|Is there a way to elimate false postives in Small Molecule mode?||Allison Haase||2019-11-04|
Sorry for the bother, but I was wondering if there any way to set a threshold for peak intensity in small molecule mode in Skylines.
My group uses Skyline for a GC-MS data set that uses a surrogate standard for quantification. This method has a pretty noisy baseline, especially in our blanks and double blanks, as the lack of filtering causes a lot of product ions to be present.
The issue we have is with the double blanks. Due to the noisy baseline, Skyline picks out a very small peak for the internal standard and for the other molecules of interest. Due to the calibration curve being normalized to the surrogate standard, this causes incredibly high concentration values to be reported for our double blanks. Currently we deal with this problem by deleting the Surrogate Standard peaks for double blanks, but we wish to automate this process and to make sure that peaks are not picked out when they are not actually present. Is there a way to set an intensity threshold for Skyline to pick peaks?