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

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

Hi @smdb21 The point of the change is to prevent the encoding you are describing - although I realise some people may not like it, hence it needs discussion. I am pushing the concept that a "valid" mzIdentML 1.2 file contains only "final" results. This means that if there are multiple SILists, the parser MUST process them with no exceptions. 

As further rationale  - in our pipelines (and presumably many others), we create 6-10 intermediate mzIdentML files from processing via various steps. We discard all the intermediate files before sending to PRIDE or another data consumer. The results from individual search engines prior to combining are an example of an intermediate file. A piece of reading software should (in my opinion) not have to do the work of figuring out the ranked PSMs for a given spectrum. If different SILists contain the same spectrum, then it places work on the reading software to make a judgement. 
Given that mzid 1.2 has already got pretty complicated to implement, I am arguing that this is a simplification worth having. 
Happy to revert the decision if there is general feeling that this is a crucial feature to support

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