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

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

Hi Eric,

The implementation of the BED format in that nice manuscript is done without "paying much attention" to the format itself (it is not their main focus), and considering only some of the possible use cases that one might encounter.

Cheers,

Juanan



> On 23 Mar 2016, at 03:03, Eric Deutsch <ede...@sy...> wrote:
> 
> Hi Mathias, the proBAM specification is undergoing some revisions beyond
> what was published. We have one more set of action items to apply to the
> spec and then we will be sending it around for inspection and comment. Soon
> and before the workshop I hope.
> 
> So that is the only published thing so far, but Xiaojing Wang and others are
> working within the PSI to enhance it.
> 
> But that reminds me that I recently saw this paper from David Fenyö and
> colleagues come out. I confess I haven't read it yet, but this may have some
> significant impact on the developing proBED format:
> http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.5b00870
> http://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.5b00870
> 
> Regards,
> Eric
> 
> 
> -----Original Message-----
> From: Mathias Walzer [mailto:wa...@in...]
> Sent: Tuesday, March 22, 2016 6:57 AM
> To: Mass spectrometry standard development
> <psi...@li...>
> Subject: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
> 
> Hi all,
> 
> just a quick thought on the proteogenomics part, see attachment.
> 
> Is http://www.mcponline.org/content/15/3/1164.full#sec-1 the only source for
> an official definition of proBAM?
> 
> Best,
> Mathias
> 
> ----- Original Message -----
> From: "Andy Jones" <And...@li...>
> To: psi...@li...,
> psi...@li..., psi...@li...
> Sent: Monday, 21 March, 2016 12:21:29 PM
> Subject: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
> 
> 
> 
> 
> 
> 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 (24 th March) at 4pm GMT
> 
> - Next Thurs (31 st March) at 4pm GMT
> 
> Best wishes
> 
> Andy
> 
> 
> 
> 
> 
> 
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