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

[Zaia, J. <jz...@bu...>]

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

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

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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>