|The quantification of MS2 ions in SWATH analysis||sunbergsoon||2019-08-02|
Recently we compared the DIA quantification results from PeakView and Skyline, we found that the results are quite different.
We analyzed protein extracts from different developmental stages of a fly species with two replicates for each stage. We used the same spectral library to do searching in both the software. In PeakView, we exported the results using default settings and q-value cutoff=0.05. However in Skyline, we exported the results with q-value cutoff=0.05 after training a mProphet model. In skyline we used the normalized area to do quantification where the normalized method is "none".
We compared the results by computing ratio of common peptides in common proteins yielded by the two software.The comparison result is shown in attached plot. Could you please give some suggestions on explanation about the results?