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##xTract
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###Targeted extraction of ion chromatograms.
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## xTract
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### Targeted extraction of ion chromatograms.
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The software xTract[1] has been designed to extract ion chromatograms of cross-linked peptides using the xQuest/xProphet[2-4] pipeline. It uses a unique target - decoy strategy to provide statistics on the extracted ion chromatograms. For this purpose, the software mProphet[5] is used.
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![image](uploads/bf24fb00f31321b6d12e277e06dbd3a4/image.png)
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###xTract example chromatogram: Shown are the extracted isotopes and the summed isotopes (cyan).
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### xTract example chromatogram: Shown are the extracted isotopes and the summed isotopes (cyan).
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The software xTract consists of multiple programs that are executed consequtively.
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All necessary programs are located in the /bin directory and have a help section (execute the program with the -h flag).
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... | ... | @@ -17,7 +17,7 @@ All necessary programs are located in the /bin directory and have a help section |
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* xtract_normalizer.pl, generates normalization parameters using common identified peptides.
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* xtract_analyzer.pl, analyzes the extraction results and provides statistics.
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###References
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### References
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1. Walzthoeni T, Joachimiak LA, Rosenberger G, Röst HL, Malmström L, Leitner A, Frydman R, Aebersold R (2015) xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. 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. 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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