Why Can't Peptide Search Be Imported Without Full-scan MS1 Filtering?

Why Can't Peptide Search Be Imported Without Full-scan MS1 Filtering? philip remes  2020-11-03

I'm importing search results into Skyline from a DIA chromatogram building experiment. After the search results are imported, and Skyline asks to Configure the Full-Scan Settings to Import the files, I want to select 'None' for the MS1 Filtering. I thought part of the advantage of DIA is that the parent ion may not be visible in the MS1 Full Scan or may have a high probability of having interferences, so why require that it be processed? There may be no MS1 scans, or they may be of such low resolution that they are not helpful. I realize I can then cancel and import the data the usual way after setting up Transitions. But I wondered if this MS1 filtering requirement could be waved for DIA and PRM peptide search imports.


Brendan MacLean responded:  2020-11-03

Are you choosing the right option when you start File > Import > Peptide Search? I am surprised it is requiring MS1 filtering for DIA or PRM. Can you add screeshots of what you are doing and what you are seeing? I feel like I have taught with this wizard not using MS1 filtering, but maybe I am mistaken.

Thanks for pointing it out, if we truly are requiring MS1 filtering for DIA and/or PRM.


philip remes responded:  2020-11-03

Hi Brendan,

I took some screen shots here. What I had actually done (slide 2), was select PRM for the workflow, and imported a pdResult file that was 10 GB+. The search results are from DIA runs, and I want to translate these into a PRM assay, but I realize that my selection of PRM for the Workflow may have been incorrect. So next it finds some files to import, and the settings were configured, and then on the Full-Scan Settings I went and selected DIA. Perhaps this is an illegal operation if the Workflow was selected as PRM? However, if I leave the Acquisition method as Targeted, I still get the error about the MS1 filtering.

On Slide 1 though you see that if DIA is selected as the workflow, then I was able to make it past this Dialog box and import the data.

It appears to me then that if there's an issue, it's that the PRM Workflow requires MS1 filtering. I hope these slides are clear, let me know if not.


Kaipo responded:  2020-11-04

Hi Philip,
Thank you for the report and the screenshots. This bug will be fixed in the next Skyline-daily.