Extensive three-dimensional intratumor proteomic heterogeneity revealed by multiregion sampling in high-grade serous ovarian tumor specimens.
Hunt AL, Bateman NW, Barakat W, Makohon-Moore S, Hood BL, Conrads KA, Zhou M, Calvert V, Pierobon M, Loffredo J, Litzi TJ, Oliver J, Mitchell D, Gist G, Rojas C, Blanton B, Robinson EL, Odunsi K, Sood AK, Casablanca Y, Darcy KM, Shriver CD, Petricoin EF, Rao UNM, Maxwell GL, Conrads TP.
iScience. 2021 Jun 21;24(7):102757. doi: 10.1016/j.isci.2021.102757. eCollection 2021 Jul 23. PMID: 34278265
Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer.
Lee S, Zhao L, Rojas C, Bateman NW, Yao H, Lara OD, Celestino J, Morgan MB, Nguyen TV, Conrads KA, Rangel KM, Dood RL, Hajek RA, Fawcett GL, Chu RA, Wilson K, Loffredo JL, Viollet C, Jazaeri AA, Dalgard CL, Mao X, Song X, Zhou M, Hood BL, Banskota N, Wilkerson MD, Te J, Soltis AR, Roman K, Dunn A, Cordover D, Eterovic AK, Liu J, Burks JK, Baggerly KA, Fleming ND, Lu KH, Westin SN, Coleman RL, Mills GB, Casablanca Y, Zhang J, Conrads TP, Maxwell GL, Futreal PA, Sood AK.
Cell Rep. 2020 Apr 14;31(2):107502. doi: 10.1016/j.celrep.2020.03.066.PMID: 32294438
Molecular Correlates of Venous Thromboembolism (VTE) in Ovarian Cancer.
Glassman D, Bateman NW, Lee S, Zhao L, Yao J, Tan Y, Ivan C, Rangel KM, Zhang J, Conrads KA, Hood BL, Abulez T, Futreal PA, Fleming ND, Afshar-Kharghan V, Maxwell GL, Conrads TP, Chen K, Sood AK.
Cancers (Basel). 2022 Mar 15;14(6):1496. doi: 10.3390/cancers14061496.PMID: 35326647
Brain proteomic atlas of alcohol use disorder in adult males.
Teng PN, Barakat W, Tran SM, Tran ZM, Bateman NW, Conrads KA, Wilson KN, Oliver J, Gist G, Hood BL, Zhou M, Maxwell GL, Leggio L, Conrads TP, Lee MR.
Transl Psychiatry. 2023 Oct 13;13(1):318. doi: 10.1038/s41398-023-02605-0.PMID: 37833300
Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants, and therapeutically relevant pathways.
Soltis AR, Bateman NW, Liu J, Nguyen T, Franks TJ, Zhang X, Dalgard CL, Viollet C, Somiari S, Yan C, Zeman K, Skinner WJ, Lee JSH, Pollard HB, Turner C, Petricoin EF, Meerzaman D, Conrads TP, Hu H; APOLLO Research Network; Shriver CD, Moskaluk CA, Browning RF Jr, Wilkerson MD.
Cell Rep Med. 2022 Nov 15;3(11):100819. doi: 10.1016/j.xcrm.2022.100819.PMID: 36384096
Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors
Kwong-Kwok Wong, Nicholas W. Bateman, Chun Wai Ng, Yvonne T. M. Tsang, Charlotte S. Sun, Joseph Celestino, Tri V. Nguyen, Anais Malpica, R. Tyler Hillman, Jianhua Zhang, P. Andrew Futreal, Christine Rojas, Kelly A. Conrads, Brian L. Hood, Clifton L. Dalgard, Matthew D. Wilkerson, Neil T. Phippen, Thomas P. Conrads, George L. Maxwell, Anil K. Sood, David M. Gershenson
J Transl Med. 2022; 20: 606. Published online 2022 Dec 17. doi: 10.1186/s12967-022-03820-x
PMCID: PMC9758924
Strategies to recover proteins from ocular tissues for proteomics.
Patel N, Solanki E, Picciani R, Cavett V, Caldwell-Busby JA, Bhattacharya SK.
Proteomics. 2008 Mar;8(5):1055-70. doi: 10.1002/pmic.200700856. PMID: 18324731.
Label-free mass spectrometry-based relative quantification of proteins separated by one-dimensional gel electrophoresis.
Getie-Kebtie M, Lazarev A, Eichelberger M, Alterman M. Anal Biochem. 2011 Feb 15;409(2):202-12. doi: 10.1016/j.ab.2010.10.023. Epub 2010 Nov 9. PMID: 20971051.
