Fix error importing Skyline documents with Spectrum Filters #921
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
labkey-jeckels
approved these changes
Jun 27, 2024
Contributor
labkey-jeckels
left a comment
labkey-jeckels
left a comment
There was a problem hiding this comment.
Thanks for the code and test cases.
| { | ||
| if (precursor.getSpectrumFilter() != null) | ||
| { | ||
| continue; |
Contributor
There was a problem hiding this comment.
Can you add a comment describing why we skip if there are spectrum filters?
vagisha
pushed a commit
that referenced
this pull request
Nov 18, 2024
"Spectrum Filter" gets parsed from the Skyline document light:heavy ratios are not calculated for precursors that have a spectrum filter The spectrum filter is used when deciding which chromatogram to read from the .skyd file for a particular precursor. # Conflicts: # src/org/labkey/targetedms/parser/ChromatogramGroupId.java
vagisha
added a commit
that referenced
this pull request
Nov 19, 2024
* Set qcTraceName on ChromatogramGroupId. * Fix error importing Skyline documents with Spectrum Filters (#921) "Spectrum Filter" gets parsed from the Skyline document light:heavy ratios are not calculated for precursors that have a spectrum filter The spectrum filter is used when deciding which chromatogram to read from the .skyd file for a particular precursor. # Conflicts: # src/org/labkey/targetedms/parser/ChromatogramGroupId.java * Added constructor for ChromatogramGroupId that takes both qcTraceName and spectrumFilter. --------- Co-authored-by: nickshulman <nicksh@proteinms.net>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Rationale
Skyline 23.1 added the "Spectrum Filter" filter feature and some of these documents fail to be imported into Panorama.
Related Pull Requests
Changes
"Spectrum Filter" gets parsed from the Skyline document
light:heavy ratios are not calculated for precursors that have a spectrum filter
The spectrum filter is used when deciding which chromatogram to read from the .skyd file for a particular precursor.