Re: [Psidev-ms-dev] PSI MSS WG call notes

[Henk v. d. T. <h.w...@uu...>]

Dear workgroup,

I missed Gerhard's proposal, or else I would have tried to join the WG 
call. I'm happy to see the quick response!

I fully agree we should have an enumeration for the PTM-score name. On 
the other hand, if I look at the PSM scores, I see a flat list (e.g. 
Mascot:score). Would this be the naming convention of choice (like 
ProteomeDiscoverer:pRS site probability) or would the enumeration be a 
better way?

Moreover, different scores exist (at least in Proteome Discoverer) for 
different things:
pRS score
pRS probability
pRS sequence probability
Site probability

pRS score and pRS probability are the same thing, but site probability 
is specific to a modification. Can this be captured in the proposed 
scheme? Could this be applied to proteins as well?

Thanks, Henk

On 2/28/2012 5:39 PM, Eric Deutsch wrote:
>
> Notes from the MSS WG call 2012-02-28
>
> + Present: Florian, Eric, Matt, Pierre-Alain
>
> Agenda:
>
> 1) Plans and agenda for spring PSI workshop in San Diego March 12-14
>
> - Evaluate MIAPE -- Quant for SRM specifically
>
> - Evaluate mzQuantML for SRM specifically and generate examples
>
> - Assemble  guideline recommendations for the HPP
>
> + We will work together with Christoph's track on this
>
> - TraML implementations
>
> - Other
>
> 2) mzML status
>
> - No critical issues
> + Need to add an ion mobility array?
>
> + It would be good to discuss at the SD meeting how to encode ion 
> mobility data in mzML (Wed?)
>
> + There seem to be several possible ways to do it. Can we settle on one?
>
> 3) TraML status
>
> - No critical issues
>
> - Propose TraML examples for encode small molecules using BRENDA or 
> SMILES or other?
>
> 4) Discuss controlled vocabulary items
>
> - Only currently open issues appear to be PI/MSI related
>
> - Any additional terms needed to support metabolomics
>
> - CV Terms from Gerhard:
>
> [Term]
>
> id: MS:1001966
>
> name: product ion mobility
>
> def: "The mobility of an MS2 product ion, as measured by ion mobility
>
> mass spectrometry." [PSI:MS]
>
> is_a: MS:1001221 ! fragmentation information
>
> [Term]
>
> id: MS:1001967
>
> name: product ion drift time
>
> def: "The ion drift time of an MS2 product ion." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> relationship: has_units UO:0000028 ! millisecond
>
> is_a: ???????
>
> + Maybe not necessary???
>
> [Term]
>
> id: MS:1001968
>
> name: PTM scoring algorithm name
>
> def: "Name of the algorithm used for post-translational modification
>
> scoring." [PSI:MS]
>
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
>
> is_a: MS:1001471 ! peptide modification details
>
> + Instead of a free text string, this should be a parent term with 
> enumerated children.
>
> [Term]
>
> id: MS:1001969
>
> name: PTM scoring algorithm version
>
> def: "Version of the post-translational modification scoring algorithm."
>
> [PSI:MS]
>
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
>
> is_a: MS:1001471 ! peptide modification details
>
> [Term]
>
> id: MS:1001970
>
> name: PTM scoring value
>
> def: "Score value for post-translational modification." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> is_a: MS:1001143 ! search engine specific score for peptides
>
> is_a: MS:1001153 ! search engine specific score
>
> + This needs a lot more discussion
>
> 5) MIAPE -- MS
>
> - Trying to collect some final example files from Matt and Salva
>
> + We now have all the example documents for MIAPE -- MS
>
> + MIAPE -- MSI is now nearly ready
>
> + MIAPE -- MS is ready. Will be submitted by the end of the week.
>
> 6) MIAPE -- Quant
>
> - In doc process
>
> - Needs review with SRM in mind
>
> - Needs an SRM example document
>
> + Work on this in San Diego
>
> Next meeting: in person in San Diego March 12^th
>
> *From:*Eric Deutsch [mailto:Eri...@sy... 
> <mailto:Eri...@sy...>]
> *Sent:* Monday, February 27, 2012 11:47 PM
> *To:* Mass spectrometry standard development
> *Cc:* Eric Deutsch
> *Subject:* PSI MSS WG call reminder
>
> Hi everyone, this is a reminder about the PSI MSS WG teleconference 
> call tomorrow, Tuesday, at the usual time.
>
> 08:00 San Francisco
>
> 11:00 New York
>
> 16:00 London
>
> 17:00 Geneva
>
> + Germany: 08001012079
>
> + Switzerland: 0800000860
>
> + Finland: 080011569
>
> + UK: 08081095644
>
> + USA:1-866-832-8490
>
> Generic international: +44 2083222500 (UK number)
>
> access code: 297427 #
>
> Agenda:
>
> 1) Plans and agenda for spring PSI workshop in San Diego March 12-14
>
> 2) mzML status
>
> 3) TraML status
>
> 4) Discuss controlled vocabulary items
>
> 5) MIAPE -- MS
>
> 6) MIAPE -- Quant
>
> Next meeting:
>
> - in San Diego March 12
>


-- 
-------------------------------------------------------------------------------------------------------
*Henk van den Toorn, bioinformatician*
Biomolecular Mass Spectrometry and Proteomics Group
Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences
Utrecht University
Padualaan, 8
3584 CH Utrecht
The Netherlands

E-mail: h.w...@uu...
Tel: +31 30 253 6758
Fax: +31 30 253 6919
--------------------------------------------------------------------------------------------------