Molecular Correlates of Venous Thromboembolism (VTE) in Ovarian Cancer
Deanna Glassman, Nicholas W. Bateman, Sanghoon Lee, Li Zhao, Jun Yao, Yukun Tan, Cristina Ivan, Kelly M. Rangel, Jianhua Zhang, Kelly A. Conrads, Brian L. Hood, Tamara Abulez, P. Andrew Futreal, Nicole D. Fleming, Vahid Afshar-Kharghan, George L. Maxwell, Thomas P. Conrads, Ken Chen, Anil K. Sood
Cancers (Basel) 2022 Mar; 14(6): 1496. Published online 2022 Mar 15. doi: 10.3390/cancers14061496
PMCID: PMC8946269
Peptide ancestry informative markers in uterine neoplasms from women of European, African, and Asian ancestry
Nicholas W. Bateman, Christopher M. Tarney, Tamara S. Abulez, Brian L. Hood, Kelly A. Conrads, Ming Zhou, Anthony R. Soltis, Pang-Ning Teng, Amanda Jackson, Chunqiao Tian, Clifton L. Dalgard, Matthew D. Wilkerson, Michael D. Kessler, Zachary Goecker, Jeremy Loffredo, Craig D. Shriver, Hai Hu, Michele Cote, Glendon J. Parker, James Segars, Ayman Al-Hendy, John I. Risinger, Neil T. Phippen, Yovanni Casablanca, Kathleen M. Darcy, G. Larry Maxwell, Thomas P. Conrads, Timothy D. O'Connor
iScience. 2022 Jan 21; 25(1): 103665. Published online 2021 Dec 23. doi: 10.1016/j.isci.2021.103665
PMCID: PMC8753123
Proteogenomic landscape of uterine leiomyomas from hereditary leiomyomatosis and renal cell cancer patients
Nicholas W. Bateman, Christopher M. Tarney, Tamara Abulez, Anthony R. Soltis, Ming Zhou, Kelly Conrads, Tracy Litzi, Julie Oliver, Brian Hood, Paul Driggers, Coralie Viollet, Clifton Dalgard, Matthew Wilkerson, William Catherino, Chad A. Hamilton, Kathleen M. Darcy, Yovanni Casablanca, Ayman Al-Hendy, James Segars, Thomas P. Conrads, G. Larry Maxwell
Sci Rep. 2021; 11: 9371. Published online 2021 Apr 30. doi: 10.1038/s41598-021-88585-x
PMCID: PMC8087684
Biomarker panel for early detection of endometrial cancer in the Prostate, Lung, Colorectal, and Ovarian cancer screening trial.
Tarney CM, Wang G, Bateman NW, Conrads KA, Zhou M, Hood BL, Loffredo J, Tian C, Darcy KM, Hamilton CA, Casablanca Y, Lokshin A, Conrads TP, Maxwell GL. Am J Obstet Gynecol. 2019 Nov;221(5): 472.e1-472.e10. doi: 10.1016/j.ajog.2019.06.005. Epub 2019 Jul 4.PMID: 31279844
Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies
Yue Xuan, Nicholas W. Bateman, Sebastien Gallien, Sandra Goetze, Yue Zhou, Pedro Navarro, Mo Hu, Niyati Parikh, Brian L. Hood, Kelly A. Conrads, Christina Loosse, Reta Birhanu Kitata, Sander R. Piersma, Davide Chiasserini, Hongwen Zhu, Guixue Hou, Muhammad Tahir, Andrew Macklin, Amanda Khoo, Xiuxuan Sun, Ben Crossett, Albert Sickmann, Yu-Ju Chen, Connie R. Jimenez, Hu Zhou, Siqi Liu, Martin R. Larsen, Thomas Kislinger, Zhinan Chen, Benjamin L. Parker, Stuart J. Cordwell, Bernd Wollscheid, Thomas P. Conrads
Nat Commun. 2020; 11: 5248. Published online 2020 Oct 16. doi: 10.1038/s41467-020-18904-9
PMCID: PMC7568553
Identification of Putative Early Atherosclerosis Biomarkers by Unsupervised Deconvolution of Heterogeneous Vascular Proteomes
Sarah J Parker, Lulu Chen, Weston Spivia, Georgia Saylor, Chunhong Mao, Vidya Venkatraman, Ronald J. Holewinski, Mitra Mastali, Rakhi Pandey, Grace Athas, Guoqiang Yu, Qin Fu, Dana Troxlair, Richard Vander Heide, David Herrington, Jennifer E. Van Eyk, Yue Wang
J Proteome Res. 2020 Jul 2; 19(7): 2794–2806. Published online 2020 Apr 7. doi: 10.1021/acs.jproteome.0c00118 PMCID: PMC7720636
Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT-SWATH mass spectrometry.
