Publications and Presentations

Summary: 50 total publications (23 first and co-first author), 39 oral presentations, 34 poster presentations

SELECTED FIRSt and Co-First Author Publications

Deciphering O-glycoprotease substrate preferences with O-Pair Search

Molecular Omics, 2022

Measuring the multifaceted roles of mucin-domain glycoproteins in cancer

Advances in Cancer Research, 2022

Glycoproteomics

Nature Reviews Method Primers, 2022

Revealing the human mucinome

Nature Communications, 2022

Cell type-selective secretome profiling in vivo

Nature Chemical Biology, 2021

A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics

Molecular & Cellular Proteomics, 2021

O-Pair Search with MetaMorpheus for O-glycopeptide characterization

Nature Methods, 2020

Optimal Dissociation Methods Differ for N- and O-Glycopeptides

Journal of Proteome Research, 2020

Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis

Nature Communications, 2019

The Role of Electron Transfer Dissociation in Modern Proteomics

Analytical Chemistry, 2018

Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation

Journal of Proteome Research, 2017

Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling

Analytical Chemistry, 2016

First and Co-First Author Publications CONTINUED

  1. 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


  1. 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.


  1. 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**


  1. 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**


  1. 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**


  1. 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.


  1. 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.


  1. 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.


  1. 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**


  1. 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


  1. 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

  1. The Human Disease Gene LYSET is Essential for Lysosomal Enzyme Transport and Viral Infection


  1. Revealing the Human Mucinome


  1. O-Pair Search with MetaMorpheus for O-glycopeptide characterization


  1. Optimal Dissociation Methods Differ for N- and O-Glycopeptides


  1. Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation


  1. 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


  1. Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling


  1. The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation

CONTRIBUTING Author Publications

  1. Richards CM*, Jabs S*, Qiao*, Varanese L, Schweizer M, Mosen PR, Riley NM, Zengel JR, Flynn RA, Rustagi A, Widen JC, Peters CE, Ooi YS, Shi PY, Bartenschlager R, Bogyo M, Bertozzi CR, Blish CA, Winter D, Nagamine CM, Braulke T#, Carette J#. The Human Disease Gene LYSET is Essential for Lysosomal Enzyme Transport and Viral Infection. Science, 2022, 378(6615): eabn5648. doi: 10.1126/science.abn5648. **featured on journal cover**


  1. Shon DJ, Fernandez D, Riley NM, Ferracane MJ, Bertozzi CR. Structure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences. Journal of Biological Chemistry, 2022, 298(5): 101917. doi: 10.1016/j.jbc.2022.101917.


  1. 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. Proc. Natl. Acad. Sci. USA, 2022, 119(39): e2117105119. doi: 10.1073/PNAS.2117105119.


  1. Daly J, Sarkar S, Natoni A, Stark JC, Riley NM, Bertozzi CR, Carlsten M, O’Dwyer M. Targeting hypersialylation in Multiple Myeloma represents a novel approach to enhance NK cell-mediated tumor responses. Blood Advances, 2022, 6(11): 3352-2266. doi: 10.1182/bloodadvances.2021006805.


  1. 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 S. Multi-Omics Analysis of Fibroblasts from the Invasive Tumor Edge Reveals that Tumor-Stroma Crosstalk Induces O-Glycosylation of the CDK4-pRB Axis. Cancer Research, 2022, 82(4): 648-664. doi: 10.1158/0008-5472.CAN-21-1705.


  1. Pluvinage JV, Sun J, Claes C, Flynn RA, Haney MS, Iram T, Meng X, Lindemann R, Riley NM, Danhash E, Chaderevian JP, Tapp E, Gate D, Kondapavulur S, Cobos I, Chetty S, Pasca S, Berry-Kravis E, Bertozzi CR, Blurton-Jones M, Wyss-Coray T. The CD22-IGF2R interaction is a therapeutic target for microglial lysosome dysfunction in Niemann-Pick Type C. Science Translational Medicine, 2021, 13(622): eabg2919. doi: 10.1126/scitranslmed.abg2919.


  1. Peters-Clarke TM, Riley NM, Westphall MS, Syka JEP, Coon JJ. Practical Effects of Intramolecular Hydrogen Rearrangement in Electron Transfer Dissociation-Based Proteomics. Journal of the American Society of Mass Spectrometry, 2021, 33(1): 100-110. doi: 10.1021/jasms.1c00284.


  1. 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.


  1. 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.


  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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  1. 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.


  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 39)

  1. Riley NM. Deciphering O-glycoprotease substrate preferences with O-Pair Search. 24th International Mass Spectrometry Conference. August 2022, Maastricht, Netherlands. (Keynote Lecture, invited by: M Wuhrer)


  1. Riley NM. Mass Spectrometry-based Tools to Study Mucin-Domain Glycoproteins. Boston Glycobiology Discussion Group, June 2022, remote presentation at virtual meeting.


  1. Riley NM. Glycoproteomics with Real-time Mass Spectrometry. Real-time Mass Spectrometry in Proteomics and Beyond Workshop, 70th ASMS Conference, June 2022, Minneapolis, MN. (invited by: C Adams)


  1. 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


  1. 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 34)

  1. 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


  1. 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**


  1. 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.


  1. Riley NM, Bertozzi CR. Understanding Mechanisms that Regulate Glycocalyx Bulk to Promote Metastasis. The F99/K00 Awardees Meeting (NIH), January 2020, Bethesda, MD.


  1. Riley NM, Coon JJ. Analyzing and Visualizing Large-Scale Glycoproteomic Data. Glycobiology Gordon Research Conference, March 2019, Barga, Italy.