Re: [Psidev-ms-dev] Imaging mzML

[Lennart M. <len...@gm...>]

Hi Angel, PSI-MS Enthusiasts,


> I think a secondary file that encodes the data arrays in its own
> binary format is squarely outside the realm of what is possible
> without effecting the primary directive of mzML. That's not to say
> that I disagree with their methodology; I don't. I think that as an
> operational format, it is far better than straight mzML for their
> needs. But there is no way I can in good faith even entertain the idea
> that this be an official part of the mzML specification.

Right, I see your point, and considered it as well for quite some time. 
But we're faced with a situation where imzML is not a proposal - it's a 
thing that's out there, that is supported by various pieces of software, 
and is actively used and promoted by a community -- amongst others as a 
means to store and transmit MS/MS data! So whether we like it or not, it 
currently can very quickly evolve into a direct competitor with mzML. 
And on that note, I share your conviction that it has serious advantages 
over mzML in operational scenarios (see also my mail to Mike earlier).

My feeling (inspired by nothing but pragmatism) therefore is that we now 
need to prevent another two-standard system in mass spectrometry 
proteomics by seeing the two as different (thus leading to an mzML 1.0 
based imzML with a separate and speciating development cycle and CV), 
and we therefore need to find one way or another to 'integrate' things. 
We can split hairs over words like 'official' as far as I'm concerned, 
but as a community-based effort, we need to keep our finger on the pulse 
of the community as well.

So I would strongly advocate that we at least endeavour to keep open 
communication with these guys, and ensure ready 
interoperability/conversion as much as possible, which means that we 
should be schema-compliant, and that (some) of our software should 
support conversion. Whether we 'officially' endorse it or not, is then a 
different matter in my view of things.


Cheers,

lnnrt.