patch for KeyError when attempting a direct index lookup for Thermo-s…

[animesh]

…tyle composite spectrum identifiers in mzML files where scan identifiers are formatted strictly as scan=X or integer scan numbers

[Copilot]

🟡 Changes recommended

The new fallback still risks KeyError because it only tries the numeric scan as a string, which may not match readers that expect an integer scan number.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

This PR hardens spectrum lookup in preprocess_spectrum to avoid KeyError when mzML spectrum identifiers are provided in alternate “scan=X” or numeric scan-number formats.

Changes:

• Wraps reader[spec_id] access in a try/except KeyError and attempts to extract a scan number from spec_id.
• Adds fallback lookups using "scan=<n>" and <n> when the direct lookup fails.

File summaries

File	Description
AA_stat/localization.py	Adds fallback spectrum ID parsing/lookup to handle scan-based IDs and numeric scan numbers.

Review details

• Files reviewed: 1/1 changed files
• Comments generated: 1
• Review effort level: Lite

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[levitsky]

Hi,

Thanks for this contribution. I'm having trouble understanding the exact use case. Do you have an example of input for AA_stat that requires this fix? I would appreciate if you could show a snippet of PSM and mzML files, and what software produced them.

[animesh]

Hi @levitsky , thanks for AA_stat, use it all the time! Huge fan!! This is just a workaround i had to employ to make my opensearch nextflow pipeline https://github.com/animesh/opensearch work on orbitrap data, otherwise i get this error
log.txt for example?

[levitsky]

Thanks for the kind words @animesh and I'm happy it is useful! Your pipeline looks great!
I've been trying to run it locally and I have not seen the need for the patch, though. AA_stat seems to work fine on my files (I also tried the example files linked in your repo, but for me AA_stat doesn't do any localization on them). If you don't mind, I would be happy to see an example where the patch is needed.

[animesh]

Thanks for your kind words @levitsky 🙏 Most probably it is a local issue then, can you share the commands you are using to run AA_stat over the Fragpipe's output, maybe my pipeline is missing some argument/switches? I must note that the patch is required only for the orbitrap data, so i am assuming you tried the test.raw.tar files?

[levitsky]

I actually didn't run AA_stat manually but directly ran your Nextflow pipeline according to README instructions. I did it first on the test.BSA.raw.tar files, but there my search didn't find any mass shifts after filtering, so localization was not performed (technically AA_stat run passed correctly but there was no chance for it to break in localization). I then took bigger files from Orbitrap, and your pipeline completed fine on them too. I verified that AA_stat log looks normal, including localization. I followed your installation instructions but skipped the patching of localization.py.

I think the error could be triggered by specific raw files or specific version of FragPipe or its components. But in my tests the spectrum IDs in pepXML files look like spectrum="SDS_01_01.1842.1842.2" and in the calibrated mzML files they look like id="controllerType=0 controllerNumber=1 scan=1842". AA_stat already knows how to translate the former into the latter, so everything works fine for me. I used latest released versions of FragPipe and MSFragger.

[animesh]

Thanks for trying the pipelie @levitsky , glad that it worked fine at your end! I still need the patch though, probably something to do with my setup. Sorry for wasting your time though! I will close this and look forward to more cool updates from AA_stat 👍🏽