Refine-Advanced-Results-minArea dkueltz  2019-07-19

Hi Brendan, Nick,
Thanks for the new Skyline release!
It would be great if you could include another option under Refine - Advanced - Results:
Like filtering for a min dotp in the best or all sample(s) it would be great to have a similar filtering option for peak area (using the best or all samples);
This would greatly facilitate generation of assay libraries using a set of training samples. It would allow us to automatically remove peaks that are low abundance in all samples and likely to be very noisy.
We are now doing this by exporting peptide quant tables for training sample set result to csv and then identifying peptides with less than the minimal desired area, then select the ones that meet the criteria and use Refine - Accept peptides - peptides to keep. But this is cumbersome and there is a limit on how many peptides can be handled that way. It would be nice to have a more straightforward way to do this in Refine - Advanced - Results

dkueltz responded:  2019-07-19

It would be even greater if one could combine the dotp filter with an area filter such that one could require the best match to have a min dotp while also having a min area...

Nick Shulman responded:  2019-07-22
You can use the Pivot Editor in the Document Grid to find the peptides with low dot product scores.
I posted a PowerPoint showing how to do this with the ratio dot product here:

By the way, what do you mean when you say that there is a limit on how many peptides you can handle in the "Refine - Accept peptides"? This sounds like something we should fix.
-- Nick
Brendan MacLean responded:  2019-07-23
What kind of limit are you seeing on Accept Peptides? I did raise the textbox character limit to 10,000,000 on 21-May-2018 from 1,000,000. Could you possibly be using an older release (4.1 or earlier) or do you really need more than 10,000,000 characters of peptide sequence text? If so, yes, we really did not foresee this large a set of accepted candidates.

An intern in the lab is currently working on the Refine > Advanced form. I am having a hard time seeing how the minimum peak area filter fits into the current UI without being too obtrusive. If you have any ideas, please send me an image of what you have in mind. Otherwise, we will see what we can come up with. This might be possible in the 19.2 timeframe.

Thanks for your feedback.

dkueltz responded:  2019-07-28
Hi Brendan and Nick,

You are right - the limit I was referring to does no longer apply - I had experienced this before the upgrade and just tried it again - the accept peptides window seems without limit now (at least within the range I tested).

Still, it would be much more convenient and straightforward to have an option in the Refine - Advanced - Results window that allows filtering for minimal peak area (best or all samples) just like you have an option in that same window for filtering for dotp value (best or all samples). To be clear, the dotp filter option already exists in that menu - I was requesting to add one just like it for min. peptide area. Do you know what I mean?

dkueltz responded:  2019-07-28
A screenshot with the corresponding menu and a scribbled in min.area option is attached to illustrate what I mean...