Which PSMs does assign-confidence return?

[Erik Johnson]

Hello,

Thanks for crux!

I'm using `crux assign-confidence` and wondering why the resulting *.assign-confidence.target.txt contains the PSMs that it does. I couldn't find an answer to my question in the documentation.  

I'm running:
crux assign-confidence --overwrite T --output-dir june13 --fileroot 1-100 june13/comet.1-100.target.txt
(note: there's also a `comet.1-100.decoy.txt` file in the `june13` directory)

From what I understand, even if the number of PSMs per scan > 1, assign-confidence only considers the xcorr scores of the top target PSM per scan and top decoy target PSM per scan. I'd expect every scan with a target PSM to have a row in the assign-confidence output. However, it looks like some scans' PSM doesn't make it into assign-confidence's output. Here's an example and I'm attaching the files involved. Thanks for your help!

[William Stafford Noble]

I think assign-confidence is doing the target-decoy competition and only reporting targets that win the competition.  For the scans that you identified, do the decoys get higher scores than the corresponding targets?

Bill

On Fri, Jun 13, 2025 at 12:32 PM Erik Johnson <airik.k...@gmail.com> wrote:

Hello, Thanks for crux! I'm using `crux assign-confidence` and wondering why the resulting *. assign-confidence. target. txt contains the PSMs that it does. I couldn't find an answer to my question in the documentation. I'm running: crux assign-confidence

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[Erik Johnson]

Ahhh! You're absolutely right. Thank you, Bill!