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DIApasef data without iRT and precursor visualization

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DIApasef data without iRT and precursor visualization shubham  2026-03-08 16:52
 

  1. I want to see chromatograms for few peptides. I did Blank Doc -> Transition Setting, Peptide Settings -> Import Assay library.
    However, at the end it asks for iRT peptides. I don't have iRT peptides, but the retention time is available. Is there a way to extract chromatograms just by retention time? I can try creating pseudo iRT but that is very challenging as I am analyzing immuno-peptidome data and peptide intensity is very poor.

  2. Another isssue is I don't see precursor ions. I only see fragment-ions in the chromatograms. I configured Transition Setting- ion types as b,y,p and also set Full-Scan MS1 filtering as Count and 3 peaks. but I only see fragment-ions.
 
 
Brian Pratt responded:  2026-03-08 17:49

If you can share your Skyline document, we can probably figure out what's going on. Use Skyline's File > Share menu item, and include at least one of your raw data files. You may wish to separately share the text file that you used in Import Assay Library.

You can upload to http://skyline.ms/files.url , or something more private as you may prefer.

Brian Pratt
 
shubham responded:  2026-03-09 17:39

Thanks Brian. I have uploaded the files on this folder
https://drive.google.com/drive/folders/1X5XByUKV84pBlPiKNpiSmHjuCSvssGGM?usp=sharing

It has example DIA library, Skyline document and one DIA data file.

Thanks a lot for looking into this.
Shubham
 
Brian Pratt responded:  2026-03-10 16:53

I'm not sure how you got into that state, but you can enable the precursor targets using Refine > Advanced > Auto-select All.