Publications

* authors contributed equally (co-first author publications)

# co-submitting author publication

Bold purple text indicates Riley Research Group-led publications.

Non-bold publications indicate collaborative publications, with RRG members highlighted in bold purple.

To navigate to a publication, please click on the doi hyperlink provided for each.

3) Jiang Y, Rex DAB, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta ML, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry. ACS Meas. Sci. Au, 2024, in press. doi: 10.1021/acsmeasuresciau.3c00068.

2) Peters-Clarke MT, Coon JJ, Riley NM. Instrumentation at the leading edge of proteomics. Analytical Chemistry, 2024, 96(20): 7976-8010. doi: 10.1021/acs.analchem.3c04497. Pre-print available at ChemRxiv: 10.26434/chemrxiv-2023-8l72m-v2.

1) Sutherland E*, Veth TS*, Barshop WD, Russell JH, Kothlow K, Canterbury JD, Mullen C, Bergen D, Huang J, Zabrouskov V, Huguet R, McAlister GC, Riley NM. Autonomous Dissociation-type Selection for Glycoproteomics using a Real-Time Library Search. Journal of Proteome Research. 2024. doi: 10.1021/acs.jproteome.4c00723 Pre-print available at chemRxiv: 10.26434/chemrxiv-2024-qdbrr.

Book Chapters

1) Riley NM#, Malaker SA#. O-glycoproteomics: methods, challenges, and new opportunities. Glycoprotein Analysis, 2024. Editor: WB Struwe. Publisher: Royal Society of Chemistry. doi: 10.1039/9781839166433-00118.

Riley Research Group pre-prints

* authors contributed equally (co-first author publications)

# co-submitting author publication

Bold purple text indicates Riley Research Group-led publications.

Non-bold publications indicate collaborative publications, with RRG members highlighted in bold purple.

To navigate to a publication, please click on the doi hyperlink provided for each.

• Hogan RA, Pepi LE, Riley NM, Krogan NJ, Chalkley RJ. Comparative Analysis of Glycoproteomic Software Using a Tailored Glycan Database. Submitted. 2024. Pre-print available at bioRxiv: 10.1101/2024.07.24.604997.

• Veth TS*, Sutherland E*, Zhang R, Markuson KA, Duboff AG, Huang J, Bergen D, Lee AE, Melani RD, Canterbury JD, Zabrouskov V, McAlister GC, Mullen C, Riley NM. Improvements in glycoproteomics through architecture changes to the Orbitrap Tribrid MS platform. ChemRxiv. 2024. Pre-print available: 10.26434/chemrxiv-2024-4sqd3 

• Sutherland E, Veth TS, Riley NM. Revisiting the effect of trypsin digestion buffers on artificial deamidation. Submitted. 2024. Pre-print available at ChemRxiv: 10.26434/chemrxiv-2024-g66d2. 

Pre-prints from work prior to UW

• Stark JC, Gray MA, Wisnovsky SP, Ibarlucea-Benitez I, Riley NM, Ribi MK, Lustig M, Errington WJ, Bruncsics B, Sarkar CA, Valerius T, Ravetch JV, Bertozzi CR. Antibody-lectin chimeras for glyco-immune checkpoint blockade. Submitted. 2022. Pre-print available at bioRxiv: 10.1101/2022.10.26.513931.

• Ducoli L, Zarnegar B, Porter DF, Meyers R, Miao W, Riley NM, Jackrazi L, Yang Y, Li Z, Wang Y, Bertozzi CR, Flynn RA, Khavari P. irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein associations on RNA. Submitted. 2024. Pre-print available at bioRxiv: 10.1101/2024.09.27.615518.

• Tharp KM, Park S, Timblin GA, Richards AL, Berg JA, Twells NM, Riley NM, Peltan EL, Shon DJ, Stevenson E, Tsui K, Palomba F, Lefebvre AEYT, Soens RW, Ayad NME, ten Hoeve-Scott J, Healy K, Digman M, Dillin A, Bertozzi CR, Mahal LK, Swaney DL, Cantor JR, Paszek MJ, Weaver WM. The microenvironment dictates glycocalyx construction and immune surveillance. Submitted. 2023. Pre-print available at bioRxiv: 10.1101/2023.06.23.546317.

* authors contributed equally (co-first author publications)

# co-submitting author publication

Bold purple text indicates first, co-first, and co-submitting author publications from Nick

To navigate to a publication, please click on the doi hyperlink provided for each.

62) Wen RM, Stark JC, Marti GEW, Fan Z, Lyu AGarcia Marques FJ Zhang X, Riley NM, Totten SM, Bermudez A, Nolley R, Zhao H, Fong L, Engelman EG, Pitteri SJ, Bertozzi BR, Brooks JD. Sialylated glycoproteins suppress immune cell killing by binding to Siglec-7/9 in prostate cancer. Journal of Clinical Investigation, 2024, in press. doi: 10.1172/JCI180282.

