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

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

@jgriss @javizca We should leave it at it is now. The only problem is that schema should respond to this or at least reflect that. I agree that we MUST report only the interesting proteins in mztab and leave in mzidentml the rest. However, I guess the part I highlighted in the specification MUST be changed to reflect that. For example, I have this Mascot mztab file prototype which is completely mztab compliant:

https://github.com/PRIDE-Toolsuite/inspector-example-files/tree/master/mztab

They produce a valid file but not the one RECOMMENDED one. It is difficult to implement a parser or reader that can realize about this change. Then, my suggestion is that we change in the specification (which looks like a simple change but will make more consistent the file format):

Current version: Page 14 

> It is RECOMMENDED that “subset proteins” that are unlikely to have been identified SHOULD NOT be reported here.

Change to:

>  The “subset proteins” that are unlikely to have been identified MUST NOT be reported here as individual protein rows. 

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