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

[andrewrobertjones <not...@gi...>]

Here is what is written about protocols in the spec doc about the SIProtocol:

`The <SpectrumIdentification> element MUST reference a <SpectrumIdentificationProtocol> holding representative parameters used across all search engines (i.e. search tolerances, enzyme and modifications), since these are MANDATORY elements. If the same search parameters were not employed in all source searches, the parameters should be set with superset or widest values i.e. all modifications that have been searched, widest tolerances and so on. All search engines that have been employed SHOULD be represented within the <AnalysisSoftwareList>. It must also be highlighted that mzIdentML cannot be used to model the order in which the software was used (it does not support workflows).`

I realise that there is some information loss here, but as noted above, there is no way in a standard to capture all meta-data of every stage in a way that any reading software could really process and understand it. 

In terms of a wrapper format. This could be useful but I think it is overkill to consider this a way to capture all intermediate files in a workflow. In my opinion, this would for relating together quant, ident, peak list and raw files - e.g. based on the PX XML. 

I would like to get agreement on this one soon if possible. Can you give this comments thumbs up or down, and if get enough thumbs up, I will close it. If anyone still feels strongly, vote thumbs down and add another comment below. Thanks! Andy



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