|Problems with import of peak boundaries in smallmolecule mode for .wiff data||Max||2020-08-24|
i am trying to import peak boundaries for a number of data sets based on .wiff data. We have set up some small molecule transitions for small molecules and peptides (due to qunatifiaction porpuses). I have used the allready discussed workarounds for small molecules (see https://skyline.ms/issues/home/issues/details.view?issueId=671) which is perfectly working for data from e.g. waters were a single filne represents a single injection. However, in the case of AbSciex 5500 the data is stored in a single .wiff file. I added therefore the sample name (alias Sample identifier) column to the peak boundaries list as stated in the FAQ for importing peak boundaries (see here: https://skyline.ms/_webdav/home/software/Skyline/@files/tutorials/ImportingIntegrationBoundaries-2_6.pdf). Nevertheless, skyline gives me an error message back stating that the sample names are not fitting to the sample names in the raw file . We have not changed the names of the single sample upon importing in Skyline thus i am looking for help to resolve this. I know i am missing something but i can not figure it out....
Looking forward to hear from you guys!
PS: I have example files ready but can only send them confidentally.