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

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

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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