PUBLISHED WORK

(68) Vincent Chang, Isaac Lian, Ali Reza Afshari, Jeff Romano, Keira E. Mahoney, Ryan J.

Chen, Niclas G. Karlsson, Gordon W. Laurie, and Stacy A. Malaker*. Mapping galectin-3 ligands in human tear fluid establishes spliceoform-dependent lacritin binding. 2026, Communications Biology. In Press. doi.org/10.1038/s42003-026-10337-2

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(67) Sarah C. Lowery, Mikaela Ribi, Joann Chongsaritsinsuk, Isabella P. Tran, Grace

Grimsley, Rachel Stubler, Keira E. Mahoney, Taryn M. Lucas, Georgia Charkoftaki, Alvaro Santos-Neto, Nissi Varki, Vasilis Vasiliou, Michael Angelo, Richard R. Drake, and Stacy A. Malaker*. Glycosite Mapping and in situ Imaging of MUC2 Glycopeptides via On-slide Digestion with Mucinase StcE. 2026, Nature Communications. In Press. doi.org/10.1038/s41467-026-72853-3

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Spatial glycoproteomics remains technically challenging due to the complexity of glycan heterogeneity within tissues. Here, we developed an on-slide mucinase digestion strategy enabling direct imaging and glycosite mapping of MUC2 glycopeptides in tissue sections, providing new opportunities to study mucosal glycoproteins in their native spatial context.

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(66) Alexandra D. Steigmeyer‡, Joann Chongsaritsinsuk‡, and Stacy A. Malaker*.

Characterization of O-glycoproteases for Applications in Mass Spectrometry. In: Stacy A. Malaker (ed) Methods in Enzymology: Mucins. Elsevier, 2026. doi.org/10.1016/bs.mie.2026.03.004

 

(65) Shane M. Finn and Stacy A. Malaker*. Enrichment Strategies for Mucin-domain O-

glycoproteins. In: Stacy A. Malaker (ed) Methods in Enzymology: Mucins. Elsevier, 2026. doi.org/10.1016/bs.mie.2026.03.003

 

(64) Abhishek K. Singh, Balkrishna Chaube, Kathryn M. Citrin, Joseph Wayne Fowler,

Sungwoon Lee, Jonatas Catarino, James Knight, Sarah C. Lowery, Sonal Shree, Keira E. Mahoney, Nabil Boutagy, Inmaculada Ruz-Maldonado, Kathy Harry, Marya Shanabrough, Trenton Thomas Ross, Stacy A. Malaker, Yajaira Suárez, Carlos Fernández-Hernando, Kariona Grabinska, and William C. Sessa. Impaired glycosylation promotes rapid transition to hepatocellular carcinoma in model of diet-induced steatotic liver disease. 2026, Journal of Clinical Investigation. In Press. doi.org/10.1172/JCI197719

 

(63) Zhen Li, Lucia Di Vagno, Aisling Ni Cheallaigh, Meg Critcher, Douglas Sammon, Edgar

Gonzalez-Rodriguez, David C. Briggs, Nara Chung, Vincent Chang, Keira E. Mahoney, Anna Cioce, Ganka Bineva-Todd, Pei-Ying Wang, Yi-Chang Liu , Lloyd D. Murphy, Yen-Hsi Chen, Yoshiki Narimatsu, Rebecca L. Miller, Lianne I. Willems, Stacy A. Malaker, Mia L Huang, Gavin J. Miller, Erhard Hohenester, and Benjamin Schumann. Xylosyltransferase engineering to manipulate proteoglycans in mammalian cells. 2026, Nature Chemical Biology, 22: 612–621. doi.org/10.1038/s41589-025-02113-w

 

(62) Zeinab Jame-Chenarboo, Edward N. Schmidt, Madeline Crichton, Kei Takahashi-

Yamashiro, Guilherme M. Lima, Liany Luna Dulcey, Jaesoo Jung, Sabine Ivison, Chris D. St. Laurent, Jhon Enteria, Sung-Yao Lin, Susmita Sarkar, Maju Joe, Fahima Mozaneh, Reni John, Som G. Nanjappa, Stacy A. Malaker, Megan K. Levings, Jamey D. Marth, Ratmir Derda, and Matthew S. Macauley. An ultrasensitive and modulator platform to detect Siglec ligands and modulate immune cell function. 2025, Science Advances, 11(46): eadz8096. doi.org/10.1126/sciadv.adz8096

 

(61) Shane M. Finn, Keira E. Mahoney, Taryn M. Lucas, Valentina Rangel-Angarita, Ryan J.

