Publications and Presentations
Summary: 39 total publications (19 first and co-first author), 34 oral presentations, 30 poster presentations
SELECTED FIRSt and Co-First Author Publications
First and Co-First Author Publications CONTINUED
Riley NM, Malaker SA, Bertozzi CR. Electron-based dissociation is needed for O-glycopeptides derived from OpeRATOR proteolysis. Analytical Chemistry, 2020, 92(22): 14878-14884. doi: 10.1021/acs.analchem.0c02950
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, 2018, 90(14): 8553-8560. doi: 10.1021/acs.analchem.8b01638.
Riley NM, Coon JJ. The Role of Electron Transfer Dissociation in Modern Proteomics. Analytical Chemistry, 2018, 90(1): 40-64. doi: 10.1021/acs.analchem.7b04810.
Riley NM, Westphall MS, Coon JJ. Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation. Journal of the American Society of Mass Spectrometry, 2018, 29(1): 140-149. doi: 10.1007/s13361-017-1808-7. **Selected in 2020 as high impact research by JASMS Editor-in-Chief**
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, 2017, 89(12): 6358-6366. doi: 10.1021/acs.analchem.7b00213. **featured on the journal cover** **Highlighted on Genome Web**
Riley NM, Hebert AS, Durnberger G, Stanek F, Mechtler K, Westphall MS, Coon, JJ. Phosphoproteomics with Activated Ion Electron Transfer Dissociation. Analytical Chemistry, 2017, 89(12): 6367-6376. doi: 10.1021/acs.analchem.7b00212. **featured on the journal cover** **Highlighted on Genome Web**
Riley NM, Bern M, Westphall MS, Coon JJ. A Full-Featured Search Algorithm for Negative Electron Transfer Dissociation. Journal of Proteome Research, 2016, 15(8): 2768-2776. doi: 10.1021/acs.jproteome.6b00319.
Riley NM, Hebert AS, Coon JJ. Proteomics Moves into the Fast Lane. Cell Systems, 2016, 2(3): 142-143. doi: 10.1016/j.cels.2016.03.002.
Riley NM, Mullen C, Weisbrod CR, Sharma S, Senko MW, Westphall MS, Syka JEP, Coon JJ. Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation. Journal of the American Society of Mass Spectrometry, 2016, 27(3): 520-531. doi: 10.1007/s13361-015-1306-8.
Riley NM, Rush MJP, 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. Molecular & Cellular Proteomics, 2015, 14(10): 2644-60. doi: 10.1074/mcp.M115.049726. **Highlighted in Nature Methods**
Zhao Y,* Riley NM,* Sun L, Hebert AS, Yan X, Westphall MW, Rush MJP, Zhu G, Champion MM, Champion PAD, Coon JJ, Dovichi NJ. Coupling Capillary Zone Electrophoresis with Electron Transfer Dissociation and Activated Ion Electron Transfer Dissociation for Top-Down Proteomics. Analytical Chemistry, 2015, 87(10): 5422-5429. doi: 10.1021/acs.analchem.5b00883. *authors contributed equally
Riley NM, Westphall MS, Coon JJ. Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins. Analytical Chemistry, 2015, 87(14): 7109-7116. doi: 10.1021/acs.analchem.5b00881.
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RELATED MEDIA ABOUT PUBLICATIONS
O-Pair Search with MetaMorpheus for O-glycopeptide characterization
Optimal Dissociation Methods Differ for N- and O-Glycopeptides
Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation
Implementation of Activated Ion Electron Transfer Dissociation on a quadrupole-Orbitrap-linear ion trap hybrid mass spectrometer and Phosphoproteomics with Activated Ion Electron Transfer Dissociation
Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling
The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation
CONTRIBUTING Author Publications
Delaveris CS, Wilk AJ, Riley NM, Stark JC, Yang SS, Rogers AJ, Ranganath T, Nadeau KC, Stanford COVID-19 Biobank, Blish CA, Bertozzi CR. Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19. ACS Central Science. 2021, 7(4): 650-657. doi: 10.1021/acscentsci.0c01669.
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, 2021. 17, 937–946 . doi: 10.1038/s41589-021-00770-1.
Wisnovsky S, Moeckl L, Malaker SA, Pedram K, Hess G, 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. Proc. Natl. Acad. Sci. USA, 2021, 118(5): e2015024118. doi: 10.1073/pnas.2015024118.
Delaveris CS, Chiu SH, Riley NM, Bertozzi CR. Modulation of immune cell reactivity with cis-binding Siglec agonists. Proc. Natl. Acad. Sci. USA, 2021, 118 (3): e2012408118. doi: 10.1073/pnas.2012408118.
Banik SM, Pedram K, Wisnovsky S, Ahn G, Riley NM, Bertozzi CR. Lysosome targeting chimeras for the degradation of extracellular proteins. Nature, 2020, 584, 291–297. doi: 10.1038/s41586-020-2545-9.
Peters-Clarke TM, Schauer KL, Riley NM, Lodge JM, Westphall MS, Coon JJ. Optical Fiber-Enabled Photoactivation of Peptides and Proteins. Analytical Chemistry, 2020, 92, 12363-12370. doi: 10.1021/acs.analchem.0c02087.
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, 2020, 92, 10246-10251. doi: 10.1021/acs.analchem.0c00705.
Leung KK, Wilson GM, Kirkemo LL, Riley NM, Coon JJ, Wells JA. Broad and thematic remodeling of the surface glycoproteome on isogenic cells transformed with driving proliferative oncogenes. Proc. Natl. Acad. Sci. USA, 2020, 117(14): 7764-7775. doi: 10.1073/pnas.1917947117.
