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Issues with Feature Detection from RAW PRM files without searching data first

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Issues with Feature Detection from RAW PRM files without searching data first nitheshperumal  2025-12-04 10:29
 

Hi,

I have been analyzing PRM data with skyline, and have had success when first searching with another software and importing the pepXMLs. I wanted to try the Feature Detection from raw files and have not been able to get it to work. Anytime I try to do the Feature Detection I get an error saying the search failed - this is with the same data that works if I search first and import pepXML. Does the skyline team have any troubleshooting suggestions or could you point me towards additional resources to setup the Feature Detection from raw files? I am using skyline 25.1.0.237 version on windows 11.

Thanks,
Nithesh Perumal
 
 
Nick Shulman responded:  2025-12-04 10:44
If you send us your files we can try to figure out what is going on.

You can put all of your files into a .zip file and upload them here:
https://skyline.ms/files.url

It would also be helpful if you could show us some screenshots so that we can see what settings you are using when you use the "File > Search > Feature Detection" menu item.

It would also be helpful if you could send us your Skyline document. In Skyline you can use the menu item:
File > Share
to create a .zip file containing the Skyline document and supporting files.
That Skyline document is likely to be empty, but it might be helpful for you to send it to us just in case it makes a difference.

If you are seeing any sort of output when you get your error, it would also be helpful for you to send us the text of that output.
-- Nick
 
nitheshperumal responded:  2025-12-05 15:11
Hi Nick,

Thank you for the prompt response. I have uploaded the skyline document (20251205_NP_FeatureDectection) for you to review. When running the Feature Detection search I get an error message saying search failed and the search never completes (I manually cancel after waiting for awhile - attached screenshot to this message). In terms of settings I am using the same settings for the peptides and transitions as I do for importing searched results, which end up working as anticipated.

Let me know if there's any additional files or information I can provide to help with the troubleshooting.

Thanks,
Nithesh Perumal
 
Nick Shulman responded:  2025-12-05 15:32
Can you send us the file that you were trying to search?
That would be "20251120_PRM_SynthPep1_1uM_20_55gradient" or something.
You can upload it here:
https://skyline.ms/files.url
-- Nick