Shao S, Guo T, Koh CC, Gillessen S, Joerger M, Jochum W, Aebersold R. Proteomics. 2015 Nov;15(21):3711-21. doi: 10.1002/pmic.201500161. Epub 2015 Sep 10. PMID: 26287124
Proteomics of Mouse Heart Ventricles Reveals Mitochondria and Metabolism as Major Targets of a Post-Infarction Short-Acting GLP1Ra-Therapy
Juliana de Freitas Germano, Ankush Sharma, Miroslava Stastna, Chengqun Huang, Marianne Aniag, Angie Aceves, Jennifer E. Van Eyk, Robert M. Mentzer, Jr., Honit Piplani, Allen M. Andres, Roberta A. Gottlieb
Int J Mol Sci. 2021 Aug; 22(16): 8711. Published online 2021 Aug 13. doi: 10.3390/ijms22168711
PMCID: PMC8395861
Improved Protein Extractionand Protein Identification from Archival Formalin-fixed Paraffin-embedded Human Aortas
Zongming Fu, Kun Yan, Avraham Rosenberg, Zhicheng Jin, Barbara Crain, Grace Athas, Richard S Vander Heide, Timothy Howard, Allen D. Everett, David Herrington, Jennifer E. Van Eyk
Proteomics Clin Appl. Author manuscript; available in PMC 2015 Feb 25. Published in final edited form as: Proteomics Clin Appl. 2013 Apr; 7(0): 217–224. doi: 10.1002/prca.201200064 PMCID: PMC4340701
ACE overexpression in myeloid cells increases oxidative metabolism and cellular ATP
Duo-Yao Cao, Weston R. Spivia, Luciana C. Veiras, Zakir Khan, Zhenzi Peng, Anthony E. Jones, Ellen A. Bernstein, Suguru Saito, Derick Okwan-Duodu, Sarah J. Parker, Jorge F. Giani, Ajit S. Divakaruni, Jennifer E. Van Eyk, Kenneth E. Bernstein J Biol Chem. 2020 Jan 31; 295(5): 1369–1384. Published online 2019 Dec 23. doi: 10.1074/jbc.RA119.011244 PMCID: PMC6996878
High-throughput proteomic sample preparation using pressure cycling technology
Xue Cai, Zhangzhi Xue, Chunlong Wu, Rui Sun, Liujia Qian, Liang Yue, Weigang Ge, Xiao Yi, Wei Liu, Chen Chen, Huanhuan Gao, Jing Yu, Luang Xu, Yi Zhu, Tiannan Guo
Nat Protoc. 2022; 17(10): 2307–2325. Published online 2022 Aug 5. doi: 10.1038/s41596-022-00727-1
PMCID: PMC9362583
Method for Recovery and Immunoaffinity Enrichment of Membrane Proteins Illustrated with Metastatic Ovarian Cancer Tissues
Luke V. Schneider, Varsha Likhte, William H. Wright, Frances Chu, Emma Cambron, Anne Baldwin-Burnett, Jessica Krakow, Gary B. Smejkal
Int J Proteomics. 2012; 2012: 838630. Published online 2012 Jul 12. doi: 10.1155/2012/838630
PMCID: PMC3418661
Pressure-assisted sample preparation for proteomic analysis
Pawel P. Olszowy, Ariel Burns, Pawel S. Ciborowski
Anal Biochem. Author manuscript; available in PMC 2014 Jul 1.
Published in final edited form as: Anal Biochem. 2013 Jul 1; 438(1): 67–72. Published online 2013 Mar 29. doi: 10.1016/j.ab.2013.03.023 PMCID: PMC3761939
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps
Tiannan Guo, Petri Kouvonen, Ching Chiek Koh, Ludovic C Gillet, Witold E Wolski, Hannes L Röst, George Rosenberger, Ben C Collins, Lorenz C Blum, Silke Gillessen, Markus Joerger, Wolfram Jochum, Ruedi Aebersold
Nat Med. Author manuscript; available in PMC 2015 Oct 1.Published in final edited form as: Nat Med. 2015 Apr; 21(4): 407–413. Published online 2015 Mar 2. doi: 10.1038/nm.3807
PMCID: PMC4390165
Pressure cycling technology-assisted mass spectrometric quantification of gingival tissue reveals proteome dynamics during the initiation and progression of inflammatory periodontal disease
Kai Bao, Xiaofei Li, Tetsuhiro Kajikawa, Abe Toshiharu, Nathalie Selevsek, Jonas Grossmann, George Hajishengallis, Nagihan Bostanci
Proteomics. Author manuscript; available in PMC 2021 Feb 1. Published in final edited form as: Proteomics. 2020 Feb; 20(3-4): e1900253. Published online 2020 Jan 15. doi: 10.1002/pmic.201900253
PMCID: PMC7033018
Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease
Kai Bao, Xiaofei Li, Lucy Poveda, Weihong Qi, Nathalie Selevsek, Pinar Gumus, Gulnur Emingil, Jonas Grossmann, Patricia I. Diaz, George Hajishengallis, Nagihan Bostanci, Georgios N. Belibasakis
Front Cell Infect Microbiol. 2020; 10: 588155. Published online 2020 Oct 2. doi: 10.3389/fcimb.2020.588155 PMCID: PMC7566166
Pressurized Pepsin Digestion in Proteomics: AN AUTOMATABLE ALTERNATIVE TO TRYPSIN FOR INTEGRATED TOP-DOWN BOTTOM-UP PROTEOMICS*
Daniel López-Ferrer, Konstantinos Petritis, Errol W. Robinson, Kim K. Hixson, Zhixin Tian, Jung Hwa Lee, Sang-Won Lee, Nikola Tolić, Karl K. Weitz, Mikhail E. Belov, Richard D. Smith, Ljiljana Paša-Tolić
