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## xQuest/xProphet
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Identification and statistical validation of cross-linked peptides identified by MS
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Chemical cross-linking of proteins or protein complexes in combination with mass spectrometry is an increasingly used technique to obtain low resolution structural restraints.
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The software xQuest is designated to identify cross-linked peptides from LC-MS/MS spectra [1].
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#### xQuest spectrum
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![image](uploads/74e2f22b2b5fcc25540a201763ff1ae9/image.png)
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xQuest example spectrum: On the top left corner the sequence of the cross-linked peptide is shown. In the spectrum, matched common fragment ions (green) and cross-linker containing fragment ions (red) are indicated with diamonds. On the peptide sequences, matched ions are indicated with red and green ticks.
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The software xProphet is designated to estimate false discovery rates (FDRs) in cross-linking datasets [2]. The software is based on a target-decoy search strategy for cross-linked peptides.
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A detailed step by step protocol of the experimental and the computational procedure has been published [3].
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#### References
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1. Rinner O, Seebacher J, Walzthoeni T, Mueller L, Beck M, Schmidt A, Mueller M, Aebersold R (2008) Identification of cross-linked peptides from large sequence databases. Nature methods.
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2. Walzthoeni T, Claassen M, Leitner A, Herzog F, Bohn S, Förster F, Beck M, Aebersold R (2012) False discovery rate estimation for cross-linked peptides identified by mass spectrometry. Nature methods.
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3. Leitner A, Walzthoeni T, Aebersold R. (2014) Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nature protocols. |