Dear Skyline team,

I want to have a curated spectral library from 3 replicates of DDA on samples spiked with iRTs.

After building the library, I found the following problems based on manual inspection:

1- some wrong picked MS1 peaks
2- wrong ID (2min far from the peak while having ID inside the elution width of the correct MS1 peak) assigned to correct MS1 peak.

With the aim to use them for the PRM assay, neither the iRT calculator nor the spectral library could be of further use if they contain incorrect information.

Those problems are expected as I am working on highly modified histone peptides where isobaric peptides co- or nearly elute with most of the product ions are shared.

Is there a way to modify the spectral library after it is built? For instance, replace a MSMS ID chosen by BiblioSpec with one from the redundant library or adjust the RT after manually adjusting the integration boundaries to the correct MS1 peak?

The only way I see for now to fix those problems is to build an assay library and then import it to Skyline.

Thank you for the help.
Hassan