iRT Retention Time Issue

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iRT Retention Time Issue johnny perez  2018-05-03 13:52
 
Hi Brendan,

One more question about how skyline predicts peptide retention times. I've attached a chart to highlight my question. In this scenario, the same peptide elutes at different times with considerably varying ion intensities. The user selecting the correct peaks and recalibrated the iRT database shows near perfect linear regression, however, my question pertains to the yellow prediction box. How is this time predicted? It does not appear to correlate with the SSRCalc times.

All the best and thank you for your help!

Johnny
 
 
Brendan MacLean responded:  2018-05-03 14:02
You can have Skyline show a regression for whichever calculator you want. It is not necessarily the one in use. Double-check your retention time predictor and make sure it is the one you think it is. The predicted RT in the chromatogram graphs is always based on the current predictor, but the regression graph may not be showing that predictor. One clue in the graph from your screenshot is that it does not contain gray text describing the coefficients of the predictor below the coefficients of the regression.

Hope this helps. Thanks for the screenshot.

--Brendan
 
johnny perez responded:  2018-05-03 14:26
Hi Brendan,

You were 100% correct. Thank you for the much needed information.

All the best,

Johnny