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

[Alexander L. <le...@im...>]

Hi Andy,

I looked through the response letter and am fine with the text and all 
changes made to the manuscript.

Regarding the implementation of an mzIdentML export feature for xQuest, 
we are working with the OpenMS team (especially Eugen), and hopefully 
there will be some way to convert the current XML output of xQuest into 
mzIdentML 1.2.  In short, I would consider it "in progress".


Best regards,

Alexander



Jones, Andy schrieb:
>
> 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 19^th 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
>