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.pdresult fail to build skyline library

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.pdresult fail to build skyline library guo xue  2023-07-19 02:31
 

I ran Hela cell lysate with iRT spiked in and searched the data using Proteome Discoverer Sequenst which has 47k proteins. Then I used the .pdresult file to build library but it gave the error: no new peptide will be added to the database; one run was not converted due to low correlation. could you please help to understand what is the reason? thank you very much.
 
 
Nick Shulman responded:  2023-07-19 07:38
I think that error means that the iRT standard peptides were not detected in your sample.
It might mean that you chose the wrong thing in the "iRT standard peptides" dropdown on the first page of the Import Peptide Search wizard.

Here is another support request where a user reported that error and it turned out that the user had chosen the wrong iRT standard peptides:
https://skyline.ms/announcements/home/support/thread.view?rowId=29853

-- Nick