|Exporting all peaks and mass accuracy for chromatograms||thomas hopf||2017-07-24|
Dear Skyline developers,
I am trying to set up an automated evaluation scheme for peak picking outside of Skyline. For this, it would be very nice to have access to all candidate peaks and their associated mass errors. While I see that information in the GUI, I wasn't able to fully access the underlying data so far.
1) When exporting the chromatograms for all of the precursors, besides the intensities is it somehow possible to get the corresponding mass error/accuracy for each time point? In the reports, I only seem to be able to get the error for the one chosen peak per precursor.
2) For each precursor, is it possible to get a list of all candidate peaks chosen by the Skyline heuristics?
3) I seem to be able to extract some of the above information by exporting the mProphet peak features; however the associated mass errors for the mProphet candidate peaks seem to differ quite substantially from nearby Skyline peaks. How does this occur?
4) Can the mProphet features be automatically extracted using a command-line parameter?
Thanks for your help!