Creating spectral libraries from Proteome Discoverer result files

Creating spectral libraries from Proteome Discoverer result files johannes voshol  2022-03-25

I am trying to create spectral libraries from PD results, using Skyline's 'Import Peptide Search' functionality. When I import from the .pdResult file, the scores are not recognized and all set to 0. When I use the corresponding .msf file, the scores are imported, even though - obviously- they are exactly the same and have the same column name (PercolatorqValue). Is that intended behavior or is there something wrong?
A second question is about the SpecIDinFile parameter. This ends up being a strange looking float like -1602.53037. In all cases the number before the decimal point (here 1602) corresponds to the WorkflowID from PD, but the rest has no obvious relation to file ID or scan number as one would maybe expect. Do you have any info on how this parameter is calculated and/or if and how you could retrieve the actual scan number from it?
Thanks a lot for providing these great tools to the community!
Hans Voshol

Kaipo responded:  2022-03-29

Hi Hans,

We recently changed the behavior on scores from PD, so depending on which version of Skyline/BiblioSpec you are using it may differ. Most recently, we are filtering based on the TargetPeptideGroups.Confidence column if you use a score threshold of 0.01 (corresponding to confidence 3) or 0.05 (confidence 2). In these cases, scores will be unavailable like you noticed. Otherwise, we check for various columns: (in order of preference) Qvalityqvalue, PercolatorqValue, qValue, ExpectationValue.

The SpecIDinFile is based on the workflow ID from PD like you mentioned, and also the spectrum ID. I'm not sure how PD assigns spectrum IDs, but you can find them in the MSnSpectrumInfo.SpectrumID or MassSpectrumItems.ID columns.