Chen, and Stacy A. Malaker*. GlycoFASP: A Universal Method to Prepare Complex Mixtures for O-Glycoproteomic Analysis. 2025, Analytical Chemistry. 97(43): 23751–23756. doi.org/10.1021/acs.analchem.5c02666

 

We developed GlycoFASP, a streamlined sample preparation workflow that improves compatibility between complex biological samples and downstream O-glycoproteomic analysis. This broadly applicable method enhances glycopeptide recovery and analytical robustness, facilitating large-scale characterization of mucin-domain glycoproteins from diverse sample types.

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(60) Vincent Chang, Keira E. Mahoney, Isaac Lian, Ryan Chen, Nara Chung, Tor Paaske

Utheim, Niclas G. Karlsson, and Stacy A. Malaker*. In-depth analysis of the tear fluid glycoproteome reveals diverse lacritin glycosylation and spliceoforms. Journal of Biological Chemistry. 2025, 301(9): 110580. doi.org/10.1016/j.jbc.2025.110580

 

Tear fluid contains a highly dynamic and understudied glycoproteome with important implications for ocular surface biology and disease. Using advanced glycoproteomic workflows, we characterized extensive lacritin glycosylation and spliceoform diversity, revealing unexpected molecular heterogeneity within the tear proteome.

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(59) Invited article for “Celebrating the Career of Donald F. Hunt”: Keira E. Mahoney, Larry

Reser, Maria Virginia Ruiz Cuevas, Jennifer G. Abelin, Jeffrey Shabanowitz, Donald F. Hunt*, and Stacy A. Malaker*. Identification of post-translationally modified MHC class I-associated peptides as potential cancer immunotherapeutic targets. Molecular and Cellular Proteomics, 2025, 24(8): 100971. doi.org/10.1016/j.mcpro.2025.100971

     

(58) Cameron Movassaghi, Jie Sun, Yuming Jiang, Amanda Momenzadeh, Natalie Turner,

Vincent Chang, Nara Chung, Ryan Chen, Elizabeth Browne, Chuwei Lin, Devin Schweppe, Stacy A. Malaker, and Jesse Meyer. Recent Advances in Mass Spectrometry-Based Bottom-up Proteomics. Analytical Chemistry. 2025, 97(9): 4728-4749 doi.org/10.1021/acs.analchem.4c06750

 

(57) Valentina Rangel-Angarita, Joann Chongsaritsinsuk, Keira E. Mahoney, Lea M. Kim,

Ryan J. Chen, Akua A. Appah-Sampong, Isabella P. Tran, Alexandra D. Steigmeyer, Marie A. Hollenhorst, and Stacy A. Malaker*. PNGaseF-generated N-glycans adduct onto peptides in the gas phase. Journal for the American Society of Mass Spectrometry. 2025, 36 (3): 542-552. doi.org/10.1021/jasms.4c00431. 

 

(56) Invited article for “Celebrating the Career of Donald F. Hunt”: Ali Reza Afshari‡, Vincent

Chang‡, Kristina A. Thomsson, Jennifer Höglund, Ellie Browne, George Karadzhov, Keira E. Mahoney, Taryn M. Lucas, Valentina Rangel-Angarita, Henrik Ryberg, Kamlesh Gidwani, Kim Pettersson, Ola Rolfson, Lena I Björkman, Thomas Eisler, Tannin A. Schmidt, Gregory D. Jay, Stacy A. Malaker*, and Niclas G. Karlsson*. Glycoproteoforms of osteoarthritis-associated lubricin in plasma and synovial fluid. Molecular and Cellular Proteomics. 2025, 6:100923. doi: 10.1016/j.mcpro.2025.100923

 

(55) Invited review: Alexandra D. Steigmeyer‡, Sarah C. Lowery‡, Valentina Rangel-

Angarita, and Stacy A. Malaker*. Decoding Extracellular Protein Glycosylation in Human Health and Disease. Annual Reviews in Analytical Chemistry. 2025, Vol 18. doi.org/10.1146/annurev-anchem-071024-124203

 

(54) Amanda Helms, Vincent Chang, Stacy A. Malaker, and Jennifer S. Brodbelt.

Unraveling O-Glycan Diversity of Mucins: Insights from SmE Mucinase and Ultraviolet Photodissociation Mass Spectrometry. Analytical Chemistry. 2024, 96 (49), 19230-19237. doi.org/10.1021/acs.analchem.4c02011

 

(53) Joann Chongsaritsinsuk, Valentina Rangel-Angarita, Taryn M. Lucas, Keira E.

