|Skyline for unknown modifications||mprado||2018-10-17|
I am wondering if anyone knows if Skyline could be used for the identification of unknown modifications.
For that, I have been running some test to see if I could identify fragment ions without considering the precursor mass, but somehow... I cannot make it work.
Let me explain it with an example. As you can see in the picture attached, I am trying to find several fragment ions of 2 peptides that differs only in one amino acid (the Met at the N-termini): MPLYSVTVK and PLYSVTVK. If in both peptides I only use y1-y7 fragment ions (disregarding the precursor mass), they should be identified at the same retention time. As you can see in the pic attached... This doesn't happen.
For this test I am deactivating the MS1 filtering in Tools>Transition settings>Full-Scan in order to use only the MS2 fragments, but I am not sure if I am missing anything else
Thanks in advance for your help!!