Hi Valdemir, the tpp2mzid is indeed the preferred and recommended tool, not idconvert.
I think the problem quite simply is that mzIdentML is not capable of handling quant data. mzIdentML is designed only for identifications. mzQuantML and mzTab are designed for quant data. So, no tool can or should put quant data in mzIdentML.
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I should add that mzQuantML is almost universally unsupported and is not recommended.
mzTab is the PSI format recommended for quant data:
FYI, there is an effort underway to design an improved mzTab 2.0, but it is a long ways off.
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