Mol Cell Proteomics. 2011 Feb; 10(2): M110.001479. Published online 2010 Jul 12. doi: 10.1074/mcp.M110.001479 PMCID: PMC3033671
Strategies to enable large-scale proteomics for reproducible research
Rebecca C. Poulos, Peter G. Hains, Rohan Shah, Natasha Lucas, Dylan Xavier, Srikanth S. Manda, Asim Anees, Jennifer M. S. Koh, Sadia Mahboob, Max Wittman, Steven G. Williams, Erin K. Sykes, Michael Hecker, Michael Dausmann, Merridee A. Wouters, Keith Ashman, Jean Yang, Peter J. Wild, Anna deFazio, Rosemary L. Balleine, Brett Tully, Ruedi Aebersold, Terence P. Speed, Yansheng Liu, Roger R. Reddel, Phillip J. Robinson, Qing Zhong Nat Commun. 2020; 11: 3793. Published online 2020 Jul 30. doi: 10.1038/s41467-020-17641-3 PMCID: PMC7393074
Label-free quantitative SWATH-MS proteomic analysis of adult myocardial slices in vitro after biomimetic electromechanical stimulation
M. A. Zabielska-Kaczorowska, A. E. Bogucka, K. Macur, P. Czaplewska, S. A. Watson, F. Perbellini, C. M. Terracciano, R. T. Smolenski
Sci Rep. 2022; 12: 16533. Published online 2022 Oct 3. doi: 10.1038/s41598-022-20494-z
PMCID: PMC9529937
Pan-cancer proteomic map of 949 human cell lines
Emanuel Gonçalves, Rebecca C. Poulos, Zhaoxiang Cai, Syd Barthorpe, Srikanth S. Manda, Natasha Lucas, Alexandra Beck, Daniel Bucio-Noble, Michael Dausmann, Caitlin Hall, Michael Hecker, Jennifer Koh, Howard Lightfoot, Sadia Mahboob, Iman Mali, James Morris, Laura Richardson, Akila J. Seneviratne, Rebecca Shepherd, Erin Sykes, Frances Thomas, Sara Valentini, Steven G. Williams, Yangxiu Wu, Dylan Xavier, Karen L. MacKenzie, Peter G. Hains, Brett Tully, Phillip J. Robinson, Qing Zhong, Mathew J. Garnett, Roger R. Reddel
Cancer Cell. 2022 Aug 8; 40(8): 835–849.e8. doi: 10.1016/j.ccell.2022.06.010
PMCID: PMC9387775
Differential Protein Expression in Striatal D1- and D2-Dopamine Receptor-Expressing Medium Spiny Neurons
M. Shahid Mansuri, Gang Peng, Rashaun S. Wilson, TuKiet T. Lam, Hongyu Zhao, Kenneth R. Williams, Angus C. Nairn
Proteomes. 2020 Dec; 8(4): 27. Published online 2020 Oct 13. doi: 10.3390/proteomes8040027
PMCID: PMC7709116
The Effect of Pressure Cycling on Proteolytic Cleavage Efficiency, Reaction Time and Protein Sequence Coverage
E. Bonneil, J. Saba, A. Huhmer, P. Thibault, R. Biringer
J Biomol Tech. 2010 Sep; 21(3 Suppl): S51. PMCID: PMC2918217
Proteomic Comparison of Photoaged and Sun-Protected Epithelium by ANOVA and Bayes Factors
J.T. Smilowitz, B.S. Phinney, R.A. Eigenheer
J Biomol Tech. 2010 Sep; 21(3 Suppl): S51.
PMCID: PMC2918028
Establishment and validation of highly accurate formalin-fixed paraffin-embedded quantitative proteomics by heat-compatible pressure cycling technology using phase-transfer surfactant and SWATH-MS
Yasuo Uchida, Hayate Sasaki, Tetsuya Terasaki
Sci Rep. 2020; 10: 11271. Published online 2020 Jul 9. doi: 10.1038/s41598-020-68245-2
PMCID: PMC7347883
Integrated Transcriptomic and Proteomic Analysis of Human Eccrine Sweat Glands Identifies Missing and Novel Proteins
Chan Hyun Na, Neeraj Sharma, Anil K. Madugundu, Ruiqiang Chen, Melis Atalar Aksit, Gedge D. Rosson, Garry R. Cutting, Akhilesh Pandey
Mol Cell Proteomics. 2019 Jul; 18(7): 1382–1395. Published online 2019 Apr 12. doi: 10.1074/mcp.RA118.001101 PMCID: PMC6601213
DIA-Based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia
Wei Liu, Yaoting Sun, Weigang Ge, Fangfei Zhang, Lin Gan, Yi Zhu, Tiannan Guo, Kexin Liu
Mol Cell Proteomics. 2022 Feb; 21(2): 100187. Published online 2021 Dec 16. doi: 10.1016/j.mcpro.2021.100187 PMCID: PMC8800142
In-Depth Comparison of Matrigel Dissolving Methods on Proteomic Profiling of Organoids
Man Wang, Huan Yu, Ting Zhang, Lihua Cao, Yang Du, Yuhao Xie, Jiafu Ji, Jianmin Wu
Mol Cell Proteomics. 2022 Jan; 21(1): 100181. Published online 2021 Dec 3. doi: 10.1016/j.mcpro.2021.100181 PMCID: PMC8733271
Shotgun proteomics of homogenate milk reveals dynamic changes in protein abundances between colostrum, transitional, and mature milk of swine
Christina V Bradshaw, Aridany Suarez Trujillo, Sarah M Luecke, Lea D Logan, Rodrigo Mohallem, Uma K Aryal, Kara R Stewart, Theresa M Casey, Radiah C Minor
J Anim Sci. 2021 Sep; 99(9): skab240. Published online 2021 Aug 12. doi: 10.1093/jas/skab240
PMCID: PMC8477453
Inclusion of Oat and Yeast Culture in Sow Gestational and Lactational Diets Alters Immune and Antimicrobial Associated Proteins in Milk
