A learned embedding for efficient joint analysis of millions of mass spectra von Bittremieux, Wout, May, Damon H., Bilmes, Jeffrey, Noble, William Stafford

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Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings von May, Damon H, Tamura, Kaipo, Noble, William S

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Detecting Modifications in Proteomics Experiments with Param-Medic von May, Damon H, Tamura, Kaipo, Noble, William S

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Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns von Timmins-Schiffman, Emma, May, Damon H, Mikan, Molly, Riffle, Michael, Frazar, Chris, Harvey, H R, Noble, William S, Nunn, Brook L

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Statistical Inference from Multiple iTRAQ Experiments without Using Common Reference Standards von Herbrich, Shelley M, Cole, Robert N, West, Keith P, Schulze, Kerry, Yager, James D, Groopman, John D, Christian, Parul, Wu, Lee, O’Meally, Robert N, May, Damon H, McIntosh, Martin W, Ruczinski, Ingo

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Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes von Mikan, Molly P., Harvey, H. Rodger, Timmins-Schiffman, Emma, Riffle, Michael, May, Damon H., Salter, Ian, Noble, William S., Nunn, Brook L.

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Quantitative Glycoproteomics Analysis Reveals Changes in N‑Glycosylation Level Associated with Pancreatic Ductal Adenocarcinoma von Pan, Sheng, Chen, Ru, Tamura, Yasuko, Crispin, David A, Lai, Lisa A, May, Damon H, McIntosh, Martin W, Goodlett, David R, Brentnall, Teresa A

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An Alignment-Free “Metapeptide” Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing von May, Damon H, Timmins-Schiffman, Emma, Mikan, Molly P, Harvey, H. Rodger, Borenstein, Elhanan, Nunn, Brook L, Noble, William S

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MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data von Riffle, Michael, May, Damon H, Timmins-Schiffman, Emma, Mikan, Molly P, Jaschob, Daniel, Noble, William Stafford, Nunn, Brook L

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Metabolomic profiling of urine: response to a randomised, controlled feeding study of select fruits and vegetables, and application to an observational study von May, Damon H., Navarro, Sandi L., Ruczinski, Ingo, Hogan, Jason, Ogata, Yuko, Schwarz, Yvonne, Levy, Lisa, Holzman, Ted, McIntosh, Martin W., Lampe, Johanna W.

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T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity von Elyanow, Rebecca, Snyder, Thomas M, Dalai, Sudeb C, Gittelman, Rachel M, Boonyaratanakornkit, Jim, Wald, Anna, Selke, Stacy, Wener, Mark H, Morishima, Chihiro, Greninger, Alexander L, Gale, Jr, Michael, Hsiang, Tien-Ying, Jing, Lichen, Holbrook, Michael R, Kaplan, Ian M, Zahid, H Jabran, May, Damon H, Carlson, Jonathan M, Baldo, Lance, Manley, Thomas, Robins, Harlan S, Koelle, David M

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A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS von Bellew, Matthew, Coram, Marc, Fitzgibbon, Matthew, Igra, Mark, Randolph, Tim, Wang, Pei, May, Damon, Eng, Jimmy, Fang, Ruihua, Lin, ChenWei, Chen, Jinzhi, Goodlett, David, Whiteaker, Jeffrey, Paulovich, Amanda, McIntosh, Martin

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Proteins associated with pancreatic cancer survival in patients with resectable pancreatic ductal adenocarcinoma von Chen, Ru, Dawson, David W, Pan, Sheng, Ottenhof, Niki A, de Wilde, Roeland F, Wolfgang, Christopher L, May, Damon H, Crispin, David A, Lai, Lisa A, Lay, Anna R, Waghray, Meghna, Wang, Shouli, McIntosh, Martin W, Simeone, Diane M, Maitra, Anirban, Brentnall, Teresa A

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MRMer, an Interactive Open Source and Cross-platform System for Data Extraction and Visualization of Multiple Reaction Monitoring Experiments von Martin, Daniel B., Holzman, Ted, May, Damon, Peterson, Amelia, Eastham, Ashley, Eng, Jimmy, McIntosh, Martin

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Proteomics portrait of archival lesions of chronic pancreatitis von Pan, Sheng, Chen, Ru, Stevens, Tyler, Bronner, Mary P, May, Damon, Tamura, Yasuko, McIntosh, Martin W, Brentnall, Teresa A

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Brain-specific Proteins Decline in the Cerebrospinal Fluid of Humans with Huntington Disease von Fang, Qiaojun, Strand, Andrew, Law, Wendy, Faca, Vitor M., Fitzgibbon, Matthew P., Hamel, Nathalie, Houle, Benoit, Liu, Xin, May, Damon H., Poschmann, Gereon, Roy, Line, Stuühler, Kai, Ying, Wantao, Zhang, Jiyang, Zheng, Zhaobin, Bergeron, John J.M., Hanash, Sam, He, Fuchu, Leavitt, Blair R., Meyer, Helmut E., Qian, Xiaohong, McIntosh, Martin W.

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Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach von Pan, Sheng, Hullar, Meredith A J, Lai, Lisa A, Peng, Hong, May, Damon H, Noble, William S, Raftery, Daniel, Navarro, Sandi L, Neuhouser, Marian L, Lampe, Paul D, Lampe, Johanna W, Chen, Ru

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Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi von Krayushkina, Dasha, Timmins-Schiffman, Emma, Faux, Jessica, May, Damon H., Riffle, Michael, Harvey, H. Rodger, Nunn, Brook L.

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Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework von Blank, Clemens, Easterly, Caleb, Gruening, Bjoern, Johnson, James, Kolmeder, Carolin A, Kumar, Praveen, May, Damon, Mehta, Subina, Mesuere, Bart, Brown, Zachary, Elias, Joshua E, Hervey, W Judson, McGowan, Thomas, Muth, Thilo, Nunn, Brook, Rudney, Joel, Tanca, Alessandro, Griffin, Timothy J, Jagtap, Pratik D

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Software Platform for Rapidly Creating Computational Tools for Mass Spectrometry-Based Proteomics von May, Damon, Law, Wendy, Fitzgibbon, Matt, Fang, Qiaojun, McIntosh, Martin

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