Re: [Psidev-pi-dev] Conference call tomorrow

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

Minutes from today
*******************

Present:

Yasset (EBI)
Andy (Liverpool)
Eric (ISB)
Julian and Gerhard (Bochum)
Lutz (Edinburgh)


-          Reviewed section 5.3 of spec doc

o   Multiple search engines text looks rather daunting – ACTION: Andy to add a figure and simplify text if possible

-          Pre-fractionation:

o   Various guidelines but these are mainly notes for implementers, should be simple for readers given that all reading software should load all PSMs from all lists flagged as “final PSM list”

o   ACTION: Gerhard, can you check whether the validator has any logic for checking whether a given spectrum identification (combination of spectrumID and spectrumRef) is unique within the “final PSM lists” – a file should be flagged as invalid if the same spectrum appears more than once

-          Peptide-level scores:

o   Various discussion about whether we should continue with the hacked method.

o   Yasset strongly expressed the view that Peaks, Thermo etc are only just getting mzid 1.1 export going; if we make schema changes, it will be disastrous for relations with these companies

o   General agreement to support peptide-level scores through the CV param mechanism proposed, rather than making more radical changes

-          Mod-localization for peptide scores:

o   Discussed that this cannot currently be supported

o   Proposal to try and see if this will work under current peptide-level CVparam mechanism e.g. by having new CV terms for “peptide:A-score” etc, as well as “a-score” for PSM-based mod localization scoring

-          Validation software – Gerhard said that most mzid 1.2 features are in there now

o   ACTION: Gerhard to add this to the SVN and send round a link

-          Crosslinking:

o   We are going to add the CV terms needed to PSI-MS, since it is proving difficult to get terms in Unimod or PSI-MOD without a lot more discussion

-          Completing mzid 1.2, Need example files:

o   ACTION: Lutz to update XL files

o   ACTION: Andy’s group to make peptide-level stats example file; and multiple search example file

o   ACTION: Marc/Harald to make examples for peptide-level stats and mod localization (and both together if possible)

o   ACTION: All – send necessary CV updates to the PSI-MS-vocab list so Gerhard can get these added

-          Manuscript:

o   ACTION: Andy to make a start on this; send to Juan and Yasset for help pulling together

Please let me know if I missed anything,
Best wishes
Andy



From: Jones, Andy [mailto:And...@li...]
Sent: 14 January 2015 17:02
To: ''psi...@li...' (psi...@li...)'
Subject: [Psidev-pi-dev] Conference call tomorrow

Hi all,

Conference call to progress mzIdentML at 4pm UK time tomorrow, http://www.timeanddate.com/worldclock/fixedtime.html?iso=20150115T16&p1=%3A&ah=1

Dial in details:
+ Germany: 08001012079
+ Switzerland: 0800000860
+ UK: 08081095644
+ Generic international: +44 2083222500 (UK number)
+ US: 877-420-0272
access code: 297427

Agenda:


1.       Brief summary of current status of mzid 1.2

2.       Review of specification document: https://code.google.com/p/psi-pi/source/browse/trunk/specification_document/specdoc1_2/mzIdentML1.2-draft.doc

3.       Discussion of open items:

a.       Various issues with the mzid 1.2 encoding identified by Harald (see email forwarded separately)

4.       Plan for completing mzid 1.2 and writing manuscript

5.       AOB

Please send me additional items for discussion,
Best wishes
Andy