Mahoney, Olivia M. Enny, Mitchelle Katemauswa, and Stacy A. Malaker*. Quantification and site-specific analysis of co-occupied N- and O-glycopeptides. Journal of Proteome Research. 2024, 23(12), 5449-5461. doi.org/10.1021/acs.jproteome.4c00574

 

(52) Abdul Zafar, Sandhya Sridhar, Ganka Bineva-Todd, Anna Cioce, Nadia Abdulla, Vincent

Chang, Stacy A. Malaker, David S. Hewings, and Benjamin Schumann*. Expanding the repertoire of monosaccharides for cell-specific bioorthogonal tagging of glycoproteins. RSC Chemical Biology. 2024, 5 (10), 1002-1009 doi.org/10.1039/D4CB00093E

 

(51) Nicholas M. Rileyǂ* and Stacy A. Malakerǂ*. O-glycoproteomics: methods, challenges,

and new opportunities.  In: Struwe, W. (ed) Glycoprotein Analysis. Royal Society of Chemistry Publishing, 2024. Cambridge, United Kingdom. doi.org/10.1039/9781839166433-00118

 

(50) Keira E. Mahoney, Vincent Chang, Ryan Chen, Nara Chung, Valentina Rangel-

Angarita, Devon Kohler, Kiyoko Aoki-Kinoshita, Frédérique Lisacek, Nichollas E. Scott,  Nicholas M. Riley*, and Stacy A. Malaker*. Second community evaluation of glycoproteomic informatics solutions. Nature Methods. 2024, Accepted in principle, study ongoing. doi.org/10.6084/m9.figshare.27095782.v1

 

(49) Invited protocol: Keira E. Mahoney and Stacy A. Malaker*. Analysis of mucin-domain

glycoproteins using mass spectrometry. Current Protocols. 2024,4, e1100. doi.org/10.1002/cpz1.1100

 

(48) Invited perspective: Stacy A. Malaker*. Glycoproteomics: charting new territory in mass

spectrometry and glycobiology. Journal of Mass Spectrometry. 2024, 59 (6), e5034. doi.org/10.1002/jms.5034

 

(47) Courtney Rivet-Noor, Andrea R Merchak, Caroline Render, Naudia Gay, Rebecca M.

Beiter, Ryan Brown, Austin Keeler, G. Brett Moreau, Sihan Li, Deniz E. Olgun, Rachel Ofer,  Alexandra D. Steigmeyer, Keira E. Mahoney, Tobey Mihn Huu Phan, Kiranmayi Vemuri, Lei Chen, Jung-Bum Shin, Stacy A. Malaker, Chris Deppmann, Michael Verzi, and Alban Gaultier. Stress-Induced Mucin 13 Reductions Drive Intestinal Microbiome Shifts and Despair Behaviors. Brain, Behavior, and Immunity. 2024, S0889-1591(24)00309-X. doi: 10.1016/j.bbi.2024.03.028.

 

(46) Keira E. Mahoney, Vincent Chang, Taryn M. Lucas, Krystyna Maruszko, and Stacy A.

Malaker*. Mass Spectrometry-Compatible Elution Technique Enables an Improved Mucin-Selective Enrichment Strategy to Probe the Mucinome. Analytical Chemistry. 2024, 96(13):5242-5250. doi.org/10.1021/acs.analchem.3c05762

 

Selective enrichment remains a critical bottleneck in the analysis of mucin-domain glycoproteins from complex biological samples. In this work, we developed an improved mucin-selective enrichment workflow featuring a mass spectrometry-compatible elution strategy that enhances recovery, sensitivity, and downstream glycoproteomic analysis of mucin-domain proteins.

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(45) Joann Chongsaritsinsuk‡, Alexandra D. Steigmeyer‡, Keira E. Mahoney‡, Mia A.

Rosenfeld‡, Taryn M. Lucas, Courtney M. Smith, Alice Li, Deniz Ince, Fiona L. Kearns, Alexandria S. Battison, Marie A. Hollenhorst, D. Judy Shon, Katherine H. Tiemeyer, Victor Attah, Catherine Kwon, Carolyn R. Bertozzi, Michael J. Ferracane, Mark A. Lemmon, Rommie E. Amaro, and Stacy A. Malaker*. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nature Communications. 2023, 14: 6169. doi.org/10.1038/s41467-023-41756-y Human Proteome Organization (HUPO) Early Career Research Manuscript Competition – First Place Award

 

This study combined mucinase-enabled glycoproteomics, structural biology, and molecular dynamics simulations to characterize glycosylation patterns across TIM-family immune checkpoint receptors. Our findings demonstrated that O-glycans influence receptor structural dynamics and highlighted glycosylation as an important regulator of immune signaling.

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(44) Valentina Rangel-Angarita, Keira E. Mahoney, Catherine Kwon, Raibat Sarker, Taryn

M. Lucas, and Stacy A. Malaker*. False positive glycopeptide identification via in-FAIMS fragmentation. JACS Au. 2023, 3(9): 2498–2509. doi.org/10.1021/jacsau.3c00264

 

(43) Michael J. Hollander, Stacy A. Malaker, Nicholas M. Riley, Idalia Perez, Nayla M. Abney,

Melissa A. Gray, Julia E. Maxson, Jennifer R. Cochran, and Carolyn R. Bertozzi. Mutational screens highlight glycosylation as a modulator of colony-stimulating factor 3 receptor (CSF3R) activity. Journal of Biological Chemistry. 2023, 299(6): 104755. doi.org/10.1016/j.jbc.2023.104755

 

(42) Kayvon Pedram, D. Judy Shon, Gabrielle S. Tender, Natalia R. Mantuano, Jason J.

