Targeted extraction of ion chromatograms.
The software xTract 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 is used.
xTract example chromatogram: Shown are the extracted isotopes and the summed isotopes (cyan).
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).
- xtract_add_precursor_intensity.pl, extracts the precursor intensities from the MS2 headers and adds it to the input ID file.
- xtract_prep.pl, prepares the folderstructures for the ion chromatogram extraction.
- xtract_decoys.pl, creates decoy peptides based on the target IDs.
- xtract_run.pl, executes the xtract.pl program.
- xtract_merger.pl, merges the results and runs the statistical analysis of peak groups by mProphet.
- xtract_normalizer.pl, generates normalization parameters using common identified peptides.
- xtract_analyzer.pl, analyzes the extraction results and provides statistics.
- 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.
- 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.
- 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.
- 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.
- Reiter et al. (2011) mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nature methods.