Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-Treated Pancreatic Beta Cells

Authors: Gluth, Austin ^{1, 2}, Li, Xiaolu ¹, Gritsenko, Marina A. ¹, Gaffrey, Matthew J. ¹, Kim, Doo Nam ¹, Lalli, Priscila M. ¹, Chu, Rosalie K. ¹, Day, Nicholas J. ¹, Sagendorf, Tyler J. ¹, Monroe, Matthew E. ¹, Feng, Song ¹, Liu, Tao ¹, Yang, Bin ², Qian, Wei-Jun ¹, Zhang, Tong ^{1, ∗}

Source: In Molecular & Cellular Proteomics December 2024 23(12)

A deep redox proteome profiling workflow and its application to skeletal muscle of a Duchenne Muscular Dystrophy model

Authors: Day, Nicholas J., Zhang, Tong, Gaffrey, Matthew J., Zhao, Rui, Fillmore, Thomas L., Moore, Ronald J., Rodney, George G., Qian, Wei-Jun

Source: In Free Radical Biology and Medicine 20 November 2022 193 Part 1:373-384

Distinctive carbon repression effects in the carbohydrate-selective wood decay fungus Rhodonia placenta

Authors: Zhang, Jiwei, Meng Markillie, Lye, Mitchell, Hugh D, Gaffrey, Matthew J, Orr, Galya, Schilling, Jonathan S.

Source: In Fungal Genetics and Biology April 2022 159

Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress

Authors: Li, Xiaolu, Day, Nicholas J., Feng, Song, Gaffrey, Matthew J., Lin, Tai-Du, Paurus, Vanessa L., Monroe, Matthew E., Moore, Ronald J., Yang, Bin, Xian, Ming, Qian, Wei-Jun

Source: In Redox Biology October 2021 46

Protein thiol oxidation in the rat lung following e-cigarette exposure

Authors: Wang, Juan, Zhang, Tong, Johnston, Carl J., Kim, So-Young, Gaffrey, Matthew J., Chalupa, David, Feng, Guanqiao, Qian, Wei-Jun, McGraw, Matthew D., Ansong, Charles

Source: In Redox Biology October 2020 37

Stochiometric quantification of the thiol redox proteome of macrophages reveals subcellular compartmentalization and susceptibility to oxidative perturbations

Authors: Duan, Jicheng, Zhang, Tong, Gaffrey, Matthew J., Weitz, Karl K., Moore, Ronald J., Li, Xiaolu, Xian, Ming, Thrall, Brian D., Qian, Wei-Jun

Source: In Redox Biology September 2020 36

Rosette core fungal resistance in Arabidopsis thaliana

Authors: Dai, Yanwan, Ogilvie, Huw A., Liu, Yuan, Huang, Michael, Markillie, Lye Meng, Mitchell, Hugh D., Borrego, Eli J., Kolomiets, Michael V., Gaffrey, Matthew J., Orr, Galya, Chehab, E. Wassim, Mao, Wan-Ting, Braam, Janet

Source: Planta, 2019 Dec 01. 250(6), 1941-1953.

Access URL: https://www.jstor.org/stable/48702428

Evaluation of the cytotoxic and cellular proteome impacts of food-grade TiO2 (E171) using simulated gastrointestinal digestions and a tri-culture small intestinal epithelial model

Authors: Cao, Xiaoqiong, Zhang, Tong, DeLoid, Glen M., Gaffrey, Matthew J., Weitz, Karl K., Thrall, Brian D., Qian, Wei-Jun, Demokritou, Philip

Source: In NanoImpact January 2020 17

A proteome-wide assessment of the oxidative stress paradigm for metal and metal-oxide nanomaterials in human macrophages

Authors: Zhang, Tong, Gaffrey, Matthew J., Thomas, Dennis G., Weber, Thomas J., Hess, Becky M., Weitz, Karl K., Piehowski, Paul D., Petyuk, Vladislav A., Moore, Ronald J., Qian, Wei-Jun, Thrall, Brian D.

Source: In NanoImpact January 2020 17

Automated Coupling of Nanodroplet Sample Preparation with Liquid Chromatography—Mass Spectrometry for High-Throughput Single-Cell Proteomics

Authors: Williams, Sarah M., Liyu, Andrey V., Tsai, Chia-Feng, Moore, Ronald J., Orton, Daniel J., Chrisler, William B., Gaffrey, Matthew J., Liu, Tao, Smith, Richard D., Kelly, Ryan T.

