XLink-DB 4.0: Improved Interpretation of Protein Conformational Differences and Ligand Occupancy in Large-Scale Cross-Link Data.
Andrew Keller, Anna A. Bakhtina, Juan D. Chavez, and James E Bruce J Proteome Res. DOI:10.1021/acs.jproteome.2c00109
XLink-DB 3.0: Tools for 3D Interactome Visualization.
Andrew Keller, Juan D. Chavez, Jimmy K. Eng, Zorian Thornton, and James E Bruce J Proteome Res. DOI:10.1021/acs.jproteome.8b00703
XLink-DB 2.0: Integrated, large-scale structural analysis of protein crosslinking data.
Devin K Schweppe , Chunxiang Zheng , Juan D Chavez , Arti T Navare , Xia Wu , Jimmy K Eng , and James E Bruce Bioinformatics. DOI:10.1093/bioinformatics/btw232
XLink-DB: database and software tools for storing and visualizing protein interaction topology data.
Chunxiang Zheng , Chad R Weisbrod , Juan D Chavez , Jimmy K Eng , Vagisha Sharma , Xia Wu , and James E Bruce J. Proteome Res. DOI:10.1021/pr301162j
Integrative Modeling Pipeline (IMP): Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies.
Daniel Russel, Keren Lasker, Ben Webb, Javier Velazquez-Muriel, Elina Tjioe, Dina Schneidman-Duhovny, Bret Peterson, and Andrej Sali
PLoS Biology, (2012) 10(1): e1001244. | doi:10.1371/journal.pbio.1001244
xiNET: xiNET: cross-link network maps with residue resolution.
Colin W Combe, Lutz Fischer, and Juri Rappsilber
Molecular and Cellular Proteomics, April 1, 2015 Molecular & Cellular Proteomics, 14, 1137-1147. | doi:10.1074/mcp.O114.042259
Cytoscape.js: Cytoscape.js: a graph theory library for visualisation and analysis.
Max Franz, Christian T. Lopes, Gerardo Huck, Yue Dong, Onur Sumer, and Gary D. Bader
Bioinformatics, (2010) 26 (18): 2347-2348. | doi:10.1093/bioinformatics/btq430
Cytoscape Web: Cytoscape Web: an interactive web-based network browser.
Christian T. Lopes, Max Franz, Farzana Kazi, Sylva L. Donaldson, Quaid Morris, and Gary D. Bader
Bioinformatics, (2016) 32 (2): 309-311. | 10.1093/bioinformatics/btv557
6-plex_iqPIR_5prot_mix_QE_Bruce: Multiplexed Cross-Linking with Isobaric Quantitative Protein Interaction Reporter Technology.
Juan D. Chavez, Andrew Keller, Helisa H. Wippel, Jared P. Mohr, and James E. Bruce
Analytical Chemistry, 2021 Dec 21;93(50):16759-16768. PMID: 34882395
6-plex_iqPIR_HeLa_QE_Bruce: Multiplexed Cross-Linking with Isobaric Quantitative Protein Interaction Reporter Technologys.
Juan D. Chavez, Andrew Keller, Helisa H. Wippel, Jared P. Mohr, and James E. Bruce
Analytical Chemistry, 2021 Dec 21;93(50):16759-167682. PMID: 34882395
BiotinylatedSS31_Bruce: Mitochondrial protein interaction landscape of SS-31.
Juan D. Chavez, Xiao-ting Tang, M.D. Campbell, G. Reyes, P.A. Kramer, R. Stuppard, Andrew Keller, H. Zhang, P.S. Rabinovitch, D.J. Marcinek, and James E. Bruce
Proc Natl Acad Sci U S A. Volume 30, Issue 26, P15363-15373, Jun 30, 2020. PMID: 32554501
Caudal_iqPIR_TACSham_Bruce: Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart.
Arianne Caudal, Xiaoting Tang, Juan D. Chavez, Andrew Keller, Jared P. Mohr, Anna A. Bakhtina, Outi Villet, Hongye Chen, Bo Zhou, Matthew A. Walker, Rong Tian, and James E. Bruce
Nature Cardiovascular Res., 2022 Sep1; 9, 855-866. | doi:10.1074/mcp.M112.024497
Chavezetal_MolCellProteomics2013: Protein Interactions, Post-translational Modifications and Topologies in Human Cells.
Juan D. Chavez, Chad R. Weisbrod, Chunxiang Zheng, Jimmy K. Eng and James E. Bruce
Mol Cell Proteomics, 12, 1451-1467. | doi:10.1074/mcp.M112.024497
ChavezCellSystems2017_BruceLab: Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue.
