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Missing remove transition peaks... for document grid actions

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Missing remove transition peaks... for document grid actions roman sakson  2022-02-06 12:31
 

Hi Nick,

I created a custom report (attached below) that I use to review some parameters of my MRM data on transition level. One of the things I do is to grab area and background, export it to Excel to calculate Background/Area and then I am pasting it back in via a custom "Signal_to_Noise" Annotation column. Then, I review transitions with a S/N below my desired value and I would like to be able to delete them in bulk, same way I would do via right click -> remove peak on single transition view level. However, in the document grid I can only find actions to remove peptide or precursor peaks but not transition peaks. I am probably doing something wrong. I hope that I explained it well enough, I could also provide an example sky.zip.

Thank you,
Roman
 
 
Nick Shulman responded:  2022-02-06 12:46
Roman,

The reason that Skyline does not have a "Remove Transition Peaks" menu item is that we did not think that it was valid thing to do with your data.

If you remove a transition peak from a particular replicate, then it no longer makes sense to compare total peak areas between replicates. (Actually, I guess if you are normalizing by ratio to heavy, then it probably still would be valid to compare different sets of transition peak areas between different replicates, but, in most cases, it's not valid to remove a transition peak from a single replicate.)

If you see that a particular transition in a particular replicate has bad signal to noise, it would be more valid to either completely discard the replicate (which is what "Remove Precursor Peaks" would do) or to mark the transition as non-quantitative so that the transition peak area is excluded from all of the replicates.

Are you sure that you want to remove the peak for one transition in one replicate? What were you planning on doing with the numbers after that?
-- Nick
 
roman sakson responded:  2022-02-06 12:56
Nick,

I completely agree with you, it is probably not a wise thing to do (even though I do have heavy standards, but still). I just thought that I am doing something wrong, since "Remove transition peaks" was mentioned in the Issue 511: https://skyline.ms/issues/home/issues/details.view?issueId=511&_docid=issue%3A511

Again, since it is not there it is probably best this way. Thank you once again, also for the incredibly short response time.
Roman