|Instrument tab and full scan tab contradictions||edith serrano||2017-02-23|
I am using Skyline 188.8.131.5293 (64 bit) and I have a couple of questions
1) I know that my sample is coming trough between 40 and 65 minutes and after that is just the wash so I set those limits on the instrument tab of the transition settings. On the full scan tab I tick Use only scans within 4 min of predicted RT.
I created a calculator and predictor based on this gradient and applied it to a library acquired with a longer one. In general the prediction is good but some peptides are supposed to appear after those 65 minutes. These chromatograms are imported even though I set the instrument limit and the data is obviously horrible. My fear is that those fake peaks are messing with the peak picking model. Is there any way to really limit the time of the imported chromatogram?
2) Other peptides that are supposed to appear after those 65 minutes figure as non measured. Do they have any effect on the model?
3) The predicted RT and time window don't appear in my chromatogram graph even though Retention time prediction is ticked.
I attach some pictures that I hope help understand the problems.
Thanks a lot