That error is saying that it was looking for a file whose name starts with "260624_LP_Chymo_PCDH15" and which ended with any of a number of different things including ".raw" or ".mzML".

Do you have a file called "260624_LP_Chymo_PCDH15.raw" or "260624_LP_Chymo_PCDH15.mzML" that you could copy into the same folder as your .msf file?
-- Nick

Dear Nick,

Thank you - yes my .raw files all start with "260624_LP_Chymo_PCDH15".

I managed to "solve" the problem for this one sample (multiple .raw files) by reprocessing .raw files individually, exporting individual pepxml's and compiling the .sky file from multiple pepxml's.

Just guessing here, but I believe this could be related to how the .raw, .msf and/or pepxml are named.

Adnan

I would have expected only one of your .raw files to start with "260624_LP_Chymo_PCDH15".

If you have many .raw files which start with "260624_LP_Chymo_PCDH15", then I imagine that these raw files have another "." in them, and that is confusing Skyline and BiblioSpec.

The filenames that Skyline extracts chromatograms from often have a different filename extension from the files which the peptide search engine searched. For instance, users often want to extract chromatograms from the original .raw files, but the peptide search engine only knew how to handle .mzML files.
For this reason, when Skyline is deciding whether some peptide search results correspond to a particular .raw file, Skyline typically ignores everything after the first "." character in the filenames.
I suspect BiblioSpec is doing something similar and is looking for .raw files whose names are missing everything after the first dot.

-- Nick