Literature DB >> 22772728

Identification of cross-linked peptides from complex samples.

Bing Yang1, 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.   

Abstract

We have developed pLink, software for data analysis of cross-linked proteins coupled with mass-spectrometry analysis. pLink reliably estimates false discovery rate in cross-link identification and is compatible with multiple homo- or hetero-bifunctional cross-linkers. We validated the program with proteins of known structures, and we further tested it on protein complexes, crude immunoprecipitates and whole-cell lysates. We show that it is a robust tool for protein-structure and protein-protein-interaction studies.

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Year:  2012        PMID： 22772728     DOI： 10.1038/nmeth.2099

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  18 in total

1.  Structure and function of archaeal box C/D sRNP core proteins.

Authors:  Mohamed Aittaleb; Rumana Rashid; Qiong Chen; John R Palmer; Charles J Daniels; Hong Li
Journal:  Nat Struct Biol       Date:  2003-04

2.  A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis.

Authors:  François Dragon; Jennifer E G Gallagher; Patricia A Compagnone-Post; Brianna M Mitchell; Kara A Porwancher; Karen A Wehner; Steven Wormsley; Robert E Settlage; Jeffrey Shabanowitz; Yvonne Osheim; Ann L Beyer; Donald F Hunt; Susan J Baserga
Journal:  Nature       Date:  2002-06-09       Impact factor: 49.962

3.  Structural and thermodynamic analysis of the GFP:GFP-nanobody complex.

Authors:  Marta H Kubala; Oleksiy Kovtun; Kirill Alexandrov; Brett M Collins
Journal:  Protein Sci       Date:  2010-12       Impact factor: 6.725

4.  Identification of cross-linked peptides from large sequence databases.

Authors:  Oliver Rinner; Jan Seebacher; Thomas Walzthoeni; Lukas N Mueller; Martin Beck; Alexander Schmidt; Markus Mueller; Ruedi Aebersold
Journal:  Nat Methods       Date:  2008-03-09       Impact factor: 28.547

5.  Structural basis for site-specific ribose methylation by box C/D RNA protein complexes.

Authors:  Jinzhong Lin; Shaomei Lai; Ru Jia; Anbi Xu; Liman Zhang; Jing Lu; Keqiong Ye
Journal:  Nature       Date:  2011-01-27       Impact factor: 49.962

6.  An isotopically coded CID-cleavable biotinylated cross-linker for structural proteomics.

Authors:  Evgeniy V Petrotchenko; Jason J Serpa; Christoph H Borchers
Journal:  Mol Cell Proteomics       Date:  2010-07-09       Impact factor: 5.911

7.  Vectors for co-expression of two genes in Caenorhabditis elegans.

Authors:  Li-Wei Lee; Hsiao-Wen Lo; Szecheng J Lo
Journal:  Gene       Date:  2010-02-10       Impact factor: 3.688

8.  High-definition macromolecular composition of yeast RNA-processing complexes.

Authors:  Nevan J Krogan; Wen-Tao Peng; Gerard Cagney; Mark D Robinson; Robin Haw; Gouqing Zhong; Xinghua Guo; Xin Zhang; Veronica Canadien; Dawn P Richards; Bryan K Beattie; Atanas Lalev; Wen Zhang; Armaity P Davierwala; Sanie Mnaimneh; Andrei Starostine; Aaron P Tikuisis; Jorg Grigull; Nira Datta; James E Bray; Timothy R Hughes; Andrew Emili; Jack F Greenblatt
Journal:  Mol Cell       Date:  2004-01-30       Impact factor: 17.970

9.  The genetics of Caenorhabditis elegans.

Authors:  S Brenner
Journal:  Genetics       Date:  1974-05       Impact factor: 4.562

10.  Bacteriome.org--an integrated protein interaction database for E. coli.

Authors:  Chong Su; Jose M Peregrin-Alvarez; Gareth Butland; Sadhna Phanse; Vincent Fong; Andrew Emili; John Parkinson
Journal:  Nucleic Acids Res       Date:  2007-10-16       Impact factor: 16.971
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  261 in total

1.  Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry.

Authors:  Fan Liu; Dirk T S Rijkers; Harm Post; Albert J R Heck
Journal:  Nat Methods       Date:  2015-09-28       Impact factor: 28.547

2.  Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification.

Authors:  Matthew M Makowski; Esther Willems; Pascal W T C Jansen; Michiel Vermeulen
Journal:  Mol Cell Proteomics       Date:  2015-11-11       Impact factor: 5.911

3.  Evidence for Two Distinct Binding Sites for Lipoprotein Lipase on Glycosylphosphatidylinositol-anchored High Density Lipoprotein-binding Protein 1 (GPIHBP1).

Authors:  Mart Reimund; Mikael Larsson; Oleg Kovrov; Sergo Kasvandik; Gunilla Olivecrona; Aivar Lookene
Journal:  J Biol Chem       Date:  2015-04-14       Impact factor: 5.157

4.  Matching cross-linked peptide spectra: only as good as the worse identification.

Authors:  Michael J Trnka; Peter R Baker; Philip J J Robinson; A L Burlingame; Robert J Chalkley
Journal:  Mol Cell Proteomics       Date:  2013-12-12       Impact factor: 5.911

Review 5.  Chemical cross-linking in the structural analysis of protein assemblies.

Authors:  Feixia Chu; Daniel T Thornton; Hieu T Nguyen
Journal:  Methods       Date:  2018-05-30       Impact factor: 3.608

6.  Structural features of the TatC membrane protein that determine docking and insertion of a twin-arginine signal peptide.

Authors:  Anne-Sophie Blümmel; Friedel Drepper; Bettina Knapp; Ekaterina Eimer; Bettina Warscheid; Matthias Müller; Julia Fröbel
Journal:  J Biol Chem       Date:  2017-10-31       Impact factor: 5.157

7.  Bifunctional cross-linking approaches for mass spectrometry-based investigation of nucleic acids and protein-nucleic acid assemblies.

Authors:  M Scalabrin; S M Dixit; M M Makshood; C E Krzemien; Daniele Fabris
Journal:  Methods       Date:  2018-05-10       Impact factor: 3.608

8.  Chemical Crosslinking Mass Spectrometry Reveals the Conformational Landscape of the Activation Helix of PPARγ; a Model for Ligand-Dependent Antagonism.

Authors:  Jie Zheng; Cesar Corzo; Mi Ra Chang; Jinsai Shang; Vinh Q Lam; Richard Brust; Anne-Laure Blayo; John B Bruning; Theodore M Kamenecka; Douglas J Kojetin; Patrick R Griffin
Journal:  Structure       Date:  2018-08-23       Impact factor: 5.006

9.  Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking.

Authors:  Eric D Merkley; Erin S Baker; Kevin L Crowell; Daniel J Orton; Thomas Taverner; Charles Ansong; Yehia M Ibrahim; Meagan C Burnet; John R Cort; Gordon A Anderson; Richard D Smith; Joshua N Adkins
Journal:  J Am Soc Mass Spectrom       Date:  2013-02-20       Impact factor: 3.109

10.  Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states.

Authors:  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
Journal:  Elife       Date:  2016-03-08       Impact factor: 8.140
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