|Orbitrap DIA search using converted Spectronaut library||zhangfangfei||2021-08-02|
Hi Skyline Support team,
I used a converted library from Spectronaut for the DIA analysis.,by importing the transition list, other steps referring the instruction here https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/DIA-QE-20_1.pdf. The mProphet capture is in the attached. It seems to me a failed search with greyed RT difference and dot product. We got a very poor CV by replicates, low cross-correlations by retention time and quantification comparing with other DIA search results. The results are much better on other datasets.
What do you think could be the problem ? My guess would be 1) the neural loss ions or other ions are setting not properly from the converted Spectronaut library 2) retention time alignment failed (there displayed the RT in the library ) 3) the size of library is too large (300K precursors) 4)Is the Skyline Batch relevant for the DIA analysis?
As the library is very large, any operations took a long time. I would like to know your suggestions in how to quickly probe into the problem in quantification.
Thanks for your support