Re: [Psidev-pi-dev] [HUPO-PSI/mzTab] Protein group (#20)

[Yasset Perez-R. <not...@gi...>]

@andrewrobertjones @mvaudel 

The current implementation of mzTab we RECOMMEND the the proteins group should be reported in this way:

Protein Accession    .... Ambiguity members 
Protein 1                   .... Protein 2, Protein 3. .

Protein Accession field MUST be unique and this is the only constrains we made in the format. Then a writer can just give us a file like:

 1 - Software writers also report Protein 2, Protein 3..because the file format allow that. Including all the
      nice information about those proteins scores, sequences, ranks, etc. Then the reader should figure 
      it out whats going on in the file, example: 
      Protein Accession    .... Ambiguity members  opt_global_cv_MS:1001301_protein_rank
      Protein 1                   .... Protein 2, Protein 3                              1
      Protein 2                   ....                NULL                                     2
      Protein 3                   ....                NULL                                     3

Then, readers and community in general needs to know what the writers was proposing and also open the field to represent the protein inference information. 

If we keep the current specification, we need to restrict this cases, because then would be imposible to handle the files, unless we add CVTerms to verbose all possible combinations.  

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