| Year |
Citation |
Score |
| 2024 |
Van Vranken JG, Li J, Mintseris J, Gadzuk-Shea M, Gygi SP, Schweppe DK. Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays. Biorxiv : the Preprint Server For Biology. PMID 38328090 DOI: 10.1101/2024.01.26.577428 |
0.499 |
|
| 2023 |
Keele GR, Zhang JG, Szpyt J, Korstanje R, Gygi SP, Churchill GA, Schweppe DK. Global and tissue-specific aging effects on murine proteomes. Cell Reports. 42: 112715. PMID 37405913 DOI: 10.1016/j.celrep.2023.112715 |
0.55 |
|
| 2023 |
Yu Q, Liu X, Keller MP, Navarrete-Perea J, Zhang T, Fu S, Vaites LP, Shuken SR, Schmid E, Keele GR, Li J, Huttlin EL, Rashan EH, Simcox J, Churchill GA, ... Schweppe DK, et al. Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression. Nature Communications. 14: 555. PMID 36732331 DOI: 10.1038/s41467-023-36269-7 |
0.757 |
|
| 2023 |
Mitchell DC, Kuljanin M, Li J, Van Vranken JG, Bulloch N, Schweppe DK, Huttlin EL, Gygi SP. A proteome-wide atlas of drug mechanism of action. Nature Biotechnology. PMID 36593396 DOI: 10.1038/s41587-022-01539-0 |
0.721 |
|
| 2021 |
Huttlin EL, Bruckner RJ, Navarrete-Perea J, Cannon JR, Baltier K, Gebreab F, Gygi MP, Thornock A, Zarraga G, Tam S, Szpyt J, Gassaway BM, Panov A, Parzen H, Fu S, ... ... Schweppe DK, et al. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell. PMID 33961781 DOI: 10.1016/j.cell.2021.04.011 |
0.778 |
|
| 2021 |
Paulo JA, Schweppe DK. Advances in quantitative high-throughput phosphoproteomics with sample multiplexing. Proteomics. e2000140. PMID 33455035 DOI: 10.1002/pmic.202000140 |
0.322 |
|
| 2021 |
Kuljanin M, Mitchell DC, Schweppe DK, Gikandi AS, Nusinow DP, Bulloch NJ, Vinogradova EV, Wilson DL, Kool ET, Mancias JD, Cravatt BF, Gygi SP. Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries. Nature Biotechnology. PMID 33398154 DOI: 10.1038/s41587-020-00778-3 |
0.798 |
|
| 2020 |
Rad R, Li J, Mintseris J, O'Connell J, Gygi SP, Schweppe DK. Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage. Journal of Proteome Research. PMID 33190505 DOI: 10.1021/acs.jproteome.0c00563 |
0.737 |
|
| 2020 |
Hauseman ZJ, Harvey EP, Newman CE, Wales TE, Bucci JC, Mintseris J, Schweppe DK, David L, Fan L, Cohen DT, Herce HD, Mourtada R, Ben-Nun Y, Bloch NB, Hansen SB, et al. Homogeneous Oligomers of Pro-apoptotic BAX Reveal Structural Determinants of Mitochondrial Membrane Permeabilization. Molecular Cell. PMID 32533918 DOI: 10.1016/J.Molcel.2020.05.029 |
0.725 |
|
| 2020 |
Jedrychowski MP, Lu GZ, Szpyt J, Mariotti M, Garrity R, Paulo JA, Schweppe DK, Laznik-Bogoslavski D, Kazak L, Murphy MP, Gladyshev VN, Gygi SP, Chouchani ET, Spiegelman BM. Facultative protein selenation regulates redox sensitivity, adipose tissue thermogenesis, and obesity. Proceedings of the National Academy of Sciences of the United States of America. PMID 32358195 DOI: 10.1073/Pnas.2001387117 |
0.607 |
|
| 2020 |
Yu Q, Xiao H, Jedrychowski MP, Schweppe DK, Navarrete-Perea J, Knott J, Rogers J, Chouchani ET, Gygi SP. Sample multiplexing for targeted pathway proteomics in aging mice. Proceedings of the National Academy of Sciences of the United States of America. PMID 32332170 DOI: 10.1073/Pnas.1919410117 |
