fail to import peptide search into skyline due to the retention time problem. chengkang  2020-03-04

I was trying to import my maxquant peptide search into the DDA in skyline, however, after I selected the .raw file of the search, an error message popped out:"The document specific spectral library does not have valid retention times. Please check your peptide search pipeline or contact Skyline support to ensure retention times appear in your spectral libraries." Can anyone help me out?


Nick Shulman responded:  2020-03-04

I believe that the error means that some of the peptides in your peptide search results had retention times that were less than or equal to zero.

Here is a thread where someone had the same error, and they found it helpful to cancel out of the Import Peptide Search wizard after getting that error, and instead use "Import > Fasta" and then "Import > Results":

It would be helpful if we could take a look at your maquant peptide search results so that we can see if we are doing anything wrong. I suspect we should try to come up with a more helpful error message that says which peptide(s) have invalid retention times.

Can you send us your "msms.txt" and also your "mqpar.xml" and "modifications.xml" files if you have them.

If those files are less than 50MB, you can attach them to this support request.

Otherwise, you can upload them here:
-- Nick
chengkang responded:  2020-03-05
Dear Nick,

Thank you for your reply.

Yes, this solution helps. But I would lost the valuable “ID” value from the maxquant run, which provided RT information of MS2 matching. Can this problem be fixed?

unfortunately, I tried to do the same type of library search importation from my previous data, which was able to be imported successfully, however, it fails again. I noticed that I had updated skyline recently, does it matter? That might be something wrong with my setting in skyline, and not from my search result, nor my .Raw file. Do you agree?

chengkang responded:  2020-03-05
Hi Nick,

And I did checked my msms.txt file after Maxquant run, it did show the retention time value for all detected peptides as well.