Re: [Psidev-ms-dev] [CompMS] Re: [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the Date

[Eric D. <eri...@is...>]

Hi Robert, great, thanks for contributing! We will try to schedule a
specific session for this and announce it so that everyone knows when it is
in advance.



Thanks,

Eric





*From:* co...@go... <co...@go...> *On Behalf Of *Robert
Chalkley
*Sent:* Monday, November 25, 2019 9:01 AM
*To:* Zaia, Joseph <jz...@bu...>; Jones, Andy <And...@li...>;
psi...@eb...; ps...@eb...; Mass spectrometry standard
development <psi...@li...>;
psi...@li...; Co...@go...
*Subject:* [CompMS] Re: [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the
Date



I would also be keen to be involved in discussions about supporting
glycopeptide data.

Robert

On 11/22/2019 11:21 AM, Zaia, Joseph wrote:

Dear All,



I would like to initiate discussion for expanding the use cases for
proteomics to include complex protein glycosylation.  Glycosylation is as a
rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition,
the glycan dissociates during tandem MS experiments.  The software and data
standards need to be expanded to include the glycosylation size,
heterogeneity, and tandem MS dissociation.  At present, quantitative
software (Skyline and others) do not recognize glycosylation.  Without this
recognition the quantitative tools developed for peptides cannot be adapted
without tedious effort on the part of the user.  Therefore, there is need
to expand the manner by which peptides are represented informatically.  It
is important that glycopeptides be included in the use cases for mzIdentML
and mzQuant.  It is also important that spectral library generating
software be expanded to allow glycosylated peptides to facilitate use of
data independent experiments for glycoproteins.



Would it be possible for me to communicate these ideas at the PSI Workshop
in San Diego?



Thank you.



Joe Zaia

*From:* Jones, Andy <And...@li...>
<And...@li...>
*Sent:* Thursday, November 21, 2019 11:29 AM
*To:* psi...@eb...; ps...@eb...; Mass spectrometry standard
development <psi...@li...>
<psi...@li...>; psi...@li...;
Co...@go...
*Subject:* [Psidev-pi-dev] PSI2020 - Save the Date



Hi all,



We are pleased to announce that the 2020 Annual workshop for the Proteomics
Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to
Thurs 26th March 2020. The workshop will focus on developing data standards
related to mass spectrometry for spectral libraries, the universal spectrum
identifier, quality control and capturing study metadata, and in the
molecular interactions side on mapping standards to Cytoscape. We will also
be welcoming the new PSI work group – Intrinsically Disordered Proteins
(IDP).



Please save the date if you might be interested to attend, we are always
pleased to welcome new groups into the PSI. The registration page will be
made available in the coming weeks.



Best wishes

Andy Jones on behalf of the PSI steering committee





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Robert Chalkley PhD

Adjunct Professor

Genentech Hall, N474A

Tel: 415 476 5189

Fax: 415 502 1655



Mass Spectrometry Facility

University of California San Francisco

600 16th Street,

Genentech Hall, suite N472A

San Francisco, CA 94143-2240







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