|Title||»||Ignore full-scan settings for retention time prediction when importing SRM data|
|Assigned To||»||Nick Shulman|
Not necessarily yours, but maybe you can fix it. We just saw a lot of confusion, and I actually needed a debugger to figure out what was going on when a course instructor at the targeted proteomics course in SF had a document with Full-Scan settings that specified extraction around MS/MS IDs, and then imported SRM data. She got very surprising peak picking results, mostly peaks picked at the latest possible edge of her chromatogram range. It turned out this was due to using a spectral library from a longer gradient. Skyline was including the MS/MS ID times in retention time prediction, and Skyline was often predicting far ahead in the future from the chromatogram range.
We should improve our check for whether to use MS/MS ID times in retention time prediction to avoid accidentally using it based on the Full-Scan tab when the data being imported is SRM.