61) Goyette MA*, Stevens LE*, DePinho, C, Seehawer MT, Li Z, Wilde CM, Li R, Qiu X, Pyke AL, Lim K, Tender GS, Northey J, Riley NM, Long HW, Bertozzi CR, Weaver VM, Polyak K. Cancer-stromal cell interactions in breast cancer brain metastases induce glycocalyx-mediated resistance to HER2-targeting therapies. Proc. Natl. Acad. Sci. USA, 2024, 121(20): e2322688121. doi: 10.1073/pnas.2322688121.

60) Stewart N, Daly J, Krishnamoorthy V, Stark JC, Riley NM, Bertozzi CR, Wisnovsky S. The glyco-immune checkpoint receptor Siglec-7 interacts with T-cell ligands to regulate T-cell activation and signaling. Journal of Biological Chemistry, 2023, 300(2): 105579. doi: 10.1016/j.jbc.2023.105579.

59) Ahn G, Riley NM, Kamber R, Wisnovsky S, Bassik MC, Banik SM#, Bertozzi CR#. Elucidating cellular determinants of targeted membrane protein degradation by lysosome targeting chimeras. Science, 2023, 382(6668). doi: 10.1126/science.adf6249.

58) Peltan EL, Riley NM, Flynn RA, Roberts DS, Bertozzi CR. Galectin-3 does not interact wth RNA directly. Glycobiology, 2023, 34(1): cwad076. doi: 10.1093/glycob/cwad076.

57) Delaveris, CS, Wang CL, Riley NM, Kulkarni RU, Bertozzi CR. Microglia mediate contact-independent neuronal remodeling via secreted Neuraminidase-3 associated with extracellular vesicles. ACS Central Science, 2023, 9(11): 2108-2114: 10.1101/2023.08.21.554214.

56) 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, Huang D, Weaver VM, Laübli H, Bertozzi CR. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins. Nature Biotechnology, 2023. doi: 10.1038/s41587-023-01840-6.

55) Wei W*, Riley NM*, Lyu X*, Shen X, Guo J, Zhao M, Moya-Garzon MD, Basu H, Tung A, Li VL, Huang W, Svensson KJ, Snyder MP, Bertozzi CR, Long JZ. Organism-wide secretome mapping uncovers pathways of tissue crosstalk in exercise. Cell Metabolism, 2023, S1550-4131(23)00138-9. doi: 10.1016/j.cmet.2023.04.011.

54) 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. Journal of Biological Chemistry, 2023, 299(6): 104755. doi: 10.1016/j.jbc.2023.104755.

53) Boyce M, Malaker SA, Riley NM, Kohler JJ. The 2022 Nobel Prize in Chemistry – sweet!. Glycobiology, 2023, in press, doi: 10.1093/glycob/cwad016.

52) Smith BAH*, Deutzmann A*, Correa KM, Delaveris CS, Dhanasekaran R, Dove CG, Sullivan DK, Wisnovsky SP, Stark JC, Pluvinage JV, Swaminathan S, Riley NM, Rajan A, Majeti R, Felsher DW, Bertozzi CR. MYC driven synthesis of Siglec ligands is a novel glyco-immune checkpoint. Proc. Natl. Acad. Sci. USA, 2023, 120 (11): e2215376120. doi: 10.1073/pnas.2215376120.

51) Riley NM#, Bertozzi CR#. Deciphering O-glycoprotease substrate preferences with O-Pair Search. Molecular Omics, 2022, 18: 908-922. doi: 10.1039/D2MO00244B.

50) Riley NM#, Wu R, Bertozzi CR, Brooks JD, Pitteri SJ#. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Advances in Cancer Research, 2022, 157, 83-121. doi: 10.1016/bs.acr.2022.09.001.

49) 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.

48) 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.

47) Bagdonaite I*, Malaker SA*, Polasky DA*, Riley NM*, Schjoldager K, Vakhrushev SY, Halim A, Aoki-Kinoshita KF, Nesvizhskii AI, Bertozzi CR, Wandall H, Parker BL, Thaysen-Andersen M, Scott NE. Glycoproteomics. Nature Reviews Method Primers, 2022, 2: 48. doi: 10.1038/s43586-022-00128-4. 

46) Malaker SA*, Riley NM*, Shon DJ, Pedram K, Krishnan V, Dorigo O, Bertozzi CR. Revealing the human mucinome. Nature Communications, 2022, 13: 3542. doi: 10.1038/s41467-022-31062-4.

45) 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.

44) 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.

43) 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.

42) Wei W*, Riley NM*, Lyu X, Bertozzi CR, Long JZ. Protocol for labeling, enrichment, and proteomic profiling of cell type-specific plasma proteins in mice. STAR Protocols, 2021, 2(4): 101014. doi: 10.1016/j.xpro.2021.101014.

41) 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.

40) 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.

39) 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.