Northey, Kevin J. Metcalf, Simon P. Wisnovsky, Nicholas M. Riley, Giovanni C. Forcina, Stacy A. Malaker, Angel Kuo, Benson M. George, Caitlyn L. Miller, Kerriann M. Casey, José G. Vilches-Moure, Davey Huang, Valerie M. Weaver, Heinz Laübli, and Carolyn R. Bertozzi. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins. Nature Biotechnology. 2023. doi.org/10.1038/s41587-023-01840-6

Featured in Trends in Pharmacological Science “Spotlight Article”: Liza L. Greenburg, Deborah Fass. Shearing of surface mucin saps tumor cell strength. doi.org/10.1016/j.tips.2023.08.011

 

(41) Xin Huang, Thomas Nero, Ranjuna Weerasekera, Katherine Matej, Alex Hinbest,

Zhaowei Jiang, Rebecca Lee, Longjun Wu, Cecilia Chak, Hapinder Nijjer, Isabella Gibaldi, Hang Yang, Nathan Gamble, Wai-Leung Ng, Stacy A. Malaker, Kaelyn Sumigray, Rich Olson, and Jing Yan. Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization. Nature Communications. 2023, 14(1): 2104. doi.org/10.1038/s41467-023-37660-0

 

(40) Michael Boyce, Stacy A. Malaker, Nicholas M. Riley, Jennifer Kohler. The 2022 Nobel

Prize in Chemistry – sweet! Glycobiology. 2023, 33(3): 178-181. 

doi.org/10.1093/glycob/cwad016

 

(39) Edgar Gonzalez-Rodriguez, Mia Zol-Hanlon, Ganka Bineva-Todd, Andrea Marchesi,

Mark Skehel, Keira E. Mahoney, Chloë Roustan, Annabel Borg, Lucia Di Vagno, Svend Kjaer, Antoni G. Wrobel, Donald J. Bentone, Philipp Nawrath, Sabine L. Flitsch, Dhira Joshi, Andrés Manuel González-Ramírez, Katalin A. Wilkinson, Robert J. Wilkinson, Ramón Hurtado-Guerrerom, Stacy A. Malaker, and Benjamin Schumann. O-Linked Sialoglycans Modulate the Proteolysis of SARS-CoV-2 Spike and Contribute to the Mutational Trajectory in Variants of Concern. ACS Central Science. 2023, 9(3): 393-404. doi.org/10.1021/acscentsci.2c01349

 

(38) Marie A. Hollenhorst, Katherine H. Tiemeyer, Keira E. Mahoney, Kazuhiro Aoki, Mayumi

Ishihara, Sarah C. Lowery, Valentina Rangel-Angarita, Carolyn R. Bertozzi, and Stacy A. Malaker*. Comprehensive analysis of glycoprotein Ibα ectodomain glycosylation. Journal of Thrombosis and Haemostasis, 2023, 21(4): 995-1009. doi.org/10.1101/ 2022.07.19.500646

 

(37) Invited article for STAR Protocols: Beatriz Calle, Edgar Gonzalez-Rodriguez, Keira E.

Mahoney, Anna Cioce, Chloe Roustan, Helen Flynn, Stacy A. Malaker, and Benjamin Schumann. Bump-and-hole engineering of human polypeptide N-acetylgalactosamine transferases to dissect their protein substrates and glycosylation sites in the living cell. STAR Protocols. 2023, 4 (1): 101974. doi: 10.1016/j.xpro.2022.101974

 

(36) Anna Cioce, Beatriz Calle, Tatiana Rizou, Sarah C. Lowery, Victoria Bridgeman, Keira

E. Mahoney, Andrea Marchesi, Ganka Bineva-Todd, Helen Flynn, Zhen Li, Omur Y. Tastan, Chloe Roustan, Thomas M. Wood, Tessa Keenan, Peter Both, Kun Huang, Fabio Parmeggiani, Ambrosius P. Snijders, Mark Skehel, Svend Kjaer, Martin A. Fascione, Carolyn R. Bertozzi, Sabine Flitsch, Stacy A. Malaker, Ilaria Malanchi, and Benjamin Schumann. Cell-specific Bioorthogonal Tagging of Glycoproteins. Nature Communications. 2022, 13 (6237). doi.org/10.1038/s41467-022-33854-0

 

(35) Brendon J. Medley, Leif Leclaire, Nicole Thompson, Keira E. Mahoney, Benjamin