Barry Donovan, Aridany Suarez-Trujillo, Theresa Casey, Uma K. Aryal, Dawn Conklin, Leonard L. Williams, Radiah C. Minor
Animals (Basel) 2021 Feb; 11(2): 497. Published online 2021 Feb 14. doi: 10.3390/ani11020497
PMCID: PMC7918739
A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer’s disease
Gennifer E. Merrihew, Jea Park, Deanna Plubell, Brian C. Searle, C. Dirk Keene, Eric B. Larson, Randall Bateman, Richard J. Perrin, Jasmeer P. Chhatwal, Martin R. Farlow, Catriona A. McLean, Bernardino Ghetti, Kathy L. Newell, Matthew P. Frosch, Thomas J. Montine, Michael J. MacCoss
Sci Data. 2023; 10: 206. Published online 2023 Apr 14. doi: 10.1038/s41597-023-02057-7
PMCID: PMC10104800
Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer’s disease
Zhi Huang, Gennifer E. Merrihew, Eric B. Larson, Jea Park, Deanna Plubell, Edward J. Fox, Kathleen S. Montine, Caitlin S. Latimer, C. Dirk Keene, James Y. Zou, Michael J. MacCoss, Thomas J. Montine
Nat Commun. 2023; 14: 2747. Published online 2023 May 12. doi: 10.1038/s41467-023-38376-x
PMCID: PMC10182086
Isolation and Characterization of Membrane Vesicles from Lactobacillus Species
Julie C. Caruana, Scott N. Dean, Scott A. Walper
Bio Protoc. 2021 Sep 5; 11(17): e4145. Published online 2021 Sep 5. doi: 10.21769/BioProtoc.4145
PMCID: PMC8443458
An integrated approach for identification of a panel of candidate genes arbitrated for invasion and metastasis in oral squamous cell carcinoma
Samapika Routray, Ravindra Kumar, Keshava K. Datta, Vinuth N. Puttamallesh, Aditi Chatterjee, Harsha Gowda, Neeta Mohanty, Rupesh Dash, Anshuman Dixit
Sci Rep. 2021; 11: 6208. Published online 2021 Mar 18. doi: 10.1038/s41598-021-85729-x
PMCID: PMC7973753
Nanosac, a Non-Cationic and Soft Polyphenol Nanocapsule, Enables Systemic Delivery of siRNA to Solid Tumors
Hyungjun Kim, Simseok A. Yuk, Alexandra M. Dieterly, Soonbum Kwon, Jinho Park, Fanfei Meng, Hytham H. Gadalla, Maria Jose Cadena, L. Tiffany Lyle, Yoon Yeo
ACS Nano. Author manuscript; available in PMC 2021 Apr 6.
Published in final edited form as: ACS Nano. 2021 Mar 23; 15(3): 4576–4593. Published online 2021 Mar 1. doi: 10.1021/acsnano.0c08694 PMCID: PMC8023695
Pressure-Assisted Protein Extraction: A Novel Method for Recovering Proteins from Archival Tissue for Proteomic Analysis
Carol B. Fowler, Timothy J. Waybright, Timothy D. Veenstra, Timothy J. O’Leary, Jeffrey T. Mason
J Proteome Res. 2012 Apr 6; 11(4): 2602–2608. Published online 2012 Feb 21. doi: 10.1021/pr201005t
PMCID: PMC3320745
High‐throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification
Yi Zhu, Tobias Weiss, Qiushi Zhang, Rui Sun, Bo Wang, Xiao Yi, Zhicheng Wu, Huanhuan Gao, Xue Cai, Guan Ruan, Tiansheng Zhu, Chao Xu, Sai Lou, Xiaoyan Yu, Ludovic Gillet, Peter Blattmann, Karim Saba, Christian D. Fankhauser, Michael B. Schmid, Dorothea Rutishauser, Jelena Ljubicic, Ailsa Christiansen, Christine Fritz, Niels J. Rupp, Cedric Poyet, Elisabeth Rushing, Michael Weller, Patrick Roth, Eugenia Haralambieva, Silvia Hofer, Chen Chen, Wolfram Jochum, Xiaofei Gao, Xiaodong Teng, Lirong Chen, Qing Zhong, Peter J. Wild, Ruedi Aebersold, Tiannan Guo
Mol Oncol. 2019 Nov; 13(11): 2305–2328. Published online 2019 Sep 18. doi: 10.1002/1878-0261.12570
PMCID: PMC6822243
Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins
Peter Blattmann, Vivienne Stutz, Giulia Lizzo, Joy Richard, Philipp Gut, Ruedi Aebersold
Sci Data. 2019; 6: 190011. Published online 2019 Feb 12. doi: 10.1038/sdata.2019.11
PMCID: PMC6371892
A repository of assays to quantify 10,000 human proteins by SWATH-MS
George Rosenberger, Ching Chiek Koh, Tiannan Guo, Hannes L. Röst, Petri Kouvonen, Ben C. Collins, Moritz Heusel, Yansheng Liu, Etienne Caron, Anton Vichalkovski, Marco Faini, Olga T. Schubert, Pouya Faridi, H. Alexander Ebhardt, Mariette Matondo, Henry Lam, Samuel L. Bader, David S. Campbell, Eric W. Deutsch, Robert L. Moritz, Stephen Tate, Ruedi Aebersold
Sci Data. 2014; 1: 140031. Published online 2014 Sep 16. doi: 10.1038/sdata.2014.31
PMCID: PMC4322573
Sample preparation for two-dimensional gel electrophoresis using pressure cycling technology
Gary B. Smejkal, Frank A. Witzmann, Heather Ringham, Deena Small, Susan F. Chase, James Behnke, Edmund Ting
Anal Biochem. Author manuscript; available in PMC 2013 Sep 11.
