Re: [Psidev-pi-dev] Spec doc

[Juan A. V. <ju...@eb...>]

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
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