Only coeluting product ions as quantitative (extended)

Only coeluting product ions as quantitative (extended) Tobi  2018-12-17

Dear Skyline team,

I noticed that setting the "Quantitative" checkbox also works with copy and paste, but no matter if done by copy and paste or by manual clicking, it seems impossible to get the same checkboxes as in the Coeluting column because of constant recalculations overwriting manually set checkboxes (in PRM)

For just a single file one could think of exporting and reimporting a transition list filtered for coeluting product ions, but for a larger experiment, this is not feasible. Is it possible to somehow fix the quantitative column to make it directly susceptible to manual editing (in general just setting "not coeluting" to "not quantitative")? Is there a smarter way to do that?

I know about unchecking integrate all, but it would be much better to have full control over the quantitative state of a transition compared to just removing the target from the target list which impacts all datasets.

The attached file shows what would be the desired output, its just not fully implementable for a whole experiment.

Thank you for all thoughts and ideas on this topic.


Brendan MacLean responded:  2018-12-17

Hi Tobi,
Are you saying that you see the checked state of the "Quantitative" column change after you set it for a transition? This should not be the case and would be considered a bug if it is.

The "Coeluting" column, on the other hand, should be read-only and is actually a peak statistic like "Peak Area", which should get recalculated if you change your peaks. I can't tell whether you are trying to edit this column or not. If that even appears to work temporarily, then this also would be considered a bug. You should not be able to set the value of this column.

Can you clarify a little bit? Maybe also post some screenshots of what you are seeing and better explain what you are hoping for or expecting relative to those screenshots.

Thanks for your continued feedback.


Tobi responded:  2018-12-17

Dear Brendan,

skyline seems to apply a manual editing of "quantitative" to all imported raw files (in the screenshot setting one y7 transition to not quantitative will automatically set it the same way for the 2nd imported raw file). In my case it sometimes takes several seconds or even a second click in the document grid to refresh the documents grid, creating the illusion of overwriting previously set checkmarks. It still interferes with manual editing when several files are in one skyline document if you want different information for one kind of ion in different datasets. (recreating checkmarks as in coelution column)

The coeluting column is indeed read-only but the true/false output can be copied into excel etc. . It would be ideal to copy/paste the coelution state over the quantitative state to create chromatograms and quantification as indicated in the 2nd screenshot. In this case it was possible to somehow get the correct quantitative checkmarks into the documents grid, but the problem remains that it is not possible to have the exact same checkmark pattern as the coelution column and doing so semi-automatic would be perfect.

Do you have a better solution to filter PRM experiments for coeluting transitions?

Hope this serves as a feedback but we can stay in contact if you want.

Best, tobias

Nick Shulman responded:  2018-12-17

The "Quantitative" property lives on the Transition, whereas the "Coeluting" property is on the Transition Result.
If you are displaying both Quantitative and Coeluting on the same view in the Document Grid, then Skyline will duplicate the Quantitative values for each replicate. The Quantitative property cannot have a different value for different replicates.

If you did have a different set of quantitative transitions in different replicates, it would not really make sense to try to compare total peak areas across replicates.

It sounds like what you want to do is remove the transition peak from the replicates that match some criteria. I actually just implemented this feature last week, and it will appear in the next update of Skyline-Daily. There is going to be a "Actions" button on the Document Grid which allows you to do things such as "Remove Transition Peak" from all of the selected rows.

-- Nick
Brendan MacLean responded:  2018-12-17
Yeah. What Nick said. It sounds like you are getting confused by the tabular layout of information in the Document Grid. Nick and I, of course, have a clear understanding of what properties belong to what objects in a tree-like or relational-database-like schema. But, just because you can see values like "Precursor m/z" replicated for every transition peak doesn't mean they can be different.

If you look closely at your Document Grid and changes just one "Quantitative" entry when showing many replicates, and then press the Enter key to commit the value and the ROW, you will see all replicates for that transition change their "Quantitative" checkboxes also.

If you a "Quantitative" property change seems to take time to commit without locking up the Skyline UI, then you most likely are not causing the necessary ROW-level commit after making the change. Pressing the Enter key is one of the best ways of guaranteeing this. Look closely at the row heading at the far left of the grid. If you see a little pencil icon in that gray row heading, then you are still in edit mode and your changes have not been committed and will not be committed until you do something to commit them like selecting a new row or pressing the Enter key.

We probably will not stick with having a method for removing single peak transition integration, as Nick described on the Document Grid. Why would you want that option at a single file level, single transition level? We tend to think much more in terms of either:
1. Removing a transition from quantitative consideration across all replicates (the point of the "Quantitative" property)
2. Removed all peak area for a single precursor in a single replicate from consideration (the normal Remove Peak behavior)

Thanks again for your feedback.

Tobi responded:  2018-12-18
Dear Brendan and Nick,

thank you very much for the extensive explanation and feedback, it is very helpful.

The Enter key works nicely when working on the documents grid, it solves the refreshing issue perfectly, so no bug or anything like that.

I can completely follow and understand the reasoning to cross-link the quantitative property of transitions across files, so it might not work out as i imagined but this is ok. The new feature sounds very helpful and I am super excited to see how it will be.

Thank you very much for the outstanding support!
roman sakson responded:  2020-05-12
Dear Skyline Team,

I decided to add to this older thread instead of opening a new one. I recently also came across the "coeluting" property on the transition result and I would like to know how exactly Skyline decides whether to check it or not for a particular run. I am just wondering whether it could be used to automatically flag interferences in larger documents?

Thank you!

Nick Shulman responded:  2020-05-12
Here's a thread where we talked about all of the criteria that Skyline considers when deciding whether a particular Transition Result is "coeluting":

It was always intended to be something that you used when doing SRM method development. I am not sure how well it would work for detecting interference in large documents.
-- Nick
roman sakson responded:  2020-05-12
Hi Nick,

thank you, it was not clear to me that this is also an mProphet feature.

Thank you for the quick reply!