dissociation Sequencing of Increasingly Sulfated Glycosaminoglycan Oligosaccharides on an Orbitrap Mass Spectrometer. Journal of the American Society For Mass Spectrometry. PMID 28589488 DOI: 10.1007/S13361-017-1709-9  0.504
2017 Riley NM, Hebert AS, Dürnberger G, Stanek F, Mechtler K, Westphall MS, Coon JJ. Phosphoproteomics with Activated Ion Electron Transfer Dissociation. Analytical Chemistry. PMID 28383256 DOI: 10.1021/Acs.Analchem.7B00212  0.694
2017 Riley NM, Westphall MS, Hebert AS, Coon JJ. Implementation of Activated Ion Electron Transfer Dissociation on a quadrupole-Orbitrap-linear ion trap hybrid mass spectrometer. Analytical Chemistry. PMID 28383247 DOI: 10.1021/Acs.Analchem.7B00213  0.696
2017 Rush MJ, Riley NM, Westphall MS, Syka JE, Coon JJ. Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation. Journal of the American Society For Mass Spectrometry. PMID 28349437 DOI: 10.1007/S13361-017-1600-8  0.498
2016 Weisenhorn EM, Van't Erve TJ, Riley NM, Hess JR, Raife TJ, Coon JJ. Multi-omics evidence for inheritance of energy pathways in red blood cells. Molecular & Cellular Proteomics : McP. PMID 27777340 DOI: 10.1074/mcp.M116.062349  0.406
2016 Riley NM, Bern M, Westphall MS, Coon JJ. A full-featured search algorithm for negative electron transfer dissociation. Journal of Proteome Research. PMID 27402189 DOI: 10.1021/Acs.Jproteome.6B00319  0.508
2016 McIlwain SJ, Peris D, Sardi M, Moskvin OV, Zhan F, Myers KS, Riley NM, Buzzell A, Parreiras LS, Ong IM, Landick R, Coon JJ, Gasch AP, Sato TK, Hittinger CT. Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research. G3 (Bethesda, Md.). 6: 1757-66. PMID 27172212 DOI: 10.1534/G3.116.029389  0.376
2016 Riley NM, Hebert AS, Coon JJ. Proteomics Moves into the Fast Lane. Cell Systems. 2: 142-143. PMID 27135360 DOI: 10.1016/J.Cels.2016.03.002  0.676
2016 Horton JL, Martin OJ, Lai L, Riley NM, Richards AL, Vega RB, Leone TC, Pagliarini DJ, Muoio DM, Bedi KC, Margulies KB, Coon JJ, Kelly DP. Mitochondrial protein hyperacetylation in the failing heart. Jci Insight. 2. PMID 26998524 DOI: 10.1172/Jci.Insight.84897  0.395
2015 Riley NM, Mullen C, Weisbrod CR, Sharma S, Senko MW, Zabrouskov V, Westphall MS, Syka JE, Coon JJ. Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation. Journal of the American Society For Mass Spectrometry. PMID 26589699 DOI: 10.1007/S13361-015-1306-8  0.512
2015 Riley NM, Coon JJ. Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling. Analytical Chemistry. PMID 26539879 DOI: 10.1021/Acs.Analchem.5B04123  0.392
2015 Riley NM, Rush MJ, Rose CM, Richards AL, Kwiecien NW, Bailey DJ, Hebert AS, Westphall MS, Coon JJ. The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD). Molecular & Cellular Proteomics : McP. 14: 2644-60. PMID 26193884 DOI: 10.1074/Mcp.M115.049726  0.75
2015 Rose CM, Rush MJ, Riley NM, Merrill AE, Kwiecien NW, Holden DD, Mullen C, Westphall MS, Coon JJ. A Calibration Routine for Efficient ETD in Large-Scale Proteomics. Journal of the American Society For Mass Spectrometry. PMID 26111518 DOI: 10.1007/S13361-015-1183-1  0.461
2015 Riley NM, Westphall MS, Coon JJ. Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins. Analytical Chemistry. PMID 26067513 DOI: 10.1021/Acs.Analchem.5B00881  0.491
2015 Zhao Y, Riley NM, Sun L, Hebert AS, Yan X, Westphall MS, Rush MJ, Zhu G, Champion MM, Mba Medie F, Champion PA, Coon JJ, Dovichi NJ. Coupling capillary zone electrophoresis with electron transfer dissociation and activated ion electron transfer dissociation for top-down proteomics. Analytical Chemistry. 87: 5422-9. PMID 25893372 DOI: 10.1021/Acs.Analchem.5B00883  0.705
2014 Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, Merrill AE, Smith LM, Hebert AS, Westphall MS, Pagliarini DJ, Garcia BA, Coon JJ. Neutron-encoded mass signatures for quantitative top-down proteomics. Analytical Chemistry. 86: 2314-9. PMID 24475910 DOI: 10.1021/Ac403579S  0.748
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