Re: [Psidev-pi-dev] mzid 1.2 reviews

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

Hi all,

I agree with Eric on this. The more clarity the better. What about? 

[Term]
id: MS:1001842
name: peptide PSM count (peptide as the raw peptide sequence)
def: "The number of MS2 spectra identified for a given peptide (considering the raw peptide sequence, and merging all charge states, modifications in the same peptide sequence are not considered separately) in spectral counting." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
is_a: MS:1002015 ! spectral count peptide level quantitation

[Term]
id: MS:1001xxx
name: peptide PSM count (peptide as the combination between peptide sequence and modifications)
def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence plus modifications, and merging all charge states) in spectral counting." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
is_a: MS:1002015 ! spectral count peptide level quantitation

[Term]
id: MS:1001xxx
name: peptide PSM count (peptide as the combination between peptide sequence, modifications and charge state)
def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence and modifications, and one single charge state) in spectral counting." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
is_a: MS:1002015 ! spectral count peptide level quantitation

Of course more variants would need to be created if we would want to mix the definitions above with different charge states, but I think these three definitions would be ok. 

What happens also in the case of ambiguity in the modification position? So, it could be even more complex. But I think this level is probably ok for the current state of things.

Cheers,

Juan



> On 17 Jan 2017, at 15:08, Eric Deutsch <ede...@sy...> wrote:
> 
> This is pretty good, but I think we should make it completely clear whether it is the number of PSMs per peptide sequence, per peptide with modifications, or per peptide ion (including separate charge states). The plain word peptide is often used as a standin for any of these 3 concepts..
>  
> Thanks,
> Eric
>  
>  
> From: mayerg97 [mailto:ger...@ru... <mailto:ger...@ru...>] 
> Sent: Tuesday, January 17, 2017 4:39 AM
> To: Jones, Andy; psi...@li... <mailto:psi...@li...>
> Cc: Juan Antonio Vizcaino (ju...@eb... <mailto:ju...@eb...>); Perkins, Simon; 'Harald Barsnes'; 'Yasset Perez-Riverol'; to...@eb... <mailto:to...@eb...>; jul...@ru... <mailto:jul...@ru...>; mar...@ru... <mailto:mar...@ru...>; lfi...@st... <mailto:lfi...@st...>; ju...@ed... <mailto:ju...@ed...>; Eugen Netz; Mathias Walzer; Oliver Kohlbacher; le...@im... <mailto:le...@im...>; 'Robert Chalkley'; Ghali, Fawaz; sma...@pr... <mailto:sma...@pr...>; 'Eric Deutsch; psi...@li... <mailto:psi...@li...>
> Subject: Re: mzid 1.2 reviews
>  
> Hi Andy,
> 
> yes we did a CV restructuring, see https://github.com/HUPO-PSI/mzIdentML/issues/25 <https://github.com/HUPO-PSI/mzIdentML/issues/25>,
> but I think this problem is not related to the restructuring.
> 
> What about
> 
> [Term]
> id: MS:1001842
> name: peptide PSM count
> def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI]
> xref: value-type:xsd\:int "The allowed value-type for this CV term."
> is_a: MS:1001805 ! quantification datatype
> is_a: MS:1002015 ! spectral count peptide level quantitation
> 
> Best regards,
> Gerhard
> 
> 
> 
> Am 11.01.2017 um 16:56 schrieb Jones, Andy:
>> Hi all,
>>  
>> (Sent to PSI-PI mailing list plus authors of the mzid paper, in case any of you are not on the mailing list).
>>  
>> We have received 5 reviews of the mzid 1.2 specifications via the PSI process, as well as the 2 reviews received on the manuscript from MCP, for which it makes sense to consider together. I think most of these can be addressed fairly simply. I have already fixed a few typos in the specification document that were identified, and made one or two other sensible clarifications to wording. These changes have been checked into GitHub. I have started response documents to both processes in the relevant zip files. 
>>  
>> If you would like to contribute, please could you send me any feedback within one week (by 19th Jan) if possible. After that point, I will submit the mzid 1.2 specs back to the PSI process (for which Sylvie the editor recommended minor corrections), unless anything comes up that needs extensive further discussion. Once they are accepted, I will resubmit the paper to MCP, as reporting the mzid 1.2 final specifications.
>>  
>> Just flagging a few points for specific people to address:
>>  
>> -          Robert and Alexander: one of the reviewer asks whether your cross-linking software will export mzid 1.2, anything you can say here?
>> -          Fawaz – one of the reviewers seemed to find some validation errors with some of our mzid 1.2 files, please could you take a look
>> -          Juan – one of the MCP reviewers suggests we change the figures. Can you give me a view on whether you think we need to do this? I’m of the view to make minor improvements, but not radically change them.
>> -          Gerhard – see response to MCP reviews. One of the reviewers would like to know how spectral counts can be added at the peptide-level. I think this may need a new parent term for one given CV term (see my notes in the response to reviews doc), could you take a look?
>>  
>> Best wishes
>> Andy 
>>  
>>  
>>  
>>  
>  
> -- 
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