Proteomics Standards Initiatives ProForma 2.0 Unifying the encoding of Proteoforms and Peptidoforms

Authors: LeDuc, Richard D., Deutsch, Eric W., Binz, Pierre-Alain, Fellers, Ryan T., Cesnik, Anthony J., Klein, Joshua A., Bossche, Tim Van Den, 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

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2109.11352

Anatomic nomenclature and 3-dimensional regional model of the human ovary: call for a new paradigm

Authors: O’Neill, Kathleen E., Maher, Jacqueline Y., Laronda, Monica M., Duncan, Francesca E., LeDuc, Richard D., Lujan, Marla E., Oktay, Kutluk H., Pouch, Alison M., Segars, James H., Tsui, Elizabeth L., Zelinski, Mary B., Halvorson, Lisa M., Gomez-Lobo, Veronica

Source: In American Journal of Obstetrics and Gynecology March 2023 228(3):270-275

Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor

Authors: Ives, Ashley N., Dunn, Henry A., Afsari, Hamid Samareh, dos Santos Seckler, Henrique, Foroutan, Max J., Chavez, Erica, Melani, Rafael D., Fellers, Ryan T., LeDuc, Richard D., Thomas, Paul M.

Source: Journal of the American Chemical Society. 144(50):23104-23114

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN630948974&indx=1&recIds=ETOCRN630948974

Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

Authors: 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

Source: Journal of proteome research. 21(4):1189-1195

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN629106570&indx=1&recIds=ETOCRN629106570

Anatomic nomenclature and 3-dimensional regional model of the human ovary: call for a new paradigm

Authors: O'Neill, Kathleen E., Maher, Jacqueline Y., Laronda, Monica M., Duncan, Francesca E., LeDuc, Richard D., Lujan, Marla E., Oktay, Kutluk H., Pouch, Alison M., Segars, James H., Tsui, Elizabeth L., Zelinski, Mary B., Halvorson, Lisa M., Gomez-Lobo, Veronica

Source: American journal of obstetrics and gynecology. 228(3):270-275.e4

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100188850085.0x000001&indx=1&recIds=ETOCvdc_100188850085.0x000001

Defining the NSD2 interactome: PARP1 PARylation reduces NSD2 histone methyltransferase activity and impedes chromatin binding

Alternate Title: PARylation impedes NSD2 binding to chromatin (English)

Authors: Huang, Xiaoxiao, LeDuc, Richard D., Fornelli, Luca, Schunter, Alissa J., Bennett, Richard L., Kelleher, Neil L., Licht, Jonathan D.

Source: In Journal of Biological Chemistry 16 August 2019 294(33):12459-12471

Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics

Authors: LeDuc, Richard D. ^{‡, **}, Fellers, Ryan T. ^‡, Early, Bryan P. ^{‡, §}, Greer, Joseph B. ^‡, Shams, Daniel P. ^¶, Thomas, Paul M. ^{‡, §}, Kelleher, Neil L. ^{‡, §, ‖, ‡‡}

Source: In Molecular & Cellular Proteomics April 2019 18(4):796-805

Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk

Authors: 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.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2018 Apr . 115(16), 4140-4145.

Access URL: https://www.jstor.org/stable/26508831

Multidimensional Top-Down Proteomics of Brain-Region-Specific Mouse Brain Proteoforms Responsive to Cocaine and Estradiol

Authors: Park, Hae-Min, Satta, Rosalba, Davis, Roderick G., Goo, Young Ah, LeDuc, Richard D., Fellers, Ryan T., Greer, Joseph B., Romanova, Elena V., Rubakhin, Stanislav S., Tai, Rex

Source: Journal of proteome research. 18(11):3999-4012

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN622132230&indx=1&recIds=ETOCRN622132230

ProSight Annotator: Complete control and customization of protein entries in UniProt XML files

Authors: Greer, Joseph B., Early, Bryan P., Durbin, Kenneth R., Patrie, Steven M., Thomas, Paul M., Kelleher, Neil L., LeDuc, Richard D., Fellers, Ryan T.

Source: Proteomics. 22(11-12)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100154004492.0x000001&indx=1&recIds=ETOCvdc_100154004492.0x000001

The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins

Authors: Riley, Nicholas M., Sikora, Jacek W., Seckler, Henrique S., Greer, Joseph B., Fellers, Ryan T., LeDuc, Richard D., Westphall, Michael S., Thomas, Paul M., Kelleher, Neil L., Coon, Joshua J.

