Exporting p, q, or e values in Peptide Quantification Report?

Exporting p, q, or e values in Peptide Quantification Report? lparsons  2019-04-24

I imported MaxQuant results into Skyline, and now I would like to export a Peptide Quantification report. I've found all the fields that I'm looking for except for the peptide score (from MaxQuant) itself. Is there a way to get this?

In this case I have 6 samples, so I would expect there could be 6 p, q, or e values for each of them, which would be fine. Or do I have to do a different report in order to get these?

thank you

Brendan MacLean responded:  2019-05-22

Unfortunately, these scores are not preserved for every ID in the non-redundant library, the way we preserve the retention times at which the ID spectra were acquired. Maybe we should also be keeping these scores, but we are currently only keeping them for the best spectrum chosen as the non-redundant library spectrum, i.e. the one used to calculate dotp for SRM, PRM and DIA data. Even for the non-redundant spectra, we don't really expose the scores you are interested in. The reports have values "Library Score 1", "Library Score 2", and "Library Score 3", but these appear to be for stored values used by the "Rank peptides by" setting for peptides, e.g. Spectrum count.

It probably would not be much work to add something like "Library Cutoff Score", which does get stored in the spectral library itself, but it is that inverse score PEP (posterior error probability) for MaxQuant, which doesn't look much like q, p or e values.

Sorry, I don't have a better answer for you. Part of why we have been able to support spectral library building for 20+ search pipelines is that don't try to preserve all of the information these tools produce.

Thanks for posting your question to the Skyline support board.