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Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling.

Larance M, Kirkwood KJ, Tinti M, Brenes Murillo A, Ferguson MA, Lamond AI.

Mol Cell Proteomics. 2016 Jul;15(7):2476-90. doi: 10.1074/mcp.O115.055467. Epub 2016 Apr 25.


Characterization of Dynamic UbR-Proteasome Subcomplexes by In vivo Cross-linking (X) Assisted Bimolecular Tandem Affinity Purification (XBAP) and Label-free Quantitation.

Yu C, Yang Y, Wang X, Guan S, Fang L, Liu F, Walters KJ, Kaiser P, Huang L.

Mol Cell Proteomics. 2016 Jul;15(7):2279-92. doi: 10.1074/mcp.M116.058271. Epub 2016 Apr 25.


Quantitative Proteomics Analysis of VEGF-Responsive Endothelial Protein S-Nitrosylation Using Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and LC-MS/MS.

Zhang HH, Lechuga TJ, Chen Y, Yang Y, Huang L, Chen DB.

Biol Reprod. 2016 May;94(5):114. doi: 10.1095/biolreprod.116.139337. Epub 2016 Apr 13.


Open-gate mutants of the mammalian proteasome show enhanced ubiquitin-conjugate degradation.

Choi WH, de Poot SA, Lee JH, Kim JH, Han DH, Kim YK, Finley D, Lee MJ.

Nat Commun. 2016 Mar 9;7:10963. doi: 10.1038/ncomms10963.


Characterization of the 26S proteasome network in Plasmodium falciparum.

Wang L, Delahunty C, Fritz-Wolf K, Rahlfs S, Helena Prieto J, Yates JR, Becker K.

Sci Rep. 2015 Dec 7;5:17818. doi: 10.1038/srep17818.


Formaldehyde crosslinking: a tool for the study of chromatin complexes.

Hoffman EA, Frey BL, Smith LM, Auble DT.

J Biol Chem. 2015 Oct 30;290(44):26404-11. doi: 10.1074/jbc.R115.651679. Epub 2015 Sep 9. Review.


Facilitated Tau Degradation by USP14 Aptamers via Enhanced Proteasome Activity.

Lee JH, Shin SK, Jiang Y, Choi WH, Hong C, Kim DE, Lee MJ.

Sci Rep. 2015 Jun 4;5:10757. doi: 10.1038/srep10757.


Histidine 114 Is Critical for ATP Hydrolysis by the Universally Conserved ATPase YchF.

Rosler KS, Mercier E, Andrews IC, Wieden HJ.

J Biol Chem. 2015 Jul 24;290(30):18650-61. doi: 10.1074/jbc.M114.598227. Epub 2015 May 27.


Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth.

Mertz J, Tan H, Pagala V, Bai B, Chen PC, Li Y, Cho JH, Shaw T, Wang X, Peng J.

Mol Cell Proteomics. 2015 Jul;14(7):1898-910. doi: 10.1074/mcp.M114.045898. Epub 2015 Apr 30.


Synthesis of two new enrichable and MS-cleavable cross-linkers to define protein-protein interactions by mass spectrometry.

Burke AM, Kandur W, Novitsky EJ, Kaake RM, Yu C, Kao A, Vellucci D, Huang L, Rychnovsky SD.

Org Biomol Chem. 2015 May 7;13(17):5030-7. doi: 10.1039/c5ob00488h.


Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry.

Navare AT, Chavez JD, Zheng C, Weisbrod CR, Eng JK, Siehnel R, Singh PK, Manoil C, Bruce JE.

Structure. 2015 Apr 7;23(4):762-73. doi: 10.1016/j.str.2015.01.022. Epub 2015 Mar 19.


BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes.

Alekseyenko AA, McElroy KA, Kang H, Zee BM, Kharchenko PV, Kuroda MI.

Curr Protoc Mol Biol. 2015 Jan 5;109:21.30.1-32. doi: 10.1002/0471142727.mb2130s109.


A new in vivo cross-linking mass spectrometry platform to define protein-protein interactions in living cells.

Kaake RM, Wang X, Burke A, Yu C, Kandur W, Yang Y, Novtisky EJ, Second T, Duan J, Kao A, Guan S, Vellucci D, Rychnovsky SD, Huang L.

Mol Cell Proteomics. 2014 Dec;13(12):3533-43. doi: 10.1074/mcp.M114.042630. Epub 2014 Sep 24.


A pipeline for determining protein-protein interactions and proximities in the cellular milieu.

Subbotin RI, Chait BT.

Mol Cell Proteomics. 2014 Nov;13(11):2824-35. doi: 10.1074/mcp.M114.041095. Epub 2014 Aug 29.


Defining dynamic protein interactions using SILAC-based quantitative mass spectrometry.

Wang X, Huang L.

Methods Mol Biol. 2014;1188:191-205. doi: 10.1007/978-1-4939-1142-4_14.


Autoubiquitination of the 26S proteasome on Rpn13 regulates breakdown of ubiquitin conjugates.

Besche HC, Sha Z, Kukushkin NV, Peth A, Hock EM, Kim W, Gygi S, Gutierrez JA, Liao H, Dick L, Goldberg AL.

EMBO J. 2014 May 16;33(10):1159-76. doi: 10.1002/embj.201386906. Epub 2014 May 8.


Advanced methods for the analysis of chromatin-associated proteins.

Guillen-Ahlers H, Shortreed MR, Smith LM, Olivier M.

Physiol Genomics. 2014 Jul 1;46(13):441-7. doi: 10.1152/physiolgenomics.00041.2014. Epub 2014 May 6. Review.


Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification.

Alekseyenko AA, Gorchakov AA, Kharchenko PV, Kuroda MI.

Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2488-93. doi: 10.1073/pnas.1400648111. Epub 2014 Feb 3.


Developing new isotope-coded mass spectrometry-cleavable cross-linkers for elucidating protein structures.

Yu C, Kandur W, Kao A, Rychnovsky S, Huang L.

Anal Chem. 2014 Feb 18;86(4):2099-106. doi: 10.1021/ac403636b. Epub 2014 Feb 6.


A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification.

Verkest A, Abeel T, Heyndrickx KS, Van Leene J, Lanz C, Van De Slijke E, De Winne N, Eeckhout D, Persiau G, Van Breusegem F, Inzé D, Vandepoele K, De Jaeger G.

Plant Physiol. 2014 Mar;164(3):1122-33. doi: 10.1104/pp.113.229617. Epub 2014 Jan 22.

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