Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Multiple search engine encoding (#5)

[Salvador M. de B. <not...@gi...>]

I am not sure about this change. I think is quite common to have more than one search over the same dataset (same spectra), using different parameters (such as HEAVY fixed masses, or PTM search) and then to apply an statistical validation over all of them, resulting in a single protein and peptide list, which means a single resulting file. In this case there is not final PSM list, all of them are final. The final protein list will contain PSMs from all of these searches. So I don't see the reason in this case to have to split into several mzIdentML files. What do you think?

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