Published in final edited form as: Anal Biochem. 2007 Apr 15; 363(2): 309–311. Published online 2007 Jan 27. doi: 10.1016/j.ab.2007.01.033 PMCID: PMC3769960
Application of pressure cycling technology to tissue sample preparation for 2-DE.
Ringham H, Bell RL, Smejkal GB, Behnke J, Witzmann FA.
Electrophoresis. 2007 Mar;28(6):1022-4. doi: 10.1002/elps.200600434.PMID: 17300130
Systems Biology Studies of Adult Paragonimus Lung Flukes Facilitate the Identification of Immunodominant Parasite Antigens
Samantha N. McNulty, Peter U. Fischer, R. Reid Townsend, Kurt C. Curtis, Gary J. Weil, Makedonka Mitreva
PLoS Negl Trop Dis. 2014 Oct; 8(10): e3242. Published online 2014 Oct 16. doi: 10.1371/journal.pntd.0003242 PMCID: PMC4199545
An Ixodes scapularis cell line with a predominantly neuron-like phenotype
Jonathan D. Oliver, Adela S. Oliva Chávez, Roderick F. Felsheim, Timothy J. Kurtti, Ulrike G. Munderloh
Exp Appl Acarol. Author manuscript; available in PMC 2016 Jul 1.
Published in final edited form as: Exp Appl Acarol. 2015 Jul; 66(3): 427–442. Published online 2015 Apr 17. doi: 10.1007/s10493-015-9908-1
PMCID: PMC4449809
Cigarette Smoke Triggers Loss of Corneal Endothelial Cells and Disruption of Descemet's Membrane Proteins in Mice
Muhammad Ali, Shahid Y. Khan, Yura Jang, Chan Hyun Na, C. Conover Talbot, Jr, John D. Gottsch, James T. Handa, S. Amer Riazuddin
Invest Ophthalmol Vis Sci. 2021 Mar; 62(3): 3. Published online 2021 Mar 2. doi: 10.1167/iovs.62.3.3
PMCID: PMC7938020
An Ultra-Sensitive Immunoassay for Quantifying Biomarkers in Breast Tumor Tissue
Carol B. Fowler, Yan-Gao Man, Jeffrey T. Mason
J Cancer. 2014; 5(2): 115–124. Published online 2014 Jan 5. doi: 10.7150/jca.8084
PMCID: PMC3909766
Proteomics-based investigation of cerebrovascular molecular mechanisms in cerebral amyloid angiopathy by the FFPE-LMD-PCT-SWATH method
Takumi Handa, Hayate Sasaki, Masaki Takao, Mitsutoshi Tano, Yasuo Uchida
Fluids Barriers CNS. 2022; 19: 56. Published online 2022 Jul 1. doi: 10.1186/s12987-022-00351-x
PMCID: PMC9250250
Proteomic signatures of myeloid derived suppressor cells from liver and lung metastases reveal functional divergence and potential therapeutic targets
Nicholas A. DaSilva, Benjamin J. Barlock, Prajna Guha, Chandra C. Ghosh, Catherine E. Trebino, Jodi L. Camberg, Steven C. Katz, David C. Rowley
Cell Death Discov. 2021; 7: 232. Published online 2021 Sep 4. doi: 10.1038/s41420-021-00621-x
PMCID: PMC8418613
Oligosarcomas, IDH-mutant are distinct and aggressive
Abigail K. Suwala, Marius Felix, Dennis Friedel, Damian Stichel, Daniel Schrimpf, Felix Hinz, Ekkehard Hewer, Leonille Schweizer, Hildegard Dohmen, Ute Pohl, Ori Staszewski, Andrey Korshunov, Marco Stein, Thidathip Wongsurawat, Pornsuk Cheunsuacchon, Sith Sathornsumetee, Christian Koelsche, Clinton Turner, Emilie Le Rhun, Angelika Mühlebner, Philippe Schucht, Koray Özduman, Takahiro Ono, Hiroaki Shimizu, Marco Prinz, Till Acker, Christel Herold-Mende, Tobias Kessler, Wolfgang Wick, David Capper, Pieter Wesseling, Felix Sahm, Andreas von Deimling, Christian Hartmann, David E. Reuss
Acta Neuropathol. 2022; 143(2): 263–281. Published online 2021 Dec 30. doi: 10.1007/s00401-021-02395-z PMCID: PMC8742817
Distinct brain regional proteome changes in the rTg-DI rat model of cerebral amyloid angiopathy
Joseph M. Schrader, Feng Xu, William E. Van Nostrand
J Neurochem. Author manuscript; available in PMC 2022 Oct 1.
