Re: [Psidev-pi-dev] Spec doc

[Jones, A. <And...@li...>]

Hi all,
Thanks for all your comments, I will assemble them today and see if I can get it submitted, or at worst tomorrow,
Cheers
Andy

> -----Original Message-----
> From: Juan Antonio Vizcaíno [mailto:ju...@eb...]
> Sent: 08 June 2011 09:29
> To: Jones, Andy
> Cc: psi...@li...
> Subject: Re: [Psidev-pi-dev] Spec doc
> 
> Hi Andy,
> 
> Some comments about the spec document.
> 
> 1. I agree completety with Matt in this point. It seems contradictory:
> 
> "A PMF search and an MS-MS search of the same sample can be saved in
> the same instance document
> as long as the result is one combined protein list." seems to
> contradict the earlier statement about
> aggregating evidence between different MS levels. If we can combine
> multiple MS levels in one
> protein list, why can't we do it for MS2 and MS3 as well as we can for
> MS1 and MS2?"
> 
> 2. Neutral losses.  In Heidelberg, Eric and Pierre-Alain suggested to
> separate the ion type from the neutral loss, e.g. having CV terms "y
> ion" and "neutral loss H2O" and be able to combine them freely. In the
> multiple search engines example (at least), the neutral losses are
> encoded in the way it has been done so far. There are two choices
> then: leave the examples the way they are today (and change then
> later) or remove neutral losses from the example files.
> 
> I am aware that the new CV terms have not been created yet and that
> the CV is really a mess, so the example files cannot be modified today.
> 
> In any case, this is quite an important change that will need to be
> added/ documented properly in the future.
> 
> 3. I think it would be a good idea to provide with the example files
> (where possible), the corresponding spectra files that the mzIdentML
> examples are linking to. For some cases it is quite obvious how the
> link is done but in other cases it is not so straightforward (for
> instance .mgf) since it is based in the index in the file.
> 
> 4. Add the specific accession number for the 'unknown modification' in
> the MS CV (MS:1001460).
> 
> 5. As a suggestion, add a diagram explaining the relationships between
> the key elements in the schema, before the model in XML schema. It
> would be similar to the figures included in the first version of the
> mzIdentML publication. I know this is a spec document and not a
> tutorial, but I think it would be useful.
> 
> Cheers,
> 
> Juan
> 
> 
> 
> On 7 Jun 2011, at 08:35, Jones, Andy wrote:
> 
> > Hi all,
> >
> > I'm planning to submit the specifications tomorrow afternoon, can
> > anyone who would like to comment please do so by the end of the day
> > if possible.
> > cheers
> > Andy
> > ------------------------------------------------------------------------------
> > EditLive Enterprise is the world's most technically advanced content
> > authoring tool. Experience the power of Track Changes, Inline Image
> > Editing and ensure content is compliant with Accessibility Checking.
> > http://p.sf.net/sfu/ephox-dev2dev
> > _______________________________________________
> > Psidev-pi-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
> 
> 
> 
> 
> 
>