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

[Eric D. <ede...@sy...>]

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...]
*Sent:* Tuesday, January 17, 2017 4:39 AM
*To:* Jones, Andy; psi...@li...
*Cc:* Juan Antonio Vizcaino (ju...@eb...); Perkins, Simon; 'Harald
Barsnes'; 'Yasset Perez-Riverol'; to...@eb...;
jul...@ru...; mar...@ru...;
lfi...@st...; ju...@ed...; Eugen Netz; Mathias Walzer;
Oliver Kohlbacher; le...@im...; 'Robert Chalkley'; Ghali,
Fawaz; sma...@pr...; 'Eric Deutsch;
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,
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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