Source: Analytical chemistry. 90(14):8553-8560

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN616787583&indx=1&recIds=ETOCRN616787583

Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms Between Mouse Strains

Authors: Davis, Roderick G., Park, Hae-Min, Kim, Kyunggon, Greer, Joseph B., Fellers, Ryan T., LeDuc, Richard D., Romanova, Elena V., Rubakhin, Stanislav S., Zombeck, Jonathan A., Wu, Cong

Source: Analytical chemistry. 90(6):3802-3810

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN615339633&indx=1&recIds=ETOCRN615339633

ProForma: A Standard Proteoform Notation

Authors: LeDuc, Richard D., Schwämmle, Veit, Shortreed, Michael R., Cesnik, Anthony J., Solntsev, Stefan K., Shaw, Jared B., Martin, Maria J., Vizcaino, Juan A., Alpi, Emanuele, Danis, Paul

Source: Journal of proteome research. 17(3):1321-1325

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN615189313&indx=1&recIds=ETOCRN615189313

Integrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts

Authors: Ntai, Ioanna ^{‡, §}, LeDuc, Richard D. ^‡, Fellers, Ryan T. ^‡, Erdmann-Gilmore, Petra ^‖, Davies, Sherri R. ^‖, Rumsey, Jeanne ^‖, Early, Bryan P. ^‡, Thomas, Paul M. ^{‡, ¶}, Li, Shunqiang ^‖, Compton, Philip D. ^{‡, ‖}, Ellis, Matthew J.C. ^**, Ruggles, Kelly V. ^‡‡, Fenyö, David ^‡‡, Boja, Emily S. ^§§, Rodriguez, Henry ^§§, Townsend, R. Reid ^{‖, ¶¶}, Kelleher, Neil L. ^{‡, §, ¶, ¶¶}

Source: In Molecular & Cellular Proteomics January 2016 15(1):45-56

Quantitative proteomics and transcriptomics reveals metabolic differences in attracting and non-attracting human-in-mouse glioma stem cell xenografts and stromal cells

Authors: Wildburger, Norelle C., Lichti, Cheryl F., LeDuc, Richard D., Schmidt, Mary, Kroes, Roger A., Moskal, Joseph R., Nilsson, Carol L.

Source: In EuPA Open Proteomics September 2015 8:94-103

Quantitative Proteomics Reveals Protein–Protein Interactions with Fibroblast Growth Factor 12 as a Component of the Voltage-Gated Sodium Channel 1.2 (Nav1.2) Macromolecular Complex in Mammalian Brain*

Authors: Wildburger, Norelle C. ^{‡, §, ¶, ‡‡}, Ali, Syed R. ^‡, Hsu, Wei-Chun J. ^‖, Shavkunov, Alexander S. ^{‡, ¶}, Nenov, Miroslav N. ^‡, Lichti, Cheryl F. ^{‡, ¶}, LeDuc, Richard D. ^**, Mostovenko, Ekaterina ^{‡, ¶}, Panova-Elektronova, Neli I. ^‡, Emmett, Mark R. ^{¶, ‖}, Nilsson, Carol L. ^{‡, ¶}, Laezza, Fernanda ^{‡, ‡‡}

Source: In Molecular & Cellular Proteomics May 2015 14(5):1288-1300

High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer

Authors: 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.

Source: Journal of proteome research. 16(5):2072-2079

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN611229511&indx=1&recIds=ETOCRN611229511

A Method for Label-Free, Differential Top-Down Proteomics

Authors: Ntai, Ioanna, Toby, Timothy K., LeDuc, Richard D., Kelleher, Neil L.

Source: Methods in molecular biology. 1410:121-134

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN609411889&indx=1&recIds=ETOCRN609411889

Amyloid β Proteoforms Elucidated by Quantitative LC/MS in the 5xFAD Mouse Model of Alzheimer's Disease.

Authors: Kandi, Soumya, Cline, Erika N., Rivera, Brianna M., Viola, Kirsten L., Zhu, Jiuhe, Condello, Carlo, LeDuc, Richard D., Klein, William L., Kelleher, Neil L., Patrie, Steven M.

Source: Journal of Proteome Research; 11/3/2023, Vol. 22 Issue 11, p3475-3488, 14p

Effect of storage conditions on the stability and fermentability of enzymatic lignocellulosic hydrolysate

Authors: Jin, Mingjie, Bothfeld, William, Austin, Samantha, Sato, Trey K., La Reau, Alex, Li, Haibo, Foston, Marcus, Gunawan, Christa, LeDuc, Richard D., Quensen, John F., Mcgee, Mick, Uppugundla, Nirmal, Higbee, Alan, Ranatunga, Ruwan, Donald, Charles W., Bone, Gwen, Ragauskas, Arthur J., Tiedje, James M., Noguera, Daniel R., Dale, Bruce E., Zhang, Yaoping, Balan, Venkatesh

Source: In Bioresource Technology November 2013 147:212-220