Re: [Psidev-pi-dev] Proteomics standards for glycosylated proteins

[Gerhard M. <may...@ru...>]

Dear Joseph,

at the moment we plan for Mon 23^rd to Thurs 26^th March 2020 at UCSD in 
San Diego.

The official announcement and registration page will be posted soon on 
our HUPO-PSI website
on http://www.psidev.info/events

Cheers,
Gerhard


On 20.11.2019 21:54, Zaia, Joseph wrote:
>
> Dear Gerhard,
>
> Thank you for your reply.  I have subscribed to the PSI-PI mailing list.
>
> In principle, I am interested in attending the HUPO-PSI spring 
> meeting.  But I cannot find information about the date and location.  
> Could you send me a link?
>
> Many thanks.
>
> Joe
>
> *From:*Gerhard Mayer <may...@ru...>
> *Sent:* Wednesday, November 20, 2019 10:52 AM
> *To:* Zaia, Joseph <jz...@bu...>; psi...@li...
> *Cc:* Klein, Joshua, Adam <ja...@bu...>; Hackett, William, Edwin 
> <weh...@bu...>
> *Subject:* Re: Proteomics standards for glycosylated proteins
>
> Dear Joseph,
>
> yes, support for glycoproteomics is still missing in mzIdentML and
> I agree that this would be an important extension for a future version 
> of mzIdentML.
>
> Since the mzIdentML standard (https://github.com/HUPO-PSI/mzIdentML) 
> is a community effort
> of the Proteomics Informatics (PI) group of the HUPO-PSI 
> (http://www.psidev.info),
> I forward your request to the PSI-PI mailing list 
> (psi...@li... 
> <mailto:psi...@li...>).
> You are invited to subscribe to that list at 
> https://sourceforge.net/projects/psidev/lists/psidev-pi-dev 
> <https://sourceforge.net/projects/psidev/lists/psidev-pi-dev>
>
> Maybe you and/or your associates can attend to the next HUPO-PSI 
> spring meeting to discuss glycoproteomics support in more details?
> HUPO-PSI always welcomes new contributors for further development of 
> their standard formats.
>
> Best regards
> Gerhard Mayer
> HUPO-PSI ontology coordinator
>
> On 20.11.2019 16:26, Zaia, Joseph wrote:
>
>     Dear Gerhard,
>
>     I am writing to initiate discussion of proteomics exchange
>     standards for glycosylated proteins.  My research group develops
>     mass spectrometry based methods and bioinformatics for
>     quantification of glycoprotein glycosylation. We suggest that the
>     use cases for mzIdentML standard be expanded to include
>     site-specific protein glycosylation.  We note that the use cases
>     for the mzIdentML1 2.0 release include protein cross-linking and
>     molecular interaction data that can be inferred from
>     cross-linking.  There is a growing need to expand this to include
>     glycosylation.
>
>     Many cell surface and extracellular proteins undergo glycosylation
>     as they pass through the secretory pathway.  The glycosylation
>     reactions do not go to completion, resulting in microheterogeneity
>     at each protein glycosylation site.  Glycans are relatively large
>     chemical modifications that undergo dissociation during tandem MS
>     events.  Therefore, it is necessary to modify mzIdentML and/or
>     other exchange standards to include this reality.
>
>     We are eager to engage you and other HUPO Proteome Standards
>     Initiative members in discussing how to expand the scope or
>     exchange standards to include glycoproteins.  Can you suggest
>     stake holders who should be included in this conversation?
>
>     Many thanks!
>
>     Joe Zaia
>
>     Joseph Zaia (he/his/him)
>
>     Professor, Biochemistry
>
>     Member, Bioinformatics Program
>
>     Associate Director, Center for Biomedical Mass Spectrometry
>
>     Boston University Medical Campus
>
>     670 Albany St., Rm. 509
>
>     Boston, MA 02118
>
>     USA
>
>     Office: 1-617-358-2429
>
> -- 
>
> *----------------------------------------------------------------------*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *Research associate*
>
> *Ruhr-Universität Bochum, Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*
>
> *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496
>
> *E-Mail: *ger...@ru... <mailto:ger...@ru...>
>
> *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>
>
-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>