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

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

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...).
You are invited to subscribe to that list at 
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>