Commit 629490e2 authored by Chris Sarnowski's avatar Chris Sarnowski
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Update README.md

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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. 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.
![image](https://gitlab.ethz.ch/leitner_lab/xtract/-/wikis/uploads/bf24fb00f31321b6d12e277e06dbd3a4/image.png) ![image](https://gitlab.ethz.ch/leitner_lab/xtract/-/wikis/uploads/bf24fb00f31321b6d12e277e06dbd3a4/image.png)
xTract example chromatogram: Shown are the extracted isotopes and the summed isotopes (cyan).
### xTract Repository Wiki ### xTract Repository Wiki
More information can be found on the various pages of the xTract repository wiki: More information can be found on the various pages of the xTract repository wiki:
...@@ -14,8 +15,7 @@ More information can be found on the various pages of the xTract repository wiki ...@@ -14,8 +15,7 @@ More information can be found on the various pages of the xTract repository wiki
* [How to run](https://gitlab.ethz.ch/leitner_lab/xtract/-/wikis/How-to-run) * [How to run](https://gitlab.ethz.ch/leitner_lab/xtract/-/wikis/How-to-run)
### xTract example chromatogram: Shown are the extracted isotopes and the summed isotopes (cyan). ### Software components
The software xTract consists of multiple programs that are executed consequtively. The software xTract consists of multiple programs that are executed consequtively.
All necessary programs are located in the /bin directory and have a help section (execute the program with the -h flag). All necessary programs are located in the /bin directory and have a help section (execute the program with the -h flag).
* xtract_add_precursor_intensity.pl, extracts the precursor intensities from the MS2 headers and adds it to the input ID file. * xtract_add_precursor_intensity.pl, extracts the precursor intensities from the MS2 headers and adds it to the input ID file.
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