Something like isolation interference (%) calculation

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Shagun Gupta

Jun 23, 2022, 3:50:06 PM6/23/22
to Comet ms/ms db search support
Hi all

I was wondering if COMET searches (maybe in conjunction with something like Peptide Prophet) can provide me estimates of isolation interference or degree of co-isolated precursor ions (what the proportion of signal to noise is for the selected precursor ion in the selection window) that software like Proteome Discoverer provide? Is there an existing value provided right now that I am not familiar with yet?


Paulo C Carvalho

Jun 23, 2022, 4:01:06 PM6/23/22
to Shagun Gupta, Comet ms/ms db search support
O suggest running Yada on your thermo raw file. Those spectra with two or more z lines are multiplexed spectra. 

Should you have any questions feel free to ask. 

Paulo Costa Carvalho. 

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Jimmy Eng

Jun 23, 2022, 4:27:28 PM6/23/22
to Comet ms/ms db search support
Comet doesn't provide this information and nor does anything in the Trans-Proteomics Pipeline as far as I'm aware.  So hopefully Paulo's suggestion works for you.
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