Published in final edited form as: J Neurochem. 2021 Oct; 159(2): 273–291. Published online 2021 Aug 17. doi: 10.1111/jnc.15463
PMCID: PMC8530857
PHENOTYPIC CHARACTERIZATION OF TWO NOVEL CELL LINE MODELS OF CASTRATION RESISTANT PROSTATE CANCER.
Michael C. Haffner, Akshay Bhamidipati, Harrison K. Tsai, David M. Esopi, Ajay M. Vaghasia, Jin-Yih Low, Radhika A. Patel, Gunes Guner, Minh-Tam Pham, Nicole Castagna, Jessica Hicks, Nicolas Wyhs, Ruedi Aebersold, Angelo M. De Marzo, William G. Nelson, Tiannan Guo, Srinivasan Yegnasubramanian
Prostate. Author manuscript; available in PMC 2022 Nov 1.
Published in final edited form as: Prostate. 2021 Nov; 81(15): 1159–1171. Published online 2021 Aug 16. doi: 10.1002/pros.24210 PMCID: PMC8460612
Proteomic Characterization of Cytoplasmic Lipid Droplets in Human Metastatic Breast Cancer Cells
Alyssa S. Zembroski, Chaylen Andolino, Kimberly K. Buhman, Dorothy Teegarden
Front Oncol. 2021; 11: 576326. Published online 2021 Jun 1. doi: 10.3389/fonc.2021.576326
PMCID: PMC8204105
Molecular alterations in oral cancer using high-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue
Varshasnata Mohanty, Yashwanth Subbannayya, Shankargouda Patil, Vinuth N. Puttamallesh, Mohd. Altaf Najar, Keshava K. Datta, Sneha M. Pinto, Sameera Begum, Neeta Mohanty, Samapika Routray, Riaz Abdulla, Jay Gopal Ray, David Sidransky, Harsha Gowda, T. S. Keshava Prasad, Aditi Chatterjee
J Cell Commun Signal. 2021 Sep; 15(3): 447–459. Published online 2021 Mar 8. doi: 10.1007/s12079-021-00609-3 PMCID: PMC8222490
Proteomic Analysis of 3T3-L1 Adipocytes Treated with Insulin and TNF-α
Hayley Chan, Ketaki P. Bhide, Aditya Vaidyam, Victoria Hedrick, Tiago Jose Paschoal Sobreira, Thomas G. Sors, Ryan W. Grant, Uma K. Aryal
Proteomes. 2019 Dec; 7(4): 35. Published online 2019 Oct 20. doi: 10.3390/proteomes7040035
PMCID: PMC6958341
Characterization of longitudinal canal tissue in the acorn barnacle Amphibalanus amphitrite
Chenyue Wang, Janna N. Schultzhaus, Chris R. Taitt, Dagmar H. Leary, Lisa C. Shriver-Lake, Daniel Snellings, Samantha Sturiale, Stella H. North, Beatriz Orihuela, Daniel Rittschof, Kathryn J. Wahl, Christopher M. Spillmann
PLoS One. 2018; 13(12): e0208352. Published online 2018 Dec 10. doi: 10.1371/journal.pone.0208352
PMCID: PMC6287898
Evaluation of the potential of Pap test fluid and cervical swabs to serve as clinical diagnostic biospecimens for the detection of ovarian cancer by mass spectrometry-based proteomics
Kristin L. M. Boylan, Somaieh Afiuni-Zadeh, Melissa A. Geller, Peter A. Argenta, Timothy J. Griffin, Amy P. N. Skubitz
Clin Proteomics. 2021; 18: 4. Published online 2021 Jan 7. doi: 10.1186/s12014-020-09309-3
PMCID: PMC7792339
Inter-Regional Proteomic Profiling of the Human Brain Using an Optimized Protein Extraction Method from Formalin-Fixed Tissue to Identify Signaling Pathways
Jennilee M. Davidson, Stephanie L. Rayner, Sidong Liu, Flora Cheng, Antonio Di Ieva, Roger S. Chung, Albert Lee
Int J Mol Sci. 2023 Mar; 24(5): 4283. Published online 2023 Feb 21. doi: 10.3390/ijms24054283
PMCID: PMC10001664
Spatially resolved proteomics via tissue expansion
Lu Li, Cuiji Sun, Yaoting Sun, Zhen Dong, Runxin Wu, Xiaoting Sun, Hanbin Zhang, Wenhao Jiang, Yan Zhou, Xufeng Cen, Shang Cai, Hongguang Xia, Yi Zhu, Tiannan Guo, Kiryl D. Piatkevich
Nat Commun. 2022; 13: 7242. Published online 2022 Nov 30. doi: 10.1038/s41467-022-34824-2
PMCID: PMC9712279 ArticlePubReaderPDF–4.0MCite
Pressure cycling technology for challenging proteomic sample processing: application to barnacle adhesive.
