If you use XLinkDB to review or manage data, please cite:

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

Visit the Bruce Lab website for related pubications.

Citations for public data and tools used in XLinkDB can be found here:

Network and Structural Tools:

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

XL-MS Interaction Networks:

XLinkDB Dataset	Description	Authors	Citation	Pub. Date
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	2021-12-21
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	2021-12-21
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	2020-06-30
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	2022-09-01
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	2013-05-01
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	2018-01-24
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	2016-06-23
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	2012-07-08
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	2015-08-03
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	2019-11-19
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	2020-10-20
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	2020-10-20
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	2014-12-01
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	2019-07-03
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	2019-07-03
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	2018-08-20
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	2015-09-28
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	2018-02-01
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	2016-03-08
MangoNuclear2018_Bruce	Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. The data was analyzed with Mango and XLinkProphet and filtered for estimated 1% FDR	D. Fasci, H. van Inge, R.A. Scheltema, A.J.R. Heck	Molecular and Cellular Proteomics, 2018 Oct;17(10):2018-2033. PMID: 30021884	2018-10-01
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	2022-02-15
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	2018-05-15
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	2015-04-07
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	2015-11-19
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	2017-02-14
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	2013-02-17
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	2016-11-11
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	2013-09-17
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	2020-01-21
BakhtinaNatureAging2023_Bruce	Comparison of mito from the muscle tissue of old and young mice. 4 biological replicates	Anna A. Bakhtina, Gavin A. Pharaoh, Matthew D. Campbell, Andrew Keller, Randolph S. Stuppard, David J. Marcinek, and James E. Bruce	Nature Aging 2023 Mar;3(3):313-326 PMID: 37118428	2023-03-02
HEK_HeLa_iqPIR_ALL_data_Bruce	Quantitative comparison of in vivo cross-link levels of HEK and HeLa cells; 4 biological replicates, 2 experiments	Anna A. Bakhtina, Helisa H. Wippel, Juan D. Chavez, and James E. Bruce	J. Proteome Res. 2024, 23, 12, 5360–5371	2025-10-25
MCF-7_HeLa_iqPIR_Bruce	Quantitative comparison of in vivo cross-link levels of MCF7 and HeLa cells; 4 biological replicates, 2 experiments	Anna A. Bakhtina, Helisa H. Wippel, Juan D. Chavez, and James E. Bruce	J. Proteome Res. 2024, 23, 12, 5360–5371	2025-10-25
c2c12_mito_BKA_CATR_Bruce	BKA or CATR treatment of isolated c2c12 mitochondria	Anna A. Bakhtina, Helisa H. Wippel, Juan D. Chavez, and James E. Bruce	J. Proteome Res. 2024, 23, 12, 5360–5371	2025-10-25
Mito_iqPIR_TACsham_withDeadends_Bruce	Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart with cross-links, looplinks, and DE peptides	Andrew Keller, Xiaoting Tang, and James E. Bruce	J. Proteome Res. 2023, 22, 9, 2900–2908	2023-08-23
Urea_BSA_wBR_Bruce	Detection of conformational changes of BSA +/- bilirubin subjected to urea with quantitative cross-linking with 3 technical replicates	Martin Mathay, Andrew Keller, and James E. Bruce	Anal Chem. 2023 Jun 27;95(25):9432-9436. doi: 10.1021/acs.analchem.2c04501. Epub 2023 Jun 12. PMID: 37307416	2023-08-23
ChemBiol17AAG_Bruce	HeLa cells treated with various concentrations of 17AAG	Juan D. Chavez, Devin K. Schweppe, Jimmy K. Eng, and James E. Bruce	Cell Chem Biol. 2016 Jun 23;23(6):716-26. doi: 10.1016/j.chembiol.2016.05.012. PMID: 27341434	2016-06-23