Re: [Psidev-ms-dev] [Psidev-pi-dev] Proteogenomics update in mzid 1.2

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

Hi Gerben,

Thanks for the input. In terms of novel event peptides, it would be nice to include these as optional CV terms for mzid 1.2 (or 1.1 for that matter).

I will take the proBAM 0.8 list as a starting point, and once we are happy with the list, get them added to the PSI-MS CV.
Best wishes
Andy

From: Gerben Menschaert [mailto:ger...@gm...]
Sent: 23 March 2016 14:00
To: Jones, Andy <jo...@li...>
Cc: psi...@li...; psi...@li...; psi...@li...
Subject: Re: [Psidev-pi-dev] Proteogenomics update in mzid 1.2

Hi Andy,

I won’t be able to join the 31st of March.
I looked into the CV term descriptions and these seem good to me.
I can provide you with a list of “novel event” peptides if necessary, or you can take the list from the proBAM format document.

All the best,
Gerben


On 21 Mar 2016, at 12:21, Jones, Andy <And...@li...<mailto:And...@li...>> wrote:

Hi all,
Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list.
One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches.  There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides).
Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion.
It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit:

-          This Thurs (24th March) at 4pm GMT

-          Next Thurs (31st March) at 4pm GMT
Best wishes
Andy



<Proteogenomics_CV_terms.docx>------------------------------------------------------------------------------
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