Schultzhaus JN, Dean SN, Leary DH, Hervey WJ, Fears KP, Wahl KJ, Spillmann CM.
Integr Biol (Camb). 2019 May 1;11(5):235-247. doi: 10.1093/intbio/zyz020.PMID: 31251329
Proteomic analysis reveals that aging rabbit vocal folds are more vulnerable to changes caused by systemic dehydration
Naila C. do Nascimento, Taylor W. Bailey, Andrea P. Santos, Chenwei Duan, Rodrigo Mohallem, Jackeline Franco, Uma K. Aryal, Jun Xie, Abigail Cox, M. Preeti Sivasankar
BMC Genomics. 2022; 23: 762. Published online 2022 Nov 21. doi: 10.1186/s12864-022-08975-x
PMCID: PMC9677652
Recurring exposure to low humidity induces transcriptional and protein level changes in the vocal folds of rabbits
Taylor W. Bailey, Andrea Pires dos Santos, Naila Cannes do Nascimento, Jun Xie, M. Preeti Sivasankar, Abigail Cox
Sci Rep. 2021; 11: 24180. Published online 2021 Dec 17. doi: 10.1038/s41598-021-03489-0
PMCID: PMC8683398
Tissue-Characteristic Expression of Mouse Proteome
Tian Lu, Liujia Qian, Yuting Xie, Qiushi Zhang, Wei Liu, Weigang Ge, Yi Zhu, Lijia Ma, Cheng Zhang, Tiannan Guo
Mol Cell Proteomics. 2022 Oct; 21(10): 100408. Published online 2022 Sep 2. doi: 10.1016/j.mcpro.2022.100408
PMCID: PMC9562433
RyR2/IRBIT regulates insulin gene transcript, insulin content, and secretion in the insulinoma cell line INS-1
Kyle E. Harvey, Emily K. LaVigne, Mohd Saleem Dar, Amy E. Salyer, Evan P. S. Pratt, Paxton A. Sample, Uma K. Aryal, Humaira Gowher, Gregory H. Hockerman
Sci Rep. 2022; 12: 7713. Published online 2022 May 11. doi: 10.1038/s41598-022-11276-8
PMCID: PMC9095623
Mice Placental ECM Components May Provide A Three-Dimensional Placental Microenvironment
Rodrigo da Silva Nunes Barreto, Ana Claudia Oliveira Carreira, Mônica Duarte da Silva, Leticia Alves Fernandes, Rafaela Rodrigues Ribeiro, Gustavo Henrique Doná Rodrigues Almeida, Bruna Tassia dos Santos Pantoja, Milton Yutaka Nishiyama Junior, Maria Angelica Miglino
Bioengineering (Basel) 2023 Jan; 10(1): 16. Published online 2022 Dec 22. doi: 10.3390/bioengineering10010016
PMCID: PMC9855196
Comparative tissue proteomics reveals unique action mechanisms of vaccine adjuvants
Yibo Li, Zhuofan Li, Xinyuan Chen
iScience. 2023 Jan 20; 26(1): 105800. Published online 2022 Dec 14. doi: 10.1016/j.isci.2022.105800
PMCID: PMC9813788
Distinct Brain Proteomic Signatures in Cerebral Small Vessel Disease Rat Models of Hypertension and Cerebral Amyloid Angiopathy
Joseph M Schrader, Aleksandra Stanisavljevic, Feng Xu, William E Van Nostrand
J Neuropathol Exp Neurol. 2022 Sep; 81(9): 731–745. Published online 2022 Jul 20. doi: 10.1093/jnen/nlac057
PMCID: PMC9803909
Comparative Studies to Uncover Mechanisms of Action of N-(1,3,4-oxadiazol-2-yl)benzamide Containing Antibacterial Agents
George A. Naclerio, Kenneth I. Onyedibe, Caroline W. Karanja, Uma K. Aryal, Herman O. Sintim
ACS Infect Dis. Author manuscript; available in PMC 2023 Apr 8.
Published in final edited form as: ACS Infect Dis. 2022 Apr 8; 8(4): 865–877. Published online 2022 Mar 17. doi: 10.1021/acsinfecdis.1c00613
PMCID: PMC9188027
Does DIA data contain hidden gems? A case study related to Alzheimer’s disease
Evan E. Hubbard, Lilian R. Heil, Gennifer E. Merrihew, Jasmeer P. Chhatwal, Martin R. Farlow, Catriona A. McLean, Bernardino Ghetti, Kathy L. Newell, Matthew P. Frosch, Randall J. Bateman, Eric B. Larson, C. Dirk Keene, Richard J. Perrin, Thomas J. Montine, Michael J. MacCoss, Ryan R. Julian
J Proteome Res. Author manuscript; available in PMC 2022 Jan 8.
Published in final edited form as: J Proteome Res. 2022 Jan 7; 21(1): 118–131. Published online 2021 Nov 24. doi: 10.1021/acs.jproteome.1c00558
PMCID: PMC8741752