Source: Analytical chemistry. 92(15):10588-10596

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN624435301&indx=1&recIds=ETOCRN624435301

Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling

Authors: Zhang, Tong, Gaffrey, Matthew J., Monroe, Matthew E., Thomas, Dennis G., Weitz, Karl K., Piehowski, Paul D., Petyuk, Vladislav A., Moore, Ronald J., Thrall, Brian D., Qian, Wei-Jun

Source: Journal of proteome research. 19(7):2863-2872

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN624267471&indx=1&recIds=ETOCRN624267471

Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line

Authors: Tan, Zhijing, Zhu, Jianhui, Stemmer, Paul M., Sun, Liangliang, Yang, Zhichang, Schultz, Kendall, Gaffrey, Matthew J., Cesnik, Anthony J., Yi, Xinpei, Hao, Xiaohu

Source: Journal of proteome research. 19(4):1635-1646

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN623953487&indx=1&recIds=ETOCRN623953487

Accurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-Search Delta Score Strategy

Authors: Wang, Xi, Swensen, Adam C., Zhang, Tong, Piehowski, Paul D., Gaffrey, Matthew J., Monroe, Matthew E., Zhu, Ying, Dong, Hailiang, Qian, Wei-Jun

Source: Journal of proteome research. 19(4):1863-1872

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN623953660&indx=1&recIds=ETOCRN623953660

Improving mitochondrial function with SS-31 reverses age-related redox stress and improves exercise tolerance in aged mice

Authors: Campbell, Matthew D., Duan, Jicheng, Samuelson, Ashton T., Gaffrey, Matthew J., Merrihew, Gennifer E., Egertson, Jarrett D., Wang, Lu, Bammler, Theo K., Moore, Ronald J., White, Collin C., Kavanagh, Terrance J., Voss, Joachim G., Szeto, Hazel H., Rabinovitch, Peter S., MacCoss, Michael J., Qian, Wei-Jun, Marcinek, David J.

Source: In Free Radical Biology and Medicine April 2019 134:268-281

Reference genes for accurate normalization of gene expression in wood-decomposing fungi

Authors: Zhang, Jiwei, Mitchell, Hugh D., Markillie, Lye Meng, Gaffrey, Matthew J., Orr, Galya, Schilling, Jonathan

Source: In Fungal Genetics and Biology February 2019 123:33-40

Fatiguing contractions increase protein S-glutathionylation occupancy in mouse skeletal muscle

Authors: Kramer, Philip A., Duan, Jicheng, Gaffrey, Matthew J., Shukla, Anil K., Wang, Lu, Bammler, Theo K., Qian, Wei-Jun, Marcinek, David J.

Source: In Redox Biology July 2018 17:367-376

Carrier-Assisted Single-Tube Processing Approach for Targeted Proteomics Analysis of Low Numbers of Mammalian Cells

Authors: Zhang, Pengfei, Gaffrey, Matthew J., Zhu, Ying, Chrisler, William B., Fillmore, Thomas L., Yi, Lian, Nicora, Carrie D., Zhang, Tong, Wu, Huanming, Jacobs, Jon

Source: Analytical chemistry. 91(2):1441-1451

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN618902662&indx=1&recIds=ETOCRN618902662

Signatures of cysteine oxidation on muscle structural and contractile proteins are associated with physical performance and muscle function in older adults: Study of Muscle, Mobility and Aging (SOMMA).

Authors: Day, Nicholas J., Kelly, Shane S., Lui, Li‐Yung, Mansfield, Tyler A., Gaffrey, Matthew J., Trejo, Jesse B., Sagendorf, Tyler J., Attah, Isaac K., Moore, Ronald J., Douglas, Collin M., Newman, Anne B., Kritchevsky, Stephen B., Kramer, Philip A., Marcinek, David J., Coen, Paul M., Goodpaster, Bret H., Hepple, Russell T., Cawthon, Peggy M., Petyuk, Vladislav A., Esser, Karyn A.

Source: Aging Cell; Jun2024, Vol. 23 Issue 6, p1-12, 12p

Subject Terms: CONTRACTILE proteins, CYTOSKELETAL proteins, OLDER people, PHYSICAL mobility, MUSCLE proteins, LEG muscles

Cell‐type‐specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems.

Authors: Fu, Jie, McKinley, Brian, James, Brandon, Chrisler, William, Markillie, Lye Meng, Gaffrey, Matthew J., Mitchell, Hugh D., Riaz, Muhammad Rizwan, Marcial, Brenda, Orr, Galya, Swaminathan, Kankshita, Mullet, John, Marshall‐Colon, Amy

Source: Plant Journal; Jun2024, Vol. 118 Issue 5, p1668-1688, 21p

Subject Terms: SORGHUM, GENE regulatory networks, GENETIC regulation, TRANSCRIPTOMES, SORGO, SUSTAINABILITY, ENERGY crops

Mass spectrometry-based proteomics for system-level characterization of biological responses to engineered nanomaterials

Authors: Zhang, Tong, Gaffrey, Matthew J., Thrall, Brian D., Qian, Wei-Jun

Source: Analytical and bioanalytical chemistry. 410(24):6067-6077

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100125589914.0x000001&indx=1&recIds=ETOCvdc_100125589914.0x000001