Brademan DR, Riley NM, Kwiecien NW, Coon JJ. Interactive Peptide Spectral Annotator: A Versatile Web-Based Tool for Proteomic Applications. Molecular & Cellular Proteomics, 2019, 18(8): S193-S201. doi: 10.1074/mcp.TIR118.001209.
Wagner E, 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, 2019, 14(5): e0212389. doi: 10.1371/journal.pone.0212389.
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, 2019, 15(3): e1008037. doi: 10.1371/journal.pgen.100803.
Rush MJP, Riley NM, Westsphall MS, Coon JJ. Top-Down Characterization of Proteins with Intact Disulfide Bonds Using Activated-Ion Electron Transfer Dissociation. Analytical Chemistry, 2018, 90(15): 8946-8953. doi: 10.1021/acs.analchem.8b01113.
Hebert AS, Thoing C, Riley NM, Kwiecien NW, Shishkova 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, 2018, 90(3): 2333-2340. doi: 10.1021/ acs.analchem.7b04808.
Leach III FE, Riley NM, Westphall, Coon JJ, Amster IJ. Negative electron transfer dissociation sequencing of increasingly sulfated glycosaminoglycan oligosaccharides on an Orbitrap mass spectrometer. Journal of the American Society of Mass Spectrometry, 2017, 28(9): 1844-1854. doi: 10.1007/s13361-017-1709-9.
Rush MJP, Riley NM, Westphall MS, Syka JEP, Coon JJ. Sulfur Pentafluoride is a Preferred Reagent for Negative Electron Transfer Dissociation. Journal of the American Society of Mass Spectrometry, 2017, 28(7): 1324-1332. doi: 10.1007/s13361-017-1600-8.
Horton JL, Martin OJ, Lai L, Riley NM, Richards AL, Vega RB, Leone TC, Pagliarini DJ, Coon JJ, Muoio DM, Bedi KC, Margulies KB, Kelly DP. Mitochondrial Protein Hyperacetylation in the Failing Heart. Journal of Clinical Investigation Insights, 2016, 1(2): e84897. doi: 10.1172/jci.insight.84897.
McIlwain S, Peris D, Sardi M, Moskvin O, Zhan F, Myers K, 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: Genes | Genomes | Genetics, 2016, 6(6): 1757-1766. doi: 10.1534/g3.116.029389.
Weisenhorn EMM, 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, 2016, 15(12): 3614-23. doi: 10.1074/mcp.M116.062349.
Rose CM, Rush MJP, Riley NM, Merrill AE, Kwiecien NW, Westphall MS, Coon JJ. A calibration routine for efficient ETD in large-scale proteomics. Journal of the American Society of Mass Spectrometry, 2015, 26(11): 1848-57. doi: 10.1007/s13361-015-1183-1.
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, 2014, 86(5): 2314-2319. doi: 10.1021/ac403579s.
SELECTED ORAL PRESENTAtIONS (5 of 34)
Riley NM. Glycoproteomic tools to investigate mucin domain glycoproteins. Leiden University Medical Center Glyco Series. June 2021, remote presentation at virtual meeting. (Invited by: Y. van der Burgt)
Riley NM, Wei W, Yang AC, Kim JT, Terrell SM, Li VL, Garcia Contreras M, Bertozzi CR, Long JZ. Cell type-selective secretome profiling in vivo. 2021 US Human Proteome Organization Annual Meeting. March 2021, remote presentation at virtual meeting. **Poster abstract selected for oral presentation
Riley NM, Lu L, Shortreed MR, Smith LM, Bertozzi CR. O-Pair Searching with MetaMorpheus for O-glycopeptide Characterization. 2020 Society for Glycobiology Annual Meeting, November 2020, remote presentation at virtual meeting. **Poster abstract selected for oral presentation
Riley NM, Lu L, Malaker SA, Shortreed MR, Smith LM, Bertozzi CR. Designing methods and software to suit the needs of O-glycoproteome characterization. Keystone Symposium: Proteomics in Cell Biology and Disease, September 2020, remote presentation at virtual meeting. (invited Short Talk, Received Keystone Symposia Scholarship)
Riley NM, Malaker SA, Driessen MD, Bertozzi CR. Cost-Benefit Analysis of Stepped-Energy Collisional Dissociation and Electron Transfer Dissociation Approaches for Intact Glycopeptide Characterization. Proceedings of the 67th ASMS Conference on Mass Spectrometry and Allied Topics, June 2019, Atlanta, GA.
SELECTED POSTER PRESENTAtIONS (5 of 30)
Riley NM, Wei W, Yang AC, Kim JT, Terrell SM, Li VL, Garcia Contreras M, Bertozzi CR, Long JZ. Cell type-selective secretome profiling in vivo. 2021 American Society of Biochemistry and Molecular Biology Annual Meeting. April 2021, remote presentation at virtual meeting. **Selected for ASBMB Postdoctoral Award
Riley NM, Lei L, Shortreed MR, Smith LM, Bertozzi CR. O-Pair Searching with MetaMorpheus for O-glycopeptide Characterization. Stanford University Mass Spectrometry Research Applications Symposium, October 2020, remote presentation at virtual meeting. **received poster award**
Riley NM, Lei L, Malaker SA, Shortreed MR, Smith LM, Bertozzi CR. Designing methods and software to suit the needs of O-glycoproteome characterization. Keystone Symposium: Proteomics in Cell Biology and Disease, September 2020, remote presentation at virtual meeting.
Riley NM, Bertozzi CR. Understanding Mechanisms that Regulate Glycocalyx Bulk to Promote Metastasis. The F99/K00 Awardees Meeting (NIH), January 2020, Bethesda, MD.
Riley NM, Coon JJ. Analyzing and Visualizing Large-Scale Glycoproteomic Data. Glycobiology Gordon Research Conference, March 2019, Barga, Italy.