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

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

The sending to the mailing list of my message below seemed to fail because of the zip files, please pick them up here:

https://www.dropbox.com/s/tgdojxj3h562xcy/MCP_Resubmit.zip?dl=0

https://www.dropbox.com/s/22mz4hr9rv61uwd/PSI_reviews.zip?dl=0

best wishes
Andy

From: Jones, Andy
Sent: 11 January 2017 15:56
To: 'psi...@li...' <psi...@li...>
Cc: Juan Antonio Vizcaino (ju...@eb...) <ju...@eb...>; 'ger...@ru...' <ger...@ru...>; Perkins, Simon <spe...@li...>; 'Harald Barsnes' <Har...@ui...>; 'Yasset Perez-Riverol' <yp...@eb...>; 'to...@eb...' <to...@eb...>; 'jul...@ru...' <jul...@ru...>; 'mar...@ru...' <mar...@ru...>; 'lfi...@st...' <lfi...@st...>; 'ju...@ed...' <ju...@ed...>; 'Eugen Netz' <eug...@tu...>; 'Mathias Walzer' <wa...@in...>; 'Oliver Kohlbacher' <oli...@un...>; 'le...@im...' <le...@im...>; 'Robert Chalkley' <cha...@cg...>; Ghali, Fawaz <fg...@li...>; 'sma...@pr...' <sma...@pr...>; ''Eric Deutsch' <ede...@sy...>
Subject: mzid 1.2 reviews

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