0.639 |
|
| 2020 |
Yu Q, Paulo JA, Navarrete-Perea J, McAlister GC, Canterbury JD, Bailey DJ, Robitaille AM, Huguet R, Zabrouskov V, Gygi SP, Schweppe DK. Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics. Analytical Chemistry. PMID 32250601 DOI: 10.1021/Acs.Analchem.9B05685 |
0.594 |
|
| 2020 |
Li J, Van Vranken JG, Pontano Vaites L, Schweppe DK, Huttlin EL, Etienne C, Nandhikonda P, Viner R, Robitaille AM, Thompson AH, Kuhn K, Pike I, Bomgarden RD, Rogers JC, Gygi SP, et al. TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples. Nature Methods. PMID 32203386 DOI: 10.1038/S41592-020-0781-4 |
0.763 |
|
| 2020 |
Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey DJ, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Wouters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP. Correction to Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry. Analytical Chemistry. PMID 32134636 DOI: 10.1021/acs.analchem.0c00888 |
0.497 |
|
| 2020 |
Schweppe DK, Eng JK, Yu Q, Bailey D, Rad R, Navarrete-Perea J, Huttlin EL, Erickson BK, Paulo JA, Gygi SP. Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics. Journal of Proteome Research. PMID 32126768 DOI: 10.1021/Acs.Jproteome.9B00860 |
0.756 |
|
| 2020 |
Xiao H, Jedrychowski MP, Schweppe DK, Huttlin EL, Yu Q, Heppner DE, Li J, Long J, Mills EL, Szpyt J, He Z, Du G, Garrity R, Reddy A, Vaites LP, et al. A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging. Cell. PMID 32109415 DOI: 10.1016/J.Cell.2020.02.012 |
0.726 |
|
| 2020 |
Zhong X, Wu X, Schweppe DK, Chavez JD, Mathay M, Eng JK, Keller A, Bruce JE. In Vivo Cross-Linking MS Reveals Conservation in OmpA Linkage to Different Classes of β-Lactamase Enzymes. Journal of the American Society For Mass Spectrometry. 31: 190-195. PMID 32031408 DOI: 10.1021/Jasms.9B00021 |
0.552 |
|
| 2020 |
Erickson BK, Schweppe DK, Yu Q, Rad R, Haas W, McAlister GC, Gygi SP. Parallel notched gas-phase enrichment for improved proteome identification and quantitation with fast spectral acquisition rates. Journal of Proteome Research. PMID 31990573 DOI: 10.1021/Acs.Jproteome.9B00715 |
0.562 |
|
| 2020 |
Nusinow DP, Szpyt J, Ghandi M, Rose CM, McDonald ER, Kalocsay M, Jané-Valbuena J, Gelfand E, Schweppe DK, Jedrychowski M, Golji J, Porter DA, Rejtar T, Wang YK, Kryukov GV, et al. Quantitative Proteomics of the Cancer Cell Line Encyclopedia. Cell. 180: 387-402.e16. PMID 31978347 DOI: 10.1016/J.Cell.2019.12.023 |
0.778 |
|
| 2019 |
Schweppe DK, Rusin SF, Gygi SP, Paulo JA. An optimized workflow for multiplexed phosphorylation analysis of TMT-labeled peptides using high-Field Asymmetric waveform Ion Mobility Spectrometry (FAIMS). Journal of Proteome Research. PMID 31799850 DOI: 10.1021/Acs.Jproteome.9B00759 |
0.615 |
|
| 2019 |
Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey D, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Woulters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP. Characterization and optimization of multiplexed quantitative analyses using high-field asymmetric-waveform ion mobility mass spectrometry. Analytical Chemistry. PMID 30672687 DOI: 10.1021/Acs.Analchem.8B05399 |
0.627 |
|
