Ion mobility libraries Susan Abbatiello  2021-03-23
 

Hi There!
I have a couple requests when making ion mobility libraries. Some of these features may already in there, just haven't found them yet!

  • Can the m/z of the peptide please be listed along with the sequence and the m/z in the library, please?
    -- Is it possible to select a single data file from which to "use results" for pulling CCS and 1/k0, instead of using all files (or an option to select one or use all?

Thanks!
Sue

 
 
Brian Pratt responded:  2021-03-23

Hi Sue,

These are good ideas, I'll put them into our development queue.

Thanks,

Brian Pratt

 
Brendan MacLean responded:  2021-03-23

Hi Sue,
You can certainly use just one file by using Edit > Manage Results and remove all but the file you want to use. Is this not at least a usable workaround for you?

I don't really understand this request "Can the m/z of the peptide please be listed along with the sequence and the m/z in the library, please?"

Where exactly are you referring to? I find the last part a bit confusing "and the m/z in the library". How is that different from the "m/z of the peptide"?

Maybe you could provide a screenshot with markup on what you would like to see where.

Thanks for posting feedback.

--Brendan

 
Susan Abbatiello responded:  2021-03-23

Hi Brendan,

In the ion mobility libraries (Settings, Transition Settings, Ion Mobility), the m/z of the precursors are not listed, only the sequence, CCS, 1/k0 and charge state. Having a column with the m/z of the precursors would be super helpful, especially when looking at multiple forms of the same peptide (like the Pierce 7x5 peptide standard that has 5 differentially labeled forms for each peptide sequence). Screen capture attached.

Sure, I can remove all but the one file I want to use for pulling IMS data, which is what I have been doing. It works fine, but I was just suggesting the feature to select a single file for pulling IMS data, as it would be a bit easier for a Skyline user.

Best,
Sue

 
Brendan MacLean responded:  2021-03-23

Okay. I see. I think then the final "and the m/z in the library" part adds unnecessary confusion. At least your description is what I would have guessed, without those words added.

I should note that we are showing the "modified sequence" which does differentiate between the 5 different forms of each peptide.

The existing columns are designed to mirror what we actually store in the library, and in that case, the "modified sequence" and "charge" combine to provide a unique key for each set of IMS values. This also aligns with what we store and show in iRT and Optimization libraries.

Your request to add precursor m/z would be a first move into showing informational columns which are not actually stored in the library and cannot be used in the unique key. We can certainly calculate and show the value, and I am not saying we won't do it. Just that it is a new direction and that "Modified Sequence" + "Charge" is already unique and visibly so, if you expand the columns to fit the content. Though, I can see how with long peptide sequences (with modifications specified), the precursor m/z might make a much more condensed visual key, if you have enough knowledge to use them for that.

Thanks for the clarification.

--Brendan

 
Susan Abbatiello responded:  2021-03-23

Hi Brendan,

Yes, sorry for the confusing bit - I meant "m/z to be shown with the sequence and charge (z) in the library".

The "modified sequence" is fine, but in the case of highly modified peptides, you have to stretch out the column and know what their m/z values are (or at least have a sense or some other table to make sure the sequence and m/z aligns).

Also, when I open up the prmparams.prmsqlite that skyline exports with PRM parameters for the tims-ToF method file, the m/z is listed there, not the peptide sequence. I'm trying to verify what is exported from the Skyline IMS library is what is going into the method, and Skyline shows sequence, while the prmparams.sqlite file does not. It would just help to verify!

Thanks!
Sue

 
Brendan MacLean responded:  2021-03-23

Ah. Then, I would recommend using a custom report in the Document Grid. You should be able to set up one that gives you all the fields you are interested in for every precursor that goes into your method.

I know it is awfully tempting to find everything you are looking for except on value in a table in the UI and think, if only this table had that 1 extra column, it would have everything I need. And the Document Grid provides so many options that it can be daunting, but it really is the right answer for what you just described as your use case.

Give it a try. Or for cookies, I am sure someone on the team could post a .skyr file with the report template that suits your needs. :-)

--Brendan

 
Susan Abbatiello responded:  2021-03-23

What kind of cookies? ;-)

I suspect that I will not be the only Skyline user who would need this feature, and I'm happy to start with setting it up with more steps and hoops to get it to work.

But seriously, what kind of cookies would it take to get a .skyr file?

Cheers,
Sue

 
Nick Shulman responded:  2021-03-23
Sue,

I don't think there is a way to see the predicted ion mobility (from the .imsdb file) in the Document Grid.
Skyline has all the necessary information in memory, so it would be straightforward for us to add some new columns to the Document Grid that expose it, but as far as I can tell there is currently know way to see that in the Document Grid right now.
I imagine it would be exposed as a set of columns under "Proteins > Peptides > Precursors > Predicted Ion Mobility"
> Predicted Ion Mobility Value
> Predicted Ion Mobility Units
> Predicted Collisional Cross Section
> Predicted High Energy Offset

Can you send us your .sky.zip file?
-- Nick
 
Brian Pratt responded:  2021-03-24
I'd rather see it called "Library" ion mobility value, but yes, that would be useful.

Note that you can already see this information in the context of chromatograms, or rather you can see the value that was used at the time of chromatogram extraction. This could differ from the library time if the library was changed in some manner. And of course there are times when you'd like to see those values prior to chromatogram extraction.

- Brian
 
Nick Shulman responded:  2021-03-25
Sue,

We are working on adding the library ion mobility values to the Document Grid.

You can see some screenshots and a discussion of the new feature here:
https://github.com/ProteoWizard/pwiz/pull/1504

Could you send me one of your .sky.zip files? It would be helpful if I could see how your data would look in the Document Grid.
-- Nick