Pluvinage, Matthew A. Parsons, John E. Burke, Stacy A. Malaker, Warren Wakarchuk, and Alisdair B. Boraston. A metzincin-like O-glycopeptidase from Akkermansia muciniphila requires the Tn antigen for cleavage of the peptide bond. Journal of Biological Chemistry. 2022, 298 (10): 102439. doi.org/10.1016/j.jbc.2022.102439

 

(34) Ieva Bagdonaiteǂ, Stacy A. Malakerǂ, Daniel A. Polaskyǂ, Nicholas M. Rileyǂ, Katrine

Schjoldager, Sergey Y. Vakhrushev, Adnan Halim, Kiyoko F. Aoki-Kinoshita, Alexey I Nesvizhskii, Carolyn R. Bertozzi, Hans Wandall, Benjamin L. Parker, Morten Thaysen-Andersen, and Nichollas E. Scott. Glycoproteomics. Nature Reviews Methods Primers. 2022, 2 (1): 1-29. doi.org/10.1038/s43586-022-00128-4

 

(33) Stacy A. Malaker*ǂ, Nicholas M. Rileyǂ, D. Judy Shon, Kayvon Pedram, Venkatesh

Krishnan, Oliver Dorigo, and Carolyn R. Bertozzi*. Revealing the human mucinome. Nature Communications. 2022, 13 (1): 1-13. doi.org/10.1038/s41467-022-31062-4

Featured in Trends in Microbiology “Spotlight Article”: Abigail E. Reeves, Mia L. Huang. Mucopedia 101: Capturing and assigning mucin-domain glycoproteins. doi.org/10.1016/j.tim.2022.09.004

 

Mucin-domain glycoproteins are notoriously difficult to identify using conventional proteomic workflows due to their dense and heterogeneous O-glycosylation. In this work, we developed a systematic mucinomics platform that enabled large-scale identification and classification of mucin-domain glycoproteins, providing a foundational resource for studying the human mucinome in health and disease.

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(32) Invited review for “Carbohydrate Biopolymers” Special Issue: Deniz Ince, Taryn M. Lucas,

and Stacy A. Malaker*. Current strategies for characterization of mucin-domain glycoproteins. Current Opinion in Chemical Biology. 2022, 69, 102174. doi: 10.1016/j.cbpa.2022.102174

 

(31) Yikun Yao, Girak Kim, Samantha Shafer, Zuojia Chen, Satoshi Kubo, Yanlong Ji, Jialie

Luo, Weiming Yang, Sebastian Perner, Chrysi Kanellopoulou, Ann Park, Ping Jiang, Safa Baris, Elif Karakoc Aydiner, Deniz Ertem, Daniel J. Mulde, Neil Warner, Anne M. Griffiths, Chani Topf-Olivestone, Michal Kori, Lael Werner, Jodie Ouahed, Michael Field, Chengyu Liu, Benjamin Schwarz, Sundar Ganesan, Jian Song, Henning Urlaub, Thomas Oellerich, Stacy A. Malaker, Lixin Zheng, Carolyn R. Bertozzi,  Yu Zhang, Helen Matthews, Will Montgomery, Han-Yu Shih, Jiansheng iang, Scott Snapper, Aleixo M. Muise, Dror Shouval, Ahmet Ozen , Kuan-Ting Pan, Chuan Wu, and Michael J. Lenardo. Mucus sialylation determines intestinal host-commensal homeostasis. Cell. 2022, 185 (7): 1172-1188.e28. doi.org/10.1016/j.cell.2022.02.013

 

(30) Valentina Rangel-Angarita, Keira E. Mahoney, Deniz Ince, and Stacy A. Malaker*. A

systematic comparison of current bioinformatic tools for glycoproteomics data. 2022, bioRXiv: doi.org/10.1101/2022.03.15.484528

 

(29) Daniela J. Carroll, Mary W. N. Burns, Lynda Mottram, Daniel C. Propheter, Andrew

Boucher, Gabrielle M. Lessen, Ashwani Kumar, Stacy A. Malaker, Chao Xing, Lora V. Hooper, Ulf Yrlid, Jennifer J. Kohler. Interleukin-22 (IL-22) regulates B3GNT7 expression to induce fucosylation of glycoproteins in intestinal epithelial cells. Journal of Biological Chemistry. 2022, 298 (2): 101463. doi: 10.1016/j.jbc.2021.101463

 

(28) Rajan Burt, Kimberly Lee, Borislav Dejanovic, Xiang Li, Johain Ounadjela, Anjana Rao,

Stacy A. Malaker, Steven A. Carr, and Samuel A. Myers. Novel antibodies for the simple and efficient enrichment of native O-GlcNAc modified peptides. Molecular and Cellular Proteomics. 2021, 20 100167. doi.org/10.1016/j.mcpro.2021.100167

 

(27) Sarah A. Penny, Jennifer G. Abelin, Stacy A. Malaker, Paisley T. Myers, Abu Z. Saeed,

