Re: [Psidev-ms-dev] First PSI-MS Teleconference

[Chris T. <chr...@eb...>]

Hiya. It's unfortunate that I had to keep this most recent 
version of MS from view until the MCP business had been 
discussed in Geneva; not sure things really got fully cleared up 
there but anyway we can move forwards now. The revision of MS 
that comes after all the dust has settled from this MCP business 
will indeed as you say have to be v2.1...

I hope that as well as your specific conversations about the 
commentary to go to Ralph Bradshaw you will find time to discuss 
the various general options available to us (MCP + MIAPE: MSI 
independently, MIAPE: MSI for reporting & MCP for quality, MCP 
and MIAPE: MSI to be the same thing, 'owned' by either PSI or 
ASBMB, etc etc).

Cheers, Chris.


Pierre-Alain Binz wrote:
> Hi Chris,
> as the MIAPE MS document being matched to the MCP draft guidelines is a 
> version that was available in Geneva, I will consider the doc (your 
> version 2.0) you has made available afterwards as being part of your 
> comments. The result of the comments from the people already having the 
> mapping documents or from those who still want to go through them (send 
> me an email for getting theem) will be compiled by the end of september. 
> I would ask all comments back to me by Sept 23rd. The resulting MIAPE-MS 
> doc will then have to have a version higher as 2.0 as a matter of fact 
> and to avoid any missunderstanding
> Thanks in advance.
> Pierre-Alain
> 
> 
> Chris Taylor wrote:
> 
>> Great. Thanks for the info. Sorry for being a pest :)
>>
>> I've reposted the 'final' (ha) MIAPE: MS document at 
>> http://psidev.sourceforge.net/gps/miape/MIAPE_MS_2.0.doc
>> but rather than chop the bits I mentioned in the list post earlier 
>> today to make a v2.1, I have simply coloured parts red as things 
>> turned out not to be so simple; I think it should be something for 
>> discussion on that call whether (4) is moved wholesale to MSI or only 
>> partially.
>>
>> A particular issue is that the 'quantitation' section (4b) serves 
>> partly to annotate the spectra described, to alert people to the fact 
>> that something 'funny' is going on (i.e. expect to see cleaved iTRAQ 
>> tags or allow for isotope-label/ICAT related mass shifts etc.). It is 
>> only partly there to address (in a limited way) the informatics 
>> process of quantitation itself if you see what I mean, therefore the 
>> overlap with MCP is patchy. Clearly (4a) overlaps heavily except for 
>> the location of the (infamous) raw data (e.g. parameters triggering 
>> the generation of peak lists etc.).
>>
>> Anyway I'll hang on to post the MS document until I hear opinions from 
>> people, perhaps till after the call (on the 17th?). The colour coding 
>> reflects my own preference...
>>
>> Cheers, Chris.
>>
>>
>> Pierre-Alain Binz wrote:
>>
>>> Hi Chris (and all psidev members)
>>> The MS group has decided to talk about the MCP-MIAPE docs at the next 
>>> phone call.
>>> I had prepared a set of  mapping documents between MIAPE MS, MSI and 
>>> MCP guidelines draft July 14th.
>>> For those interested in commenting on the mapping and on the content, 
>>> it's been decided that I send them the documents and will collect the 
>>> comments.
>>> So if I get emails I send the docs...
>>> Cheers,
>>> Pierre-Alain
>>>
>>> Chris Taylor wrote:
>>>
>>>> Hi all. I'll try to make this call if I can; regardless though I 
>>>> wonder if a small addition to the agenda might be desirable, namely 
>>>> to mention the 'reponse' (or whatever) to MCP? I'm assuming that as 
>>>> owner of the MIAPE: MSI document, Pierre-Alain will have a hand in 
>>>> this along with Sean and others with an interest? It may be in order 
>>>> to actually draw up a list of drafters who can do the point-by-point 
>>>> offline.
>>>>
>>>> To do my bit I will later today post the MIAPE: MS document as a 
>>>> final version, but with any sniff of informatics removed (i.e. 
>>>> profile to peak list), with a view to putting it into the MSI 
>>>> module, to better align that document with the MCP proposal. MIAPE: 
>>>> MS has been sitting around for some time now though, and so I think 
>>>> it is only fair to the contribtors to that document that they see 
>>>> something come from it.
>>>>
>>>> We should have by early next year MIAPE modules for gels and gel 
>>>> informatics, and should be moving forwards with general separations 
>>>> (everything that is not a 'classical' 1 or 2D gel) and study design. 
>>>> I'd like to see something equivalent for mass spec informatics 
>>>> sooner rather than later, whether 'owned' by MCP or us or whatever 
>>>> gets it done quickest (this is also something for the call). I'd 
>>>> also underline as several people restated in Geneva, that what might 
>>>> come under the MIAPE banner shouldn't include prescriptive methods 
>>>> for doing the work, just for reporting it.
>>>>
>>>> Cheers, Chris.
>>>>
>>>>
>>>> Randy Julian wrote:
>>>>
>>>>> The PSI-MS working group would like to organize a weekly (or 
>>>>> bi-weekly) teleconference to further the development of both the 
>>>>> mzData format as well as push forward on the results interchange 
>>>>> format proposed at Geneva as 'analysisXML'.
>>>>>
>>>>> We are new to this type of interaction, but it works well in other 
>>>>> standards organization and seems like a good way to allow wide 
>>>>> participation and create a transparent process for establishing 
>>>>> standards.
>>>>>
>>>>> The first teleconference was discussed at the Geneva meeting and 
>>>>> despite the late notice, we would like to have a 60 minute call 
>>>>> tomorrow (13 Sept) at 11:00 EST.
>>>>>
>>>>> The first call is organized by Genologics so if you would like to 
>>>>> attend, please e-mail Kent Laursen (ken...@ge...) 
>>>>> for the dialing instructions.
>>>>>
>>>>> We are planning to have these calls every two weeks, so if you miss 
>>>>> this one (due to the late notice...), we are planning another for 
>>>>> Sept 27.
>>>>>
>>>>> For the first call, I would propose the following agenda:
>>>>>
>>>>> 1. Discuss our statement of mission
>>>>> 2. Explicitly declare our deliverables
>>>>> 3. Discuss the use of the documentation of the Global Grid Forum as 
>>>>> a possible template for PSI-MS
>>>>> 4. Discuss the extension mechanism in analysisXML (see attached 
>>>>> .tgz file with the schema)
>>>>>    - what's the right balance between cvParam and sub-schema
>>>>> 5. Setting the next few calls agenda
>>>>>
>>>>> We will take notes at this call and post them to this list.
>>>>>
>>>>> Please contact me (rkj...@in...) with questions, and Kent 
>>>>> (ken...@ge...) for dialing instructions.
>>>>>
>>>>> Thanks,
>>>>> Randy Julian for the PSI-MS group
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
> 

-- 
~~~~~~~~~~~~~~~~~~~~~~~~
  chr...@eb...
  http://psidev.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~