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Literature DB >> 18327264

Identification of cross-linked peptides from large sequence databases.

Oliver Rinner¹, Jan Seebacher, Thomas Walzthoeni, Lukas N Mueller, Martin Beck, Alexander Schmidt, Markus Mueller, Ruedi Aebersold.

Abstract

We describe a method to identify cross-linked peptides from complex samples and large protein sequence databases by combining isotopically tagged cross-linkers, chromatographic enrichment, targeted proteomics and a new search engine called xQuest. This software reduces the search space by an upstream candidate-peptide search before the recombination step. We showed that xQuest can identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search.

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Year: 2008 PMID： 18327264 PMCID： PMC2719781 DOI： 10.1038/nmeth.1192

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

15 in total

1. A modular cross-linking approach for exploring protein interactions.

Authors: Michelle Trester-Zedlitz; Katsuhiko Kamada; Stephen K Burley; David Fenyö; Brian T Chait; Tom W Muir
Journal: J Am Chem Soc Date: 2003-03-05 Impact factor: 15.419

2. Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis.

Authors: D R Müller; P Schindler; H Towbin; U Wirth; H Voshol; S Hoving; M O Steinmetz
Journal: Anal Chem Date: 2001-05-01 Impact factor: 6.986

3. Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes.

Authors: Andrea Sinz
Journal: J Mass Spectrom Date: 2003-12 Impact factor: 1.982

Review 4. Chemical cross-linking and mass spectrometry for protein structural modeling.

Authors: Jaap Willem Back; Luitzen de Jong; Anton O Muijsers; Chris G de Koster
Journal: J Mol Biol Date: 2003-08-08 Impact factor: 5.469

5. Mapping low-resolution three-dimensional protein structures using chemical cross-linking and Fourier transform ion-cyclotron resonance mass spectrometry.

Authors: Gry H Dihazi; Andrea Sinz
Journal: Rapid Commun Mass Spectrom Date: 2003 Impact factor: 2.419

6. Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method.

Authors: Kara M Pearson; Lewis K Pannell; Henry M Fales
Journal: Rapid Commun Mass Spectrom Date: 2002 Impact factor: 2.419

7. Unambiguous assignment of intramolecular chemical cross-links in modified mammalian membrane proteins by Fourier transform-tandem mass spectrometry.

Authors: Petr Novak; William E Haskins; Marites J Ayson; Richard B Jacobsen; Joseph S Schoeniger; Michael D Leavell; Malin M Young; Gary H Kruppa
Journal: Anal Chem Date: 2005-08-15 Impact factor: 6.986

8. High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry.

Authors: M M Young; N Tang; J C Hempel; C M Oshiro; E W Taylor; I D Kuntz; B W Gibson; G Dollinger
Journal: Proc Natl Acad Sci U S A Date: 2000-05-23 Impact factor: 11.205

9. Probing three-dimensional structure of bovine serum albumin by chemical cross-linking and mass spectrometry.

Authors: Bill X Huang; Hee-Yong Kim; Chhabil Dass
Journal: J Am Soc Mass Spectrom Date: 2004-08 Impact factor: 3.109

10. MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides.

Authors: Birgit Schilling; Richard H Row; Bradford W Gibson; Xin Guo; Malin M Young
Journal: J Am Soc Mass Spectrom Date: 2003-08 Impact factor: 3.109

203 in total

1. In vivo application of photocleavable protein interaction reporter technology.

Authors: Li Yang; Chunxiang Zheng; Chad R Weisbrod; Xiaoting Tang; Gerhard R Munske; Michael R Hoopmann; Jimmy K Eng; James E Bruce
Journal: J Proteome Res Date: 2012-01-09 Impact factor: 4.466

2. StavroX--a software for analyzing crosslinked products in protein interaction studies.

Authors: Michael Götze; Jens Pettelkau; Sabine Schaks; Konstanze Bosse; Christian H Ihling; Fabian Krauth; Romy Fritzsche; Uwe Kühn; Andrea Sinz
Journal: J Am Soc Mass Spectrom Date: 2011-10-25 Impact factor: 3.109

3. Quaternary diamines as mass spectrometry cleavable crosslinkers for protein interactions.

Authors: Billy Clifford-Nunn; H D Hollis Showalter; Philip C Andrews
Journal: J Am Soc Mass Spectrom Date: 2011-12-01 Impact factor: 3.109

4. Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling.

Authors: Nir Kalisman; Christopher M Adams; Michael Levitt
Journal: Proc Natl Acad Sci U S A Date: 2012-02-01 Impact factor: 11.205

5. False discovery rate estimation for cross-linked peptides identified by mass spectrometry.

Authors: Thomas Walzthoeni; Manfred Claassen; Alexander Leitner; Franz Herzog; Stefan Bohn; Friedrich Förster; Martin Beck; Ruedi Aebersold
Journal: Nat Methods Date: 2012-07-08 Impact factor: 28.547

6. Identification of cross-linked peptides from complex samples.

Authors: 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
Journal: Nat Methods Date: 2012-07-08 Impact factor: 28.547

7. Topographic studies of the GroEL-GroES chaperonin complex by chemical cross-linking using diformyl ethynylbenzene: the power of high resolution electron transfer dissociation for determination of both peptide sequences and their attachment sites.

Authors: Michael J Trnka; A L Burlingame
Journal: Mol Cell Proteomics Date: 2010-09-02 Impact factor: 5.911