|Problems with MS1 extraction||frederik tellkamp||2023-06-28 07:02|
Dear Skyline support team and community,
I am trying to set up a PRM measurement. To this end I wanted to use some DDA runs to extract chromatograms and generate a transition list for PRM. One of the peptides I am particulary interested in is an N-terminal phosphopeptide.
Unfortunately, after MS1 extraction this very phosphopeptide did not appear in Skyline, whereas the unphosphorylated one did. I was puzzled and did some troubleshooting (I am new to this software I should mention here):
I noticed other prominent phosphopeptides in the data that have been extracted without problems.
I used MQ 184.108.40.206 and Skyline 220.127.116.117. I guess you may need some files, i attached the msms.txt, the mqpar.xml and the modifications.xml.
Thanks in advance your your help!