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Identification of cross-linked peptides from complex samples

by Chi, Hao , Hao, Zhiqi , Yang, Bing , Lin, Jinzhong , Li, Shuang , Chen, She , Wu, Yan-Jie , Ye, Keqiong , Fan, Sheng-Bo , He, Si-Min , Zhu, Ming , Wang, Le-Heng , Xiu, Li-Yun , Zhang, Kun , Luo, Shu-Kun , Dong, Meng-Qiu , Li, Yu-Xin , Ding, Yue-He , Chen, Hai-Feng

in 631/1647/2067 / 631/1647/527/296 / 631/1647/794 / Algorithms / Animals / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / brief-communication / Caenorhabditis elegans - chemistry / Chromatography, High Pressure Liquid / Cross-Linking Reagents - chemistry / Crosslinked polymers / Data analysis / Data Interpretation, Statistical / Databases, Protein / Escherichia coli - chemistry / False Positive Reactions / Humans / Identification and classification / Life Sciences / Mass Spectrometry / Methods / Models, Molecular / Peptides / Peptides - analysis / Peptides - chemistry / Protein Binding / Protein Conformation / Proteins / Proteomics / Proteomics - methods / Reproducibility of Results / Software / Spectrometry

2012

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2012

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2012

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Journal Article

Identification of cross-linked peptides from complex samples

Chi, Hao,

Hao, Zhiqi,

Yang, Bing,

Lin, Jinzhong,

Li, Shuang,

Chen, She,

Wu, Yan-Jie,

Ye, Keqiong,

Fan, Sheng-Bo,

He, Si-Min,

Zhu, Ming,

Wang, Le-Heng,

Xiu, Li-Yun,

Zhang, Kun,

Luo, Shu-Kun,

Dong, Meng-Qiu,

Li, Yu-Xin,

Ding, Yue-He,

Chen, Hai-Feng

2012

Overview

pLink, software for data analysis of cross-linked proteins coupled with mass spectrometry, estimates false discovery rate and enables analysis of protein complexes without extensive purification. 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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Publisher

Nature Publishing Group US,Nature Publishing Group

Subject

/ Animals

/ Biological Microscopy