Juan D. Chavez, C.F. Lee, Ariane Caudal, Andrew Keller, Rong Tian, and James E. Bruce
Cell Systems. Volume 6, Issue 1, P136-141, Jan 24, 2018. PMID: 29199018
ChavezChemBiol2016_BruceLab: In vivo conformational dynamics of Hsp90 and its interactors.
Juan Chavez, Devin K Schweppe, Jimmy K Eng and James E Bruce
Cell Chemical Biology, Cell Chem Biol. 2016 Jun 23;23(6):716-726 PMID: 27341434
Ecoli2012_BingYang: Identification of cross-linked peptides from complex samples.
Bing Yang, Yan-Jie Wu, Ming Zhu, Sheng-Bo Fan, Jinzhong Lin, Kun Zhang, Shuang Li, Hao Chi, Yu-Xin Li, Hai-Feng Chen, Shu-Kun Luo, Yue-He Ding, Le-Heng Wang, Zhiqi Hao, Li-Yun Xiu, She Chen, Keqiong Ye, Si-Min He, Meng-Qiu Dong
Nature Methods, 9, 904-906 (2012) | doi:10.1038/nmeth.2099
HeLaNatureCommunications2015_BruceLab: Quantitative interactome analysis reveals a chemoresistant edgotype.
Juan D. Chavez, Devin K. Schweppe, Jimmy K. Eng, Chunxiang Zheng, Alex Taipale, Yiyi Zhang, Kohji Takara, James E. Bruce
Nature Communications, 6, Article number:7928 | doi:10.1038/ncomms8928
HeLa_PTX_titration_Cell_Reports_2019: Cellular interactome dynamics during paclitaxel treatment.
Juan D. Chavez, Andrew Keller, Bo Zhou, Rong Tian, and James E. Bruce
Cell Reports. Volume 29, Issue 8, P2371-2383.E5, Nov 19, 2019. PMID: 31747606
iqPIR_HeLa_17AAG_Chavez2020_Bruce: Isobaric quantitative protein interaction reporter technology for comparative interactome studies.
Juan D. Chavez, Andrew Keller, Jared P. Mohr, and James E. Bruce
Analytical Chemistry. Volume 92, Issue 20, P14094-14102, Oct 20, 2020. PMID: 32969639
iqPIR_std_proteins_Chavez2020_Bruce: Isobaric quantitative protein interaction reporter technology for comparative interactome studies.
Juan D. Chavez, Andrew Keller, Jared P. Mohr, and James E. Bruce
Analytical Chemistry. Volume 92, Issue 20, P14094-14102, Oct 20, 2020. PMID: 32969639
Kaake2014MCP_Huang: A New in Vivo Cross-linking Mass Spectrometry Platform to Define Protein–Protein Interactions in Living Cells
Robyn M. Kaake, Xiaorong Wang, Anthony Burke, Clinton Yu, Wynne Kandur, Yingying Yang, Eric J. Novtisky, Tonya Second, Jicheng Duan, Athit Kao, Shenheng Guan, Danielle Vellucci, Scott D. Rychnovsky, Lan Huang
MCP 13, 3533-3543 | http://dx.doi.org/10.1074/mcp.M114.042630
KellerJProteomeRes2019_HeLaLysate_Bruce: Prediction of an Upper Limit for the Fraction of Inter-Protein Cross-Links in Large-scale In Vivo Cross-Linking Studies.
Andrew Keller, Juan D. Chavez, Kevin C. Felt, and James E. Bruce
J Proteome Res. 2019 Jul 3. doi: 10.1021/acs.jproteome.9b00189. PMID: 31267744
KellerJProteomeRes2019_HeLaInVivo_Bruce: Prediction of an Upper Limit for the Fraction of Inter-Protein Cross-Links in Large-scale In Vivo Cross-Linking Studies.
Andrew Keller, Juan D. Chavez, Kevin C. Felt, and James E. Bruce
J Proteome Res. 2019 Jul 3. doi: 10.1021/acs.jproteome.9b00189. PMID: 31267744
KellerBioinformatics2018_Bruce: Increased Sensitivity with Automated Validation of XL-MS Cleavable Peptide Crosslinks.
Andrew Keller, Juan D Chavez, and James E Bruce
Bioinformatics, bty720, Published online 20 August 2018. PMID: 30137231
Liu2015NatureMethods_Heck: Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry.
Fan Liu, Dirk T S Rijkers, Harm Post, Albert J R Heck
Nature Methods, 12, 1179-1184 (2015) | doi:10.1038/nmeth.3603
Liu2017MCPmousemito_Heck: The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes.