Lora G. Steadman, Dina L. Bai, Stephen T. Ward, Jeffrey Shabanowitz, Donald F. Hunt, and Mark Cobbold. Tumor infiltrating lymphocytes target HLA-I phosphopeptides derived from cancer signaling in colorectal cancer. Frontiers Immunology. 2021, 12:723566. doi.org/10.3389/fimmu.2021.723566

 

(26) Invited review for “Chemical Glycobiology” Special Issue: Valentina Rangel-Angarita and

Stacy A. Malaker*. Mucinomics as the next frontier of mass spectrometry. ACS Chemical Biology. 2021, 16(10): 1866-1883. doi.org/10.1021/acschembio.1c00384

 

This invited review highlighted emerging analytical challenges and opportunities associated with the study of mucin-domain glycoproteins. We discussed recent advances in mucin-selective proteases, glycoproteomic workflows, and bioinformatic approaches while outlining a broader vision for the development of “mucinomics” as a rapidly evolving subfield of chemical glycobiology and mass spectrometry.

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(25) Stacy A. Malakerǂ, Jusal Quanicoǂ, Antonella Raffo Romero, Firas Kobeissy,

Soulaimane Aboulouard, Dominique Tierny, Carolyn R. Bertozzi, Isabelle Fournier, and Michel Salzet. On-tissue spatially resolved glycoproteomics guided by N-glycan imaging reveal global dysregulation of canine glioma glycoproteomic landscape. Cell Chemical Biology. 2022, 29 (1): 30-42 e4. doi.org/10.1016/j.chembiol.2021.05.007

 

(24) Ryan A. Flynn, Kayvon Pedram, Stacy A. Malaker, Pedro J. Batista, Benjamin A.H. Smith,

Alex G. Johnson, Benson M. George, Karim Majzoub, Peter W. Villalta, Jan E. Carette, and Carolyn R. Bertozzi. Small RNAs are modified with N-glycans and are primarily displayed on the surface of living cells. Cell. 2021, 184(10): 3109-3124.e22. doi.org/10.1016/j.cell.2021.04.023

Featured in C&E News, HHMI News, The Scientist, Boston Children’s Hospital Innovation News, and Stanford News. 

 

(23) Invited review article: D. Judy Shon, Angel Kuo, Michael J. Ferracane, and Stacy A.

Malaker*. Classification, structural biology, and applications of mucin domain-targeting proteases. Biochemical Journal, 2021, 478(8): 1585-1603. doi.org/10.1042/bcj20200607

 

(22) Invited article for “Emerging Talent” Special Issue: Beatriz Calle‡, Ganka Bineva-Todd‡,

Andrea Marchesi‡, Helen Flynn, Mattia Ghirardello, Omur Y. Tastan, Chloe Roustan, Junwon Choi, M. Carmen Galan, Benjamin Schumann*, and Stacy A. Malaker*. Benefits of chemical sugar modifications introduced by click chemistry for glycoproteomic analyses. Journal of the American Society for Mass Spectrometry. 2021, 32(9): 3266-2375. doi.org/10.1021/jasms.1c00084

 

(21) Invited article: Neil G. Rumachik, Stacy A. Malaker*, and Nicole K. Paulk*. VectorMOD:

method for bottom-up proteomic characterization of rAAV capsid PTMs and vector impurities. Frontiers Immunology. 2021, 12: 657795. doi: 10.3389/fimmu.2021.657795

 

(20) Invited review article: Anna Coice, Stacy A. Malaker*, and Benjamin Schumann*.

Generating Orthogonal Glycosyltransferase-Nucleotide Sugar Pairs as Next Generation Glycobiology Tools. Current Opinion in Chemical Biology. 2021, 60: 66-78. doi.org/10.1016/j.cbpa.2020.09.001

 

(19) Simon P. Wisnovsky, Leonhard Mockl, Stacy A. Malaker, Kayvon Pedram, Gaelen Hess,

Nicholas M. Riley, Melissa A. Gray, Benhamin A.H. Smith, Michael C. Bassik, W.E. Moerner, and Carolyn R. Bertozzi. Genome-wide CRISPR screens reveal a specific ligand for glycan-binding immune checkpoint receptor Siglec-7. Proceedings of the National Academy of Sciences USA. 2021, 118(5): e2015024118. doi.org/10.1073/pnas.2015024118

 

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Publications Prior To Yale

 

(18) Melissa A. Gray, Michal A. Stanczak, Han Xiao, Johan F. A. Pijnenborg, Natalia R

Mantuano, Stacy A. Malaker, Payton A. Weidenbacher, Caitlyn L. Miller, Julia T. Tanzo, Green Ahn, Elliot C. Woods, Heinz Läubli, and Carolyn R. Bertozzi. Targeted desialylation overcomes glyco-immune checkpoints and potentiates the anticancer immune response in vivo. Nature Chemical Biology. 2020; doi.org/10.1038/s41589-020-0622-x

