Skyline/work/20240207 nist library rt

[meowcat]

Addresses #2755: When using NIST (MSP) spectral libraries for small molecules, the retention time is stored in the library but not added to the document.

[brendanx67]

Explicit RT is too strong a statement to take from a library where we have no idea if it comes from exactly the same chromatography. Without extra UI to specify this choice it is too strong an assumption to make by default. This is a misunderstanding of what Explicit RT means and its intended purpose.

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On Wed, Feb 7, 2024 at 12:08 AM meowcat ***@***.***> wrote: Addresses #2755 <#2755>: When using NIST (MSP) spectral libraries for small molecules, the retention time is stored in the library but not added to the document. ------------------------------ You can view, comment on, or merge this pull request online at: #2860 Commit Summary - 641774d <641774d> Skyline: import retention time from MSP libraries for small molecules - 639ef3f <639ef3f> Merge branch 'master' into Skyline/work/20240207_NIST_library_RT File Changes (1 file <https://github.com/ProteoWizard/pwiz/pull/2860/files>) - *M* pwiz_tools/Skyline/Model/AbstractModificationMatcher.cs <https://github.com/ProteoWizard/pwiz/pull/2860/files#diff-b17ef94a22253bbd0779a759f5876cb8eca9ee5ae945fc13b01a32716baeb710> (17) Patch Links: - https://github.com/ProteoWizard/pwiz/pull/2860.patch - https://github.com/ProteoWizard/pwiz/pull/2860.diff — Reply to this email directly, view it on GitHub <#2860>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACYBWUF4RYC7JRE4T6FOZ3TYSMZABAVCNFSM6AAAAABC5LJEE6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGEZDENBSG43TIMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[meowcat]

OK, I guess I need to understand the current model better then.

• If the retention time from a library is not used as Explicit Retention Time, why is it imported in the first place / what is it currently used for?
• When adding a library in "Edit Library", there is the checkbox "Use explicit peak bounds". I don't actually know what it does, but as a user I would have expected this to govern whether or not RT are imported. Currently, I see no change in the import whether or not I activate the checkbox. Does this do something else I am not aware of?
• Would it be an acceptable UI choice to have a checkbox (deactivated by default) "Add explicit retention time"?

As a background, our motivation: We maintain in-house MS2 libraries with precise RT annotated. I'm aware that I can Modify the explicit RT by hand, compound by compound, but this is a lot of work and error-prone if the user is handling 100+ compounds. On the other hand, when we start via Transition List (where the RT can be specified), I cannot add the library spectrum to a compound.

• Is there an existing workflow to add an explicit retention time (e.g. from a CSV file) in batch to molecules imported from a Spectral Library?
• Is there an existing workflow to add spectra from spectral libraries to molecules added with a Transition List (with explicit RT specified)?

This would be enough for us, but I haven't found this yet...