|Number of scans from raw data||ulisse cucchi||2021-07-29|
Hello Skyline Team,
I'm still trying to learn the basics of the software, in particular for the targeted analysis of peptides by PRM. I managed to perform all the steps well described by your tutorials, but I have an issue regarding the number of scans that are imported into Skyline from the raw data. To show you the issue I attached you 3 slides in a pdf file.
In the slide 1 you can see the peak from the raw file (two different visualizations of the same peak are showed). As you can see the peak contains over 40 scans of the same precursor (the instrument used was the Orbitrap Exploris 240 from Thermo).
In the second slide you can see how the same peak is imported into Skyline. As you can see, only few scans (less than 10) are used and the resulting peak has a lower resolution, that means also a lower accuracy when the peak is integrated.
In the third and last slide you can see the only parameter that I've found that should affect the number of scans that are imported, but the option "include all matching scans" was already selected. Since they are all very good scans from the raw file, I don't understand why Skyline is considering less than 10 of them. Is there any way to make Skyline import all the scans present in the raw file?
Thanks in advance for any answer and suggestion you may provide,
Ulisse Cucchi from Nerviano Medical Sciences (Italy)