 

(17) Nicholas M. Riley, Stacy A. Malaker, and Carolyn R. Bertozzi. 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

 

(16) Marjoke F. Debets, Omur Y. Yastan, Simon P. Wisnovsky, Stacy A. Malaker, Nikolaos

Angelis, Leonhard K.R. Moeckl, Junwon Choi, Helen Flynn, Lauren J.S. Wagner, Ganka Bineva-Todd, Aristotelis Antononopoulos, Anna Cioce, William M. Browne, Zhen Li, David C. Briggs, Holly L. Douglas, Gaelen T. Hess, Anthony J. Agbay, Chloe Roustan, Svend Kjaer, Stuart M. Haslam, Ambrosius P. Snijders, Michael C. Bassik, W.E. Moerner, Vivian S.W. Li, Carolyn R. Bertozzi, and Benjamin Schumann. Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation. Proceedings of the National Academy of Sciences USA. 2020, 117(41); 25293-25301. doi.org/10.1073/pnas.2007297117

 

(15) Neil G. Rumachik, Stacy A. Malaker, Nicole Poweleit, Lucy Maynard, Christopher M.

Adams, Ryan Leib, Giana Cirolia, Dennis Thomas, Susan Stamnes, Kathleen Holt, Patrick Sinn, Joseph L. DeRisi, Andrew P. May, and Nicole K. Paulk. Methods Matter -- Standard Production Platforms for Recombinant AAV Produce Chemically and Functionally Distinct Vectors. Molecular Therapy: Methods & Clinical Development. 2020; 18:98-118. doi.org/10.1016/j.omtm.2020.05.018

 

(14) D. Judy Shon, Stacy A. Malaker, Kayvon Pedram, Emily Yang, Venkatesh Krishnan,

Oliver Dorigo, and Carolyn R. Bertozzi. An Enzymatic Toolkit for Selective Proteolysis, Detection, and Visualization of Mucin-Domain Glycoproteins. Proceedings of the National Academy of Sciences USA. 2020; 117(35): 21299-21307. doi.org/10.1073/pnas.2012196117

 

(13) Nicholas M. Riley, Stacy A. Malaker, Marc D. Driessen, and Carolyn R. Bertozzi. Optimal

dissociation methods differ for N- and O-glycopeptides. Journal of Proteome Research. 2020; 19(8): 3286-3301. doi.org/10.1021/acs.jproteome.0c00218

Selected as ACS Editor’s Choice, Featured in JPR “Rising Stars” special issue, Among JPR’s “Most Read Articles in 2020”

 

(12) Benjamin Schumann, Stacy A. Malaker, Simon P. Wisnovsky, Marjoke F. Debets,

Anthony J. Agbay, Daniel Fernandez, Lauren J. S. Wagner, Liang Lin, Zhen Li, Junwon Choi, Douglas M. Fox, Jessie M. Peh, Melissa A. Gray, Kayvon Pedram, Jennifer J. Kohler, Milan Mrksich, and Carolyn R. Bertozzi. Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells. Molecular Cell, 2020; 78(5): 834-834. doi.org/10.1016/j.molcel.2020.03.030 

 

(11) Ryan A. Flynn, Benjamin A.H. Smith, Alex Johnson, Kayvon Pedram, Benson M. George,

Stacy A. Malaker, Karim Majzoub, Jan E. Carette, and Carolyn R. Bertozzi. Mammalian Y-RNAs are glycosylated at discrete guanosine residues with N-type glycans. bioRXiv 787614:  doi.org/10.1101/787614

Featured in Science News, C&E News, The Scientist, and Science Translational Medicine

 

(10) Junwon Choi, Lauren J. S. Wagner, Suzanne B. P. E. Timmermans, Stacy A. Malaker,

Benjamin Schumann, Melissa A. Gray, Marjoke F. Debets, Megumi Takashima, Jase Gehring, and Carolyn R. Bertozzi. Engineering Orthogonal Polypeptide GalNAc-Transferase and UDP-Sugar Pairs. Journal of the American Chemical Society. 2019; 141(34): 13442-13453. doi.org/10.1021/jacs.9b04695

 

(9) Stacy A. Malakerǂ, Kayvon Pedramǂ, Michael J. Ferracane, Barbara A. Bensing,

Venkatesh Krishnan, Christian Pett, Jin Yu, Elliot C. Woods, Jessica R. Kramer, Ulrika Westerlind, Oliver Dorigo, and Carolyn R. Bertozzi. The mucin-selective protease StcE enables molecular and functional analysis of human cancer-associated mucins. Proceedings of the National Academy of Sciences USA. 2019, 116(15): 7278-7287. doi.org/10.1073/pnas.1813020116 Featured in ChEM-H News

 

Mucin-domain glycoproteins are heavily implicated in cancer progression but remain difficult to interrogate analytically. This work demonstrated that the bacterial mucinase StcE could be leveraged as a selective biochemical tool for enrichment, visualization, and functional characterization of cancer-associated mucins, establishing a foundation for subsequent mucinomics technologies.