F. Liu, P. Löss, B.M. Rabbitts, R.S. Balaban, and A.J.R. Heck
Molecular and Cellular Proteomics, 2018 Feb;17(2):216-232. PMID: 29222160
Leiker2015Ecoli_Lei: Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states
Dan Tan, Qiang Li, Mei-Jun Zhang, Chao Liu, Chengying Ma, Pan Zhang, Yue-He Ding, Sheng-Bo Fan, Li Tao, Bing Yang, Xiangke Li, Shoucai Ma, Junjie Liu, Boya Feng, Xiaohui Liu, Hong-Wei Wang, Si-Min He, Ning Gao, Keqiong Ye, Meng-Qiu Dong, Xiaoguang Lei
eLife 2016;5:e12509 | http://dx.doi.org/10.7554/eLife.12509
Leiker2016Ecoli_Lei: Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states.
Dan Tan, et. al., and Xiaoguang Lei
Elife, 2016 Mar 8;5:e12509. PMID: 26952210
MangoNuclear2018_Bruce: Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei.
D. Fasci, H. van Inge, R.A. Scheltema, A.J.R. Heck
Molecular and Cellular Proteomics, 2018 Oct;17(10):2018-2033. PMID: 30021884
MCF7_Hsp90_6plex_Bruce: Multiplexed Isobaric Quantitative Cross-Linking Reveals Drug-Induced Interactome Changes in Breast Cancer Cells.
Helisa H. Wippel, Juan D. Chavez, Andrew Keller, and James E. Bruce
Analytical Chemistry, 2022 Feb 15;94(6):2713-2722. PMID: 35107270
MohrAnalChem2018_Bruce: Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification.
Jared P. Mohr JP, P. Perumalla, Juan D. Chavez, Jimmy K. Eng, and James E Bruce
Analytical Chemistry. 2018 May 15;15;90(10):6028-6034. PMID: 29676898
PAeruginosa_Structure2015: Probing the Protein Interaction Network of Pseudomonas aeruginosa Cells by Chemical Cross-Linking Mass Spectrometry.
Arti T. Navare, Juan D. Chavez, Chunxiang Zheng, Chad R. Weisbrod, Jimmy K. Eng, Richard Siehnel, Pradeep K. Singh, Colin Manoil, James E. Bruce
Structure, Volume 23, Issue 4, 7 April 2015, Pages 762-773 | doi:10.1016/j.str.2015.01.022
Schweppe2015ChemBio_BruceLab: Host-Microbe Protein Interactions during Bacterial Infection.
Devin K. Schweppe, Christopher Harding, Juan D. Chavez, Xia Wu, Elizabeth Ramage, Pradeep K. Singh, Colin Manoil, James E. Bruce
Cell Chemical Biology, Volume 22, Issue 11, 19 November 2015, Pages 1521-1530 | doi:10.1016/j.chembiol.2015.09.015
SchweppemousemitoPNAS2017_BruceLab: Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry.
Devin K Schweppe, Juan Chavez, CF Lee, A Caudal, SE Kruse, R Stuppard, DJ Marcinek, GS Shadel, R Tian, and James E Bruce
Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1732-1737. PMID: 28130547
Weisbrodetal_JProteomeRes2013: In Vivo Protein Interaction Network Identified with a Novel Real-Time Cross-Linked Peptide Identification Strategy.
Chad R. Weisbrod, Juan D. Chavez, Jimmy K. Eng, Li Yang, Chunxiang Zheng, James E. Bruce
J. Proteome Res., 2013, 12 (4). | doi: 10.1021/pr3011638
Wu_NatureComm2016_BruceLab: In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in antibiotic resistant bacteria.
Xia Wu, Juan Chavez, Devin Schweppe, Chunxiang Zheng, Chad Weisbrod, Jimmy Eng, Ananya Murali, Samuel Lee, Elizabeth Ramage, Larry Gallagher, Hematha Kulasekara, Mauna Edrozo, Cassandra Kamischke, Mitchell Brittnacher, Samuel Miller, Pradeep Singh, Colin Manoil, and James Bruce
Nature Communications Nov 11;7:13414 PMID: 27834373
XLdb2013_Malmstrom: Cross-Link Guided Molecular Modeling with ROSETTA
Abdullah Kahraman , Franz Herzog , Alexander Leitner, George Rosenberger, Ruedi Aebersold, Lars Malmström
PLOS One Published: September 17, 2013 | http://dx.doi.org/10.1371/journal.pone.0073411
YeastNuclei_FilteredUnion_Wilkins: Cross-linking Mass Spectrometry Analysis of the Yeast Nucleus Reveals Extensive Protein-Protein Interactions Not Detected by Systematic Two-Hybrid or Affinity Purification-Mass Spectrometry.
Tara K. Bartolec, D.L. Smith, C.N.I. Pang, Y.D. Xu, J.J. Hamey, and Mark R. Wilkins
Analytical Chemicstry. 2020 Jan 21;92(2):1874-1882. PMID: 31851481
