mzID output contains multiple SpectrumIdentificationResult tags for the same spectrum

[524D]

Hi,

When mzIdentML (mzID) output is selected, and Comet finds multiple identifications for the same spectrum, each identification is reported in a separate SpectrumIdentificationResult tag. This is seems not correct according to the mzID schema.
In the Comet output, each result is enclosed in both a SpectrumIdentificationResult and a SpectrumIdentificationItem tag. Identifications belonging to the same spectrum should however be grouped under the same SpectrumIdentificationResult.

This problem prevents Comet mzID files to be read by readMzIdData in R.

For completeness, there is another problem that prevents reading Comet output with readMzIdData, but that seems to be on the reader side.

I'm using Comet v2023.01.2

Best, Rob

[jke000]

Bob,

Thanks for reporting the issue. I'm never confident I'm writing valid mzIdentML files even if they pass the validator. I hopefully addressed both of these issues (SpectrumIdentificationResult and the "other" problem) with commits 5f6af8e and f4e0c37. For the "other" problem preventing reads by readMzIdData, I just got rid of that cvParam entry that doesn't seem useful and hopefully isn't required.

If you're willing to test the fix and need a compiled binary, let me know what OS you're using and I can compile a binary for you if helpful.

Jimmy

[524D]

Hi Jimmy,

Thanks for your very quick reply. Of course it would be great if you could send me a test version, either Windows or Linux is fine. However, I can probably only test by October 24 since I'm not at work until then.

Best, Rob

[jke000]

Rob, you can find a Linux binary at http://proteomicsresource.washington.edu/dist/comet.2023020.linux.exe

[524D]

Hi Jimmy,

The mzID output look good with the new version and also works perfectly with readMzIdData. Many thanks for the quick fix.

Rob