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(8) Invited book chapter: Stacy A. Malaker* and Michael J. Ferracane. Mass Spectrometric

Identification and Molecular Modeling of Glycopeptides Presented by MHC Class I and II Processing Pathways. In: Fulton K., Twine S. (eds) Immunoproteomics. Methods in Molecular Biology, 2019, vol 2024. Humana, New York, NY. doi: 10.1007/978-1-4939-9597-4_17

 

(7) Invited book chapter: Sarah A. Penny and Stacy A. Malaker*. Isolation of Major

Histocompatibility Complex (MHC)-Associated Peptides by Immunoaffinity Purification. In: Fulton K., Twine S. (eds) Immunoproteomics. Methods in Molecular Biology, 2019, vol 2024. Humana, New York, NY doi: 10.1007/978-1-4939-9597-4_14

 

(6) Rebecca Pavlos, Elizabeth J. McKinnon, David A. Ostrov, Bjoern Peters, Soren Buus,

David Koelle, Abha Chopra, Ryan Schutte, Craig Rive, Alec Redwood, Susana Restrepo, Austin Bracey, Thomas Kaever, Paisley T. Myers, Ellen H. Spears, Stacy A. Malaker, Jeffrey Shabanowitz, Jing Yuan, Silvana Gaudieri, Donald F. Hunt, Mary Carrington, David W. Haas, Simon Mallal, and Elizabeth J. Phillips. Shared binding specificities of HLA Class I and Class II Alleles Associate with Cutaneous Nevirapine Hypersensitivity and Identify Novel Risk Alleles. Scientific Reports. 2017 Aug 17;7(1):8653. doi: 10.1038/s41598-017-08876-0.

 

(5) Stacy A. Malakerǂ, Sarah A. Pennyǂ, Lora Steadman, Paisley T. Myers, Justin C. Loke,

Manoj Raghavan, Dina L. Bai, Jeffrey Shabanowitz, Donald F. Hunt, Mark Cobbold. Identification of glycopeptides as post-translationally modified neoantigens in leukemia. Cancer Immunology Research. 2017, 5(5): 376-384. doi: 10.1158/2326-6066.CIR-16-0280

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(4) Tobias Bergmann, Mikaela Lindvall, Erin Moore, Eugene Moore, John Sidney, Donald

Miller, Rebecca Tallmadge, Paisley T. Myers, Stacy A. Malaker, Jeffrey Shabanowitz, Nikolaus Osterrieder, Bjoern Peters, Donald F. Hunt, Douglas F. Antczak, and Alessandro Sette. Peptide binding motifs of two common equine class I MHC molecules in thoroughbred horses. Immunogenetics. 2017; 69(5): 351-358. doi: 10.1007/s00251-017-0978-6

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(3) Malcolm JW Sim, Stacy A. Malaker, Ayesha Khan, Janet M. Stowell, Jeffrey Shabanowitz,

Mary E. Peterson, Sumati Rajagopalan, Donald F. Hunt, Daniel M. Altmann, Eric O. Long, and Rosemary J. Boyton. Canonical and Cross-reactive Binding of NK Cell Inhibitory Receptors to HLA-C Allotypes Is Dictated by Peptides Bound to HLA-C. Frontiers Immunology. 2017, 8(193). doi: 10.3389/fimmu.2017.00193

 

(2) Stacy A. Malaker, Michael J. Ferracane, Florence R. Depontieu, Angela L. Zarling, Jeffrey

Shabanowitz, Dina L. Bai, Suzanne Topalian, Victor H. Engelhard, and Donald F. Hunt. Identification and Characterization of Complex Glycosylated Peptides Presented by the MHC Class II Processing Pathway in Melanoma. Journal of Proteome Research. 2017, 16(1): 228-237. doi: 10.1021/acs.jproteome.6b00496

Featured in JPR “Rising Stars” special issue

 

(1) Mark Cobbold, Hugo De La Pena, Andrew Norris, Joy Polefrone, James E. Turner, Jie

Qian, A. Michelle English, Jennifer G. Abelin, Stacy A. Malaker, Angela L. Zarling, Hsing-Wen Huang, Sarah Penny, Sylvie Freeman, Jeffrey Shabanowitz, Guy Pratt, Charles Craddock, Michael E. Williams, Donald F. Hunt, and Victor H. Engelhard. MHC Class I–Associated Phosphopeptides Are the Targets of Memory-like Immunity in Leukemia. Science Translational Medicine. 5(203) 203ra1252013. doi: 10.1126/scitranslmed.3006061