thanks for your response. Good to know that there's no limits to this brilliant software! I've run the same tests as you and it seems to work fine. I've also imported a subset of the subset as query spectra into MS-FINDER as a sanity check and it does a pretty good job matching them up. Not perfect though, which is worrying. For example, searching a series of query spectra for PC(16:0, 18:2) across varying collision energies I get five spectral matches returned from the library for query CE of 14, none for CE16 and seven for CE20. Visually inspecting the CE16 spectra there is little difference between that and adjacent CE spectra, as you would expect. So I don't understand why I get no matches. It would be great to have a variety of matching algorithms, as are available in MS-DIAL (dot product, reverse dot product, unweighted dot product, presence peak score, total MS/MS similarity score). I can't see where to vary the match factor threshold in MS-FINDER either and I can't tell what the algorithm its using is.
Do you use your own scheme for .msp keys? I am thinking I will edit the libraries to remove fields that the software doesn't use, in case those are the problem.