Retention time difference in library when using PDresult vs. msf file

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Retention time difference in library when using PDresult vs. msf file roberthardt  2019-04-23
 

Dear Skyline-Team,

I today created a spectral library from ProteomeDiscoverer 2.3 results (Mascot search engine) once using the .PDresult and once using the .msf file(s). I got quite similar results but interestingly, there is a clear retention time shift/offset when using the PDresult file. This becomes immediately apparent when looking at MS1-chromatograms, where the blue vertical peptide-ID lines are clearly "missing" the correct MS1-peak in the case of the PDresults-library.

Best

Robert

 
 
Nick Shulman responded:  2019-04-23
Can you send us your .pdresult file and your .msf file? I am not sure whether there are other files we need when building a library from these types of files. I imagine we will also need to see that .raw file in order for us to understand what is going wrong.

Files that are less than 50MB can be attached to this support request. You can upload larger files here:
https://skyline.ms/files.url

-- Nick
 
roberthardt responded:  2019-04-24
Hi Nick,

I will upload the files in a single zip-file named 190424_roberthardt.zip

Best

Robert
 
matt.chambers42 responded:  2019-04-25

Hi Robert,

I looked at your MSF and pdResult files and the problem seems to lie in your workflow. The retention times in the pdResult file have been modified. Possibly due to some alignment process. Here's a sampling to compare the times in the msf vs pdResult. You can see that the ratio starts out wildly different but as the file progresses it approaches 1. Strangely, for the 19_PRM file, the ratio starts out at 1 and then has a minor adjustment sometime later, but as the file progresses the ratio falls back toward 1. In other words, I have no idea what's going on, but it's not something we can fix in BiblioSpec. :)

RawFileScanNumberPdResultTimeMsfTimeTimeRatio
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