Removing precursors for DIA data epcasavant  2020-04-17


I am trying to run my data through MS Stats and ran into the error that said I needed to remove the precursors. I saw your answer here ( and followed the following steps you outlined:

  1. View > Document Grid
  2. Choose "Transitions" from the Views dropdown at the top of the Document Grid
  3. Right click on the "Fragment Ion" column and choose "Filter"
  4. Set the filter type to "Starts With" and type "precursor" into the textbox.

However, how do I delete the precursors? When I select them all int he document grid, it looks like it literally deletes all of my data.

Thank you,

Brendan MacLean responded:  2020-04-17

Hi Ellen,
I don't think you want to think about "deleting" anything for this. If it were me, I would edit the MSstats Input report and add a filter to it that is "Fragment Ion Type" - Does Not Equal - "precursor". You can do this in the Document Grid, by

  1. Click the "Reports" menu, choosing External Tools and clicking MSstats Input.
  2. Click the "Reports" menu, and clicking "Edit Report".
  3. Double-click on the "Fragment Ion" field in righthand pane of the Customize Report form.
  4. Click the Filter tab.
  5. Select "Fragment Ion Type" in the left-hand pane.
  6. Click the Add button.
  7. Select the operation "Does Not Equal".
  8. Enter the value, "precursor".
  9. Click the OK button.

Hope this works for you. You can see that there is already a filter of this type on "Is Decoy" - Does Not Equal - "True". This is how Skyline keeps from sending MSstats peak areas for decoy peptides.


epcasavant responded:  2020-04-17

Great! Exactly what I was looking for. Thank you Brendan. One follow-up question: how do I make sure the filter "stays". For example, when I was filtering out precursors on transitions and I close the document grid, when I re-open the document grid on transitions I still see the precursors. How does skyline "save" these filters?

Nick Shulman responded:  2020-04-17
If you add the filter by going to:
Reports dropdown > Edit Report
then the filter changes you make become part of the report definition and it will be remembered.

If you set a filter by click on columns in the Document Grid, those filters will not usually be remembered. There is a menu item that you can use to tell Skyline to remember these sorts of quick filters. There's a dropdown button next to the Reports dropdown that has a "Remember current layout" menu item on it.
-- Nick
epcasavant responded:  2020-04-17
Hi Nick- thank you! This is exactly what I needed to know.