38) 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.

37) 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.

36) 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.

35) 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, 2021, 17: 326-334. doi: 10.1038/s41589-020-00698-y.

34) Riley NM#, Bertozzi CR, Pitteri SJ#. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-based Glycoproteomics. Molecular & Cellular Proteomics, 2021, 20: 100029. doi: 10.1074/ mcp.R120.002277.

33) 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.

32) Lu L*, Riley NM*, Shortreed MR, Bertozzi CR, Smith LM. O-Pair Search with MetaMorpheus for O-glycopeptide Characterization. Nature Methods, 2020, 17: 1133-1138. doi: 10.1038/s41592-020-00985-5.

31) 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.

30) 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.

29) 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.

28) Riley NM, Malaker SA, Driessen MD, Bertozzi CR. Optimal Dissociation Methods Differ for N- and O-glycopeptides. Journal of Proteome Research, 2020, 19(8): 3286-3301. doi: 10.1021/ acs.jproteome.0c00218.

27) 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.

26) 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.

25) 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.

24) Riley NM, Hebert AS, Westphall MS, Coon JJ. Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis. Nature Communications, 2019, 10: 1311. doi: 10.1038/s41467-019-09222-w.

23) 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.

22) 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.

21) 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.

20) 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.

19) 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.

18) 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.

17) Riley NM, Westphall MS, Coon JJ. Activated Ion Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation. Journal of Proteome Research, 2017, 16(7): 2653-2659. doi: 10.1021/acs.jproteome.7b00249.

16) 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.

15) 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.

14) 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.

13) 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.

12) 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.

11) 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.

10) 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.

9) 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.

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.

7) Riley NM, Coon JJ. Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling. Analytical Chemistry, 2016, 88(1): 74–94. doi: 10.1021/acs.analchem.5b04123.

6) 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.

5) 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.

4) 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.

3) 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. 

2) 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.

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.

Prior to UW

1. Elucidating the cellular determinants of targeted membrane protein degradation by lysosome-targeting chimeras

   1. • New protein destruction target pathway, Stanford

2. Organism-wide, cell-type-specific secretome mapping of exercise training in mice

   1. • Understanding how different cell types respond to exercise could be key step toward exercise as medicine, Stanford

      • Extracellular messaging elicited by exercise, Wong, Science Signaling

      • An Exercise-induced Liver Enzyme Boosts Metabolism, Mesa, The Scientist

3. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins

   1. • A bioengineered enzyme-based scissors cuts off cancer cells’ defenses, Stanford

      • Clipping cell-surface mucins in cancer by targeted degradation, Nature Reviews Drug Discovery

      • A mucin degrader for cancer therapy, Nature Biotechnology

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

   1. • Featured on the cover of Science

      • LYSET/TMEM251- a novel key component of the mannose 6-phosphate pathway, Autophagy

      • TMEM251, a new player in lysosomal enzyme trafficking, Life Metabolism

5. Revealing the Human Mucinome

   1. • Mucopedia 101: capturing and assigning mucin-domain glycoproteins, Reeves and Huang, Trends in Microbiology

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

   1. • Getting more for less: new software solutions for glycoproteomics, Praissman and Wells, Nature Methods

      • Tools to cut the sweet layer-cake that is glycoproteomics, Marx, Nature Methods

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

   1. • ACS Editor's Choice

      • Journal of Biomolecular Techniques Article Watch

      • Top 5 most read articles in JPR in 2020

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

   1. • Selected in 2020 as high impact research by JASMS Editor-in-Chief

9. 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. • Featured on the journal cover

        1. • Highlighted on Genome Web

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

    1. • Featured on the journal cover

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

    1. • Highlighted in Nature Methods

• The Mystery of Sugar -- in Cellular Processes by  Nancy Joseph, UW College of Arts & Sciences, September 28, 2024

• Meet Assistant Professor Nick Riley by Diana Knight, Department of Chemistry, August 20, 2024

• The day my supervisor won the Nobel prize in chemistry by Nick Riley, Chemistry World Opinion Section, September 28, 2023

• ASMS 2024: An Interview with Nick Riley of the University of Washington, by Aaron Acevedo, LCGC International Magazine, May 28, 2024

  • • highlighting Nick's presentation on GlyCounter and its utility for glycoproteomics

• Investigating the Interfaces by Valerie Weingart, South Carolina Honors College, June 3, 2024

  • • highlighting Nick as the 2023 SCHC Distinguished Young Honors Alumni awardee

• Meet the Glycoscientist,  Fall 2024 newsletter from the American Chemical Society Division of Carbohydrate Chemistry & Chemical Glycobiology (CARB)

Prior to UW

• An interview with IonOpticks about using their columns for our in vivo secretome work

• A Mass Geek Moment from Mass Dynamics highlighting Nick when he was a postdoc in the Bertozzi lab

• A Badger Chemist highlight from Nick's days as a graduate student at UW-Madison