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

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

Dial-in details, call in 15 mins:

Numbers:
+ UK: 0808 109 5644
+ US: 877-420-0272
+ Belgium: 0800 509 80
+ Germany: 0800 101 2079
+ Switzerland: 0800 000 860
+ Generic international: +44 (0) 20 8322 2500 (UK number)
Access code: 297427 #

From: Jones, Andy [mailto:And...@li...]
Sent: 29 March 2016 16:10
To: psi...@li...
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2

Hi all,
Just confirming we will have a call to discuss mzid 1.2 this coming Thurs at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301
Agenda:

1.       Discussion of encoding proteogenomics results in mzid 1.2 (review of docs sent previously)

2.       General review of mzid 1.2 specifications (attached here) – please take a look in advance if you can. We will probably not have time for a full review on the call, but we will see how far we get

3.       Any other business

Juan – are you okay to start the call, and if so, can you circulate dial-in details?
Thanks
Andy



From: Binz Pierre-Alain [mailto:Pie...@ch...]
Sent: 22 March 2016 15:45
To: psi...@li...<mailto:psi...@li...>
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2

Fine for me too
Pierre-Alain

De : Eric Deutsch [mailto:ede...@sy...]
Envoyé : mardi 22 mars 2016 14:53
À : psi...@li...<mailto:psi...@li...>; Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>
Objet : Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2

That works fine for me!

From: Jones, Andy [mailto:And...@li...<mailto:And...@li...>]
Sent: Tuesday, March 22, 2016 2:49 AM
To: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2

Hi all,
I think the 24th is out for various people as an Easter-related holiday in some countries. Eric is correct, that time zones will be changing.
On the 31st, my preferred slot is actually 4pm British summer time:
http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301
This would be 8am in Seattle; 5pm Germany;  5pm Norway; (and 4pm in the independent nation state of the EBI)
Does this work for everyone?
Best wishes
Andy



From: Eric Deutsch [mailto:ede...@sy...]
Sent: 22 March 2016 03:32
To: Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc: Eric Deutsch <ede...@sy...<mailto:ede...@sy...>>
Subject: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2

Thanks, Andy, I like this idea. The times are not good for me, however. Normally 4pm London time is 8am Seattle time, but for these few weeks, 4pm London time is 9am Seattle time and I have a standing meeting I cannot change.
http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p1=1440
An hour earlier would be fine for the 24th.
I hope I’m not getting confused between 4pm GMT and London local time? I think on the 24th 16:00 GMT = 4pm local London, but on the 31st, 16:00 GMT is 5pm London time?
Thanks,
Eric

From: Jones, Andy [mailto:And...@li...<mailto:And...@li...>]
Sent: Monday, March 21, 2016 4:21 AM
To: psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
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 (24th March) at 4pm GMT

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