| 2019 |
Erickson BK, Mintseris J, Schweppe DK, Navarrete-Perea J, Erickson AR, Nusinow DP, Paulo JA, Gygi SP. Active instrument engagement combined with a real-time database search for improved performance of sample multiplexing workflows. Journal of Proteome Research. PMID 30658528 DOI: 10.1021/Acs.Jproteome.8B00899 |
0.762 |
|
| 2018 |
Rose CM, Erickson BK, Schweppe DK, Viner R, Choi J, Rogers J, Bomgarden R, Gygi SP, Kirkpatrick DS. TomahaqCompanion: A tool for the creation and analysis of isobaric label based multiplexed targeted assays. Journal of Proteome Research. PMID 30501201 DOI: 10.1021/Acs.Jproteome.8B00767 |
0.614 |
|
| 2018 |
Vreven T, Schweppe DK, Chavez JD, Weisbrod CR, Shibata S, Zheng C, Bruce JE, Weng Z. Integrating cross-linking experiments with ab initio protein-protein docking. Journal of Molecular Biology. PMID 29665372 DOI: 10.1016/J.Jmb.2018.04.010 |
0.765 |
|
| 2017 |
Bird IM, Kim SH, Schweppe DK, Caetano-Lopes J, Robling AG, Charles JF, Gygi SP, Warman ML, Smits PJ. The skeletal phenotype of Achondrogenesis type 1A is caused exclusively by cartilage defects. Development (Cambridge, England). PMID 29180569 DOI: 10.1242/Dev.156588 |
0.534 |
|
| 2017 |
Schweppe DK, Huttlin EL, Harper JW, Gygi SP. BioPlex Display: An interactive suite for large-scale, AP-MS protein-protein interaction data. Journal of Proteome Research. PMID 29054129 DOI: 10.1021/Acs.Jproteome.7B00572 |
0.77 |
|
| 2017 |
Nygren PJ, Mehta S, Schweppe DK, Langeberg LK, Whiting JL, Weisbrod CR, Bruce JE, Zhang J, Veesler D, Scott JD. Intrinsic disorder within AKAP79 fine-tunes anchored phosphatase activity toward substrates and drug sensitivity. Elife. 6. PMID 28967377 DOI: 10.7554/Elife.30872 |
0.729 |
|
| 2017 |
Huttlin EL, Bruckner RJ, Paulo JA, Cannon JR, Ting L, Baltier K, Colby G, Gebreab F, Gygi MP, Parzen H, Szpyt J, Tam S, Zarraga G, Pontano-Vaites L, Swarup S, ... ... Schweppe DK, et al. Architecture of the human interactome defines protein communities and disease networks. Nature. PMID 28514442 DOI: 10.1038/Nature22366 |
0.764 |
|
| 2017 |
Erez Z, Sorek R, Shao S, Hegde RS, Schweppe DK, Chavez JD, Bruce JE, Mizrachi E, Verbeke L, Peer YVd, Marchal K, Myburg AA, Bennett JA, Klironomos J, Payne GF, et al. Principles of Systems Biology, No. 14: Sense Codon Reassignment Boosts Protein Chemistries Cell Systems. 4: 143-143. PMID 28231445 DOI: 10.1016/J.Cels.2017.02.004 |
0.586 |
|
| 2017 |
Zhong X, Navare AT, Chavez JD, Eng JK, Schweppe DK, Bruce JE. Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers. Journal of Proteome Research. 16: 720-727. PMID 28152603 DOI: 10.1021/Acs.Jproteome.6B00752 |
0.656 |
|
| 2017 |
Schweppe DK, Chavez JD, Lee CF, Caudal A, Kruse SE, Stuppard R, Marcinek DJ, Shadel GS, Tian R, Bruce JE. Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. PMID 28130547 DOI: 10.1073/Pnas.1617220114 |
0.63 |
|
| 2017 |
Nygren PJ, Mehta S, Schweppe DK, Langeberg LK, Whiting JL, Weisbrod CR, Bruce JE, Zhang J, Veesler D, Scott JD. Author response: Intrinsic disorder within AKAP79 fine-tunes anchored phosphatase activity toward substrates and drug sensitivity Elife. DOI: 10.7554/Elife.30872.022 |
0.703 |
|
