skyline is not able identify with my iRT peptides

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skyline is not able identify with my iRT peptides Sangram  2021-12-07
 

Hello people,

I am trying to perform a (pretty straightforward) DIA analysis with 32 fractions of a cell line proteome. I performed the spectra search using PeptideShaker and yielded the results in mzid format. Now in the "Add iRT peptide" window all samples shows failed. I would like to know what implications I might have down the analysis. This is because I noticed whenever this happens and I would export a spectral library in openSWATH format, the values from RetentionTimeCalibrationScore is missing !

How can I stop this from happening ?

 
 
Nick Shulman responded:  2021-12-07
I don't know what is going on there, but if you send us your files we can figure it out.

Can you send us one (or more) of your .mzid files as well as the .mzML, or .raw or .mgf or whatever file goes along with them?
Those files will probably be too large to attach to this support request, so you can zip them up and upload them here:
https://skyline.ms/files.url

-- Nick
 
Sangram responded:  2021-12-10
Hi Nick

These analyses involve my collaborator's data so low security upload protocol is a problem. But I have them uploaded to Onedrive, may I send the link over an email.

-Sangram