the error messages when importing result file into Skyline

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the error messages when importing result file into Skyline mei chen8686  2022-04-07
 

Hello,
I have two questions related to the error messages when importing PD result files. I am using Proteome Discover 2.1. The questions are in the attached file.
Thank you,
Mei

 
 
Kaipo responded:  2022-04-07

Hi Mei,
Would you mind sharing the pdResult file? You can upload it to https://skyline.ms/files.url

Thanks,
Kaipo

 
mei chen8686 responded:  2022-04-07

Hi Keipo,
I upload the file: "ProteomFeb2022001 new one.pdResult". This is the file in my question1, a label free DDA result file.

I was also trying to upload another PD file in my questions2 into the server, but it is not able to be uploaded. This PD file is a TMT result fine. I am not sure if I can add this file in the "library" in "Peptide setting" , since there are mass shift of TMT. Do you think I can use both NIST and this TMT result together as a spectra library file?

Thank you very much for your help!
Mei

 
Kaipo responded:  2022-04-08

Hi Mei,
It looks like the name of a table has changed in PD result files, causing this issue. It will be fixed in the next release of Skyline (including a daily version, which should be soon I think).
Regarding the TMT labels, Skyline is able to work with them (modifications can be configured under Peptide Settings > Modifications).

Thanks,
Kaipo

 
mei chen8686 responded:  2022-04-21

Hi Kaipo,

Thank you for your reply. I did not make any name changes on the PD result file name.

I know you mentioned the next release version may solve this problem. I I am wondering if you could send me the steps of building DDA library for DIA from QE data, and what I should do to prevent this error message coming up. Should I change the PD result file into different format before importing into Skyline? Should I not use PD result file but directly import the raw DDA files (8 fractions) from QE into Skyline?

Skyline also does not allow me to import other my PD result file into the "library" in "Peptide setting". I got the same error message as above.

I have attached these two PD result files. The first is label free DDA library for DIA, and the second is TMT-labeled DDA.

Thank you very much,
Mei

 
mei chen8686 responded:  2022-04-21

Hi Kaipo,

Thank you for your reply. I did not make any name changes on the PD result file name.

I know you mentioned the next release version may solve this problem. While waiting for the new release, I am wondering if you could send me the steps of building DDA library for DIA from QE data, and what I should do to prevent this error message coming up. Should I change the PD result file into a different format before importing into Skyline? Should I not use PD result file but directly import the raw DDA files (8 fractions) from QE into Skyline?

Skyline also does not allow me to import other my PD result files of TMT-labeled DDA into the "library" in "Peptide setting". I got the same error message as above.

I was trying to attached the TMT-labeled DDA, but the file is too big. I hope you can help to solve the problem of uploading PD result file into Skyline.

Thank you very much,
Mei

 
Kaipo responded:  2022-04-25

Hi Mei,
The next release should fix the issue, I was able to use the PD file you shared to build a library successfully. A new Skyline-daily should be available soon (maybe this week?) with the fix. In the meantime, do you have any other formats that could be used to try to build the spectral library (e.g. perc.xml, .pep.xml, etc)?

Thanks,
Kaipo