In order for Skyline to be able to match BiblioSpec library spectra to MS1 scans Skyline needs to know at least the basenames (filenames without extensions) of the original instrument data files. Currently, Bibliospec mostly has the files from which it got the spectra. In cases like Mascot .dat files and X! Tandem XML this may already be too removed from the original files to have a hope of figuring out how MS/MS and MS1 spectra correspond with each other. When each search corresponds to just one original data file, we could require that they search result file be given the same basename as the data file, but that is not always what the tools produce, and it doesn't work for Mudpit runs.

I believe the current status is:

TPP pepXML/mzXML - done (mzXML files can contain MS1 scans and they generally have the same basenames as the original raw data files)
idpXML/mz[X]ML - done (same as above)
Scaffold mzIdentML/mzML - done? (same as above)
Mascot DAT - possible
UW SEQUEST & Percolator - possible
Protein Pilot group XML - possible?
X! Tandem XML - possible?
OMSSA pepXML - possible?
Waters MS^e - possible?
Spectrum Mill pepXML/mzXML - not possible? (these are generated from the search engine on demand and likely have little association with the original data - I'll check)

Turns out SpectrumMill is done also, since it always exports mzXML with the same basename as the raw file from which the spectra originate.

Many of these have been fixed. We are now solving these issues on a case-by-case basis.