|DDA data question
Hi Skyline team,
I am trying to use Skyline to track the performance of our System Suitability (DDA run, 15 peptide standards mix). The goal is to monitor MS1 and MS2 intensity change across the time.
Below is what I did: I searched the raw data in PMI and generated the mzid file that can be imported into Skyline. I used this mzid file to build the spectrum library. Then I set the peptide setting and transition setting based on the method edit tutorial. Then I imported all 15 peptides that I would like to monitor. Once everything is set up, I used File>Import>Result to import the raw data and try to view the results in Skyline. One thing I do not understand is that I can see all those product ion on the spectrum library, but why most of those product ions were labelled red in the Skyline? For example, if you look at the second peptide “GISNEGQNASIK”, I can see y7, y8 and y10 in the spectrum library, but these product ions were all labelled as red in the list (screenshot attached). The raw data I imported directly into Skyline is the same file I searched with PMI, so the fragment should be exactly the same. I have attached my Skyline file in case you want to take a look at the setting.
Another question is that I set in the transition setting that to monitor y, b, p ion types, why I only can see the precursor ion? I cannot find the way to display the fragment ions.
Hope I have my question expressed clearly, if you have any question or need any further information from me, please let me know.