Identification of cross-linked peptides from complex samples - PubMed (original) (raw)

doi: 10.1038/nmeth.2099. Epub 2012 Jul 8.

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

Affiliations

• PMID: 22772728
• DOI: 10.1038/nmeth.2099

Identification of cross-linked peptides from complex samples

Bing Yang et al. Nat Methods. 2012 Sep.

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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Comment in

• Evaluating protein interactions through cross-linking mass spectrometry.
  Tabb DL. Tabb DL. Nat Methods. 2012 Sep;9(9):879-81. doi: 10.1038/nmeth.2139. Nat Methods. 2012. PMID: 22936167 Free PMC article. No abstract available.

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References

1. 1. Nucleic Acids Res. 2008 Jan;36(Database issue):D632-6 - PubMed
2. 1. Mol Cell Proteomics. 2011 Feb;10(2):M110.001420 - PubMed
3. 1. Mol Cell Biol. 2008 Nov;28(21):6547-56 - PubMed
4. 1. Protein Sci. 2010 Dec;19(12):2389-401 - PubMed
5. 1. J Proteome Res. 2010 Jul 2;9(7):3384-93 - PubMed

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