De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis von Haas, Brian J, Papanicolaou, Alexie, Yassour, Moran, Grabherr, Manfred, Blood, Philip D, Bowden, Joshua, Couger, Matthew Brian, Eccles, David, Li, Bo, Lieber, Matthias, MacManes, Matthew D, Ott, Michael, Orvis, Joshua, Pochet, Nathalie, Strozzi, Francesco, Weeks, Nathan, Westerman, Rick, William, Thomas, Dewey, Colin N, Henschel, Robert, LeDuc, Richard D, Friedman, Nir, Regev, Aviv

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The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms von Hollas, Michael A R, Robey, Matthew T, Fellers, Ryan T, LeDuc, Richard D, Thomas, Paul M, Kelleher, Neil L

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Identification and Quantification of Proteoforms by Mass Spectrometry von Schaffer, Leah V., Millikin, Robert J., Miller, Rachel M., Anderson, Lissa C., Fellers, Ryan T., Ge, Ying, Kelleher, Neil L., LeDuc, Richard D., Liu, Xiaowen, Payne, Samuel H., Sun, Liangliang, Thomas, Paul M., Tucholski, Trisha, Wang, Zhe, Wu, Si, Wu, Zhijie, Yu, Dahang, Shortreed, Michael R., Smith, Lloyd M.

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Mapping intact protein isoforms in discovery mode using top-down proteomics von Tran, John C., Zamdborg, Leonid, Ahlf, Dorothy R., Lee, Ji Eun, Catherman, Adam D., Durbin, Kenneth R., Tipton, Jeremiah D., Vellaichamy, Adaikkalam, Kellie, John F., Li, Mingxi, Wu, Cong, Sweet, Steve M. M., Early, Bryan P., Siuti, Nertila, LeDuc, Richard D., Compton, Philip D., Thomas, Paul M., Kelleher, Neil L.

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Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry von Anderson, Lissa C, DeHart, Caroline J, Kaiser, Nathan K, Fellers, Ryan T, Smith, Donald F, Greer, Joseph B, LeDuc, Richard D, Blakney, Greg T, Thomas, Paul M, Kelleher, Neil L, Hendrickson, Christopher L

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Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms von LeDuc, Richard D, Deutsch, Eric W, Binz, Pierre-Alain, Fellers, Ryan T, Cesnik, Anthony J, Klein, Joshua A, Van Den Bossche, Tim, Gabriels, Ralf, Yalavarthi, Arshika, Perez-Riverol, Yasset, Carver, Jeremy, Bittremieux, Wout, Kawano, Shin, Pullman, Benjamin, Bandeira, Nuno, Kelleher, Neil L, Thomas, Paul M, Vizcaíno, Juan Antonio

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Combinatorial Modification of Human Histone H4 Quantitated by Two-dimensional Liquid Chromatography Coupled with Top Down Mass Spectrometry von Pesavento, James J., Bullock, Courtney R., LeDuc, Richard D., Mizzen, Craig A., Kelleher, Neil L.

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A Method for Label-Free, Differential Top-Down Proteomics von Ntai, Ioanna, Toby, Timothy K., LeDuc, Richard D., Kelleher, Neil L.

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An informatic framework for decoding protein complexes by top-down mass spectrometry von Skinner, Owen S, Havugimana, Pierre C, Haverland, Nicole A, Fornelli, Luca, Early, Bryan P, Greer, Joseph B, Fellers, Ryan T, Durbin, Kenneth R, Do Vale, Luis H F, Melani, Rafael D, Seckler, Henrique S, Nelp, Micah T, Belov, Mikhail E, Horning, Stevan R, Makarov, Alexander A, LeDuc, Richard D, Bandarian, Vahe, Compton, Philip D, Kelleher, Neil L

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ProSight Lite: Graphical software to analyze top‐down mass spectrometry data von Fellers, Ryan T., Greer, Joseph B., Early, Bryan P., Yu, Xiang, LeDuc, Richard D., Kelleher, Neil L., Thomas, Paul M.

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Proteomic analyses of decellularized porcine ovaries identified new matrisome proteins and spatial differences across and within ovarian compartments von Henning, Nathaniel F., LeDuc, Richard D., Even, Kelly A., Laronda, Monica M.

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Diversity of Amyloid-beta Proteoforms in the Alzheimer’s Disease Brain von Wildburger, Norelle C., Esparza, Thomas J., LeDuc, Richard D., Fellers, Ryan T., Thomas, Paul M., Cairns, Nigel J., Kelleher, Neil L., Bateman, Randall J., Brody, David L.

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The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells von Melani, Rafael D, Gerbasi, Vincent R, Anderson, Lissa C, Sikora, Jacek W, Toby, Timothy K, Hutton, Josiah E, Butcher, David S, Negrão, Fernanda, Seckler, Henrique S, Srzentić, Kristina, Fornelli, Luca, Camarillo, Jeannie M, LeDuc, Richard D, Cesnik, Anthony J, Lundberg, Emma, Greer, Joseph B, Fellers, Ryan T, Robey, Matthew T, DeHart, Caroline J, Forte, Eleonora, Hendrickson, Christopher L, Abbatiello, Susan E, Thomas, Paul M, Kokaji, Andy I, Levitsky, Josh, Kelleher, Neil L

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Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk von Ntai, Ioanna, Fornelli, Luca, DeHart, Caroline J., Hutton, Josiah E., Doubleday, Peter F., LeDuc, Richard D., van Nispen, Alexandra J., Fellers, Ryan T., Whiteley, Gordon, Boja, Emily S., Rodriguez, Henry, Kelleher, Neil L.

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A five-level classification system for proteoform identifications von Smith, Lloyd M., Thomas, Paul M., Shortreed, Michael R., Schaffer, Leah V., Fellers, Ryan T., LeDuc, Richard D., Tucholski, Trisha, Ge, Ying, Agar, Jeffrey N., Anderson, Lissa C., Chamot-Rooke, Julia, Gault, Joseph, Loo, Joseph A., Paša-Tolić, Ljiljana, Robinson, Carol V., Schlüter, Hartmut, Tsybin, Yury O., Vilaseca, Marta, Vizcaíno, Juan Antonio, Danis, Paul O., Kelleher, Neil L.

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High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer von Cleland, Timothy P, DeHart, Caroline J, Fellers, Ryan T, VanNispen, Alexandra J, Greer, Joseph B, LeDuc, Richard D, Parker, W. Ryan, Thomas, Paul M, Kelleher, Neil L, Brodbelt, Jennifer S

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Defining the NSD2 interactome: PARP1 PARylation reduces NSD2 histone methyltransferase activity and impedes chromatin binding von Huang, Xiaoxiao, LeDuc, Richard D., Fornelli, Luca, Schunter, Alissa J., Bennett, Richard L., Kelleher, Neil L., Licht, Jonathan D.

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Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer von Fornelli, Luca, Durbin, Kenneth R, Fellers, Ryan T, Early, Bryan P, Greer, Joseph B, LeDuc, Richard D, Compton, Philip D, Kelleher, Neil L

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Creating a common language for the subanatomy of the ovary von Tsui, Elizabeth L., O'Neill, Kathleen E., LeDuc, Richard D., Shikanov, Ariella, Gomez-Lobo, Veronica, Laronda, Monica M.

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The C‑Score: A Bayesian Framework to Sharply Improve Proteoform Scoring in High-Throughput Top Down Proteomics von LeDuc, Richard D, Fellers, Ryan T, Early, Bryan P, Greer, Joseph B, Thomas, Paul M, Kelleher, Neil L

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