| 2016 |
Chavez JD, Eng JK, Schweppe DK, Cilia M, Rivera K, Zhong X, Wu X, Allen T, Khurgel M, Kumar A, Lampropoulos A, Larsson M, Maity S, Morozov Y, Pathmasiri W, et al. A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. Plos One. 11: e0167547. PMID 27997545 DOI: 10.1371/Journal.Pone.0167547 |
0.665 |
|
| 2016 |
Wu X, Chavez JD, Schweppe DK, Zheng C, Weisbrod CR, Eng JK, Murali A, Lee SA, Ramage E, Gallagher LA, Kulasekara HD, Edrozo ME, Kamischke CN, Brittnacher MJ, Miller SI, et al. In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075. Nature Communications. 7: 13414. PMID 27834373 DOI: 10.1038/Ncomms13414 |
0.746 |
|
| 2016 |
Chavez JD, Schweppe DK, Eng JK, Bruce JE. In Vivo Conformational Dynamics of Hsp90 and Its Interactors. Cell Chemical Biology. 23: 716-26. PMID 27341434 DOI: 10.1016/J.Chembiol.2016.05.012 |
0.614 |
|
| 2016 |
Schweppe DK, Zheng C, Chavez JD, Navare AT, Wu X, Eng JK, Bruce JE. XLinkDB 2.0: Integrated, large-scale structural analysis of protein crosslinking data. Bioinformatics (Oxford, England). PMID 27153666 DOI: 10.1093/Bioinformatics/Btw232 |
0.666 |
|
| 2016 |
Schweppe DK, Chavez JD, Navare AT, Wu X, Ruiz B, Eng JK, Lam H, Bruce JE. Spectral library searching to identify crosslinked peptides. Journal of Proteome Research. PMID 27089058 DOI: 10.1021/Acs.Jproteome.6B00014 |
0.645 |
|
| 2016 |
Johnson ME, Grassetti AV, Taroni JN, Lyons SM, Schweppe D, Gordon JK, Spiera RF, Lafyatis R, Anderson PJ, Gerber SA, Whitfield ML. Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis. Arthritis Research & Therapy. 18: 27. PMID 26801089 DOI: 10.1186/S13075-016-0914-4 |
0.675 |
|
| 2015 |
Schweppe DK, Harding C, Chavez JD, Wu X, Ramage E, Singh PK, Manoil C, Bruce JE. Host-Microbe Protein Interactions during Bacterial Infection. Chemistry & Biology. PMID 26548613 DOI: 10.1016/J.Chembiol.2015.09.015 |
0.633 |
|
| 2015 |
Schweppe DK, Chavez JD, Bruce JE. XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking. Bioinformatics (Oxford, England). PMID 26411867 DOI: 10.1093/Bioinformatics/Btv519 |
0.64 |
|
| 2015 |
Chavez JD, Schweppe DK, Eng JK, Zheng C, Taipale A, Zhang Y, Takara K, Bruce JE. Quantitative interactome analysis reveals a chemoresistant edgotype. Nature Communications. 6: 7928. PMID 26235782 DOI: 10.1038/Ncomms8928 |
0.663 |
|
| 2013 |
Schweppe DK, Rigas JR, Gerber SA. Quantitative phosphoproteomic profiling of human non-small cell lung cancer tumors. Journal of Proteomics. 91: 286-96. PMID 23911959 DOI: 10.1016/J.Jprot.2013.07.023 |
0.671 |
|
| 2011 |
Kettenbach AN, Schweppe DK, Faherty BK, Pechenick D, Pletnev AA, Gerber SA. Quantitative phosphoproteomics identifies substrates and functional modules of Aurora and Polo-like kinase activities in mitotic cells. Science Signaling. 4: rs5. PMID 21712546 DOI: 10.1126/Scisignal.2001497 |
0.679 |
|
| 2010 |
Gerber SA, Kettenbach AN, Schweppe DK, Dragnev KH, Rigas JR. Use of quantitative proteomics to evaluate substrates and functional modules of the aurora and polo-like kinases. Journal of Clinical Oncology. 28: e13530-e13530. DOI: 10.1200/Jco.2010.28.15_Suppl.E13530 |
0.673 |
|
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