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From: Jones, A. <And...@li...> - 2019-11-21 16:29:25
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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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From: Juan A. V. <ju...@eb...> - 2019-11-25 13:04:24
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Dear Joe, Thanks for your e-mail. You are very welcome to present in San Diego. We are still discussing the agenda, but we will make sure you get a slot. Best regards, Juan > On 22 Nov 2019, at 19:21, Zaia, Joseph <jz...@bu...> 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... <mailto:And...@li...>> > Sent: Thursday, November 21, 2019 11:29 AM > To: psi...@eb... <mailto:psi...@eb...>; ps...@eb... <mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li... <mailto:psi...@li...>>; psi...@li... <mailto:psi...@li...>; Co...@go... <mailto: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 > > > -- > You received this message because you are subscribed to the Google Groups "CompMS" group. > To unsubscribe from this group and stop receiving emails from it, send an email to com...@go... <mailto:com...@go...>. > To view this discussion on the web visit https://groups.google.com/d/msgid/compms/BN7PR03MB38755FF1B30AC07417844AB8CE490%40BN7PR03MB3875.namprd03.prod.outlook.com <https://groups.google.com/d/msgid/compms/BN7PR03MB38755FF1B30AC07417844AB8CE490%40BN7PR03MB3875.namprd03.prod.outlook.com?utm_medium=email&utm_source=footer>. |
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From: Zaia, J. <jz...@bu...> - 2019-11-25 15:12:57
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Thanks, Juan. I look forward to attending the spring HUPO-PSI meeting. Joe From: Juan Antonio Vizcaino <ju...@eb...> Sent: Monday, November 25, 2019 8:04 AM To: Zaia, Joseph <jz...@bu...> Cc: Andy Jones <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go... Subject: Re: [CompMS] [Psidev-pi-dev] PSI2020 - Save the Date Dear Joe, Thanks for your e-mail. You are very welcome to present in San Diego. We are still discussing the agenda, but we will make sure you get a slot. Best regards, Juan On 22 Nov 2019, at 19:21, Zaia, Joseph <jz...@bu...<mailto:jz...@bu...>> 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...<mailto:And...@li...>> Sent: Thursday, November 21, 2019 11:29 AM To: psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto: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 -- You received this message because you are subscribed to the Google Groups "CompMS" group. To unsubscribe from this group and stop receiving emails from it, send an email to com...@go...<mailto:com...@go...>. To view this discussion on the web visit https://groups.google.com/d/msgid/compms/BN7PR03MB38755FF1B30AC07417844AB8CE490%40BN7PR03MB3875.namprd03.prod.outlook.com<https://groups.google.com/d/msgid/compms/BN7PR03MB38755FF1B30AC07417844AB8CE490%40BN7PR03MB3875.namprd03.prod.outlook.com?utm_medium=email&utm_source=footer>. |
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From: Robert C. <cha...@cg...> - 2019-11-25 17:54:03
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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...> > *Sent:* Thursday, November 21, 2019 11:29 AM > *To:* psi...@eb...; ps...@eb...; Mass spectrometry > standard development <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 23^rd to Thurs 26^th 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 > > > _______________________________________________ > Psi-announce mailing list > Psi...@eb... > https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce -- 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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From: Eric D. <eri...@is...> - 2019-11-27 03:25:55
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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 _______________________________________________ Psi-announce mailing list Psi...@eb... https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce -- 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 -- You received this message because you are subscribed to the Google Groups "CompMS" group. To unsubscribe from this group and stop receiving emails from it, send an email to com...@go.... To view this discussion on the web visit https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu <https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu?utm_medium=email&utm_source=footer> . |
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From: Zaia, J. <jz...@bu...> - 2019-11-27 15:31:26
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I have been in touch with Nathan Edwards (Georgetown University, copied). He expressed interest in attending the session to discuss supporting glycoproteomics data. Best regards, Joe From: Eric Deutsch <eri...@is...> Sent: Tuesday, November 26, 2019 7:40 PM To: Robert Chalkley <cha...@cg...>; Zaia, Joseph <jz...@bu...>; Jones, Andy <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go... Subject: Re: [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save the Date 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...<mailto:co...@go...> <co...@go...<mailto:co...@go...>> On Behalf Of Robert Chalkley Sent: Monday, November 25, 2019 9:01 AM To: Zaia, Joseph <jz...@bu...<mailto:jz...@bu...>>; Jones, Andy <And...@li...<mailto:And...@li...>>; psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto: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...><mailto:And...@li...> Sent: Thursday, November 21, 2019 11:29 AM To: psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...><mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto: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 _______________________________________________ Psi-announce mailing list Psi...@eb...<mailto:Psi...@eb...> https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce -- 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 -- You received this message because you are subscribed to the Google Groups "CompMS" group. To unsubscribe from this group and stop receiving emails from it, send an email to com...@go...<mailto:com...@go...>. To view this discussion on the web visit https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu<https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu?utm_medium=email&utm_source=footer>. |
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From: Eric D. <eri...@is...> - 2019-11-27 18:06:20
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Thanks, Joe, it looks like there is great interest. We have a workshop planning call next week and will create a slot for a session on this. The dates for the workshop are: Mon Mar 23: Tue Mar 24: Wed Mar 25: Thu Mar 26: If anyone very interested in a glycoproteomics session has any major constraints in participation on these days, please let me know and we can try to work around it to maximize participation. Thanks, Eric *From:* Zaia, Joseph <jz...@bu...> *Sent:* Wednesday, November 27, 2019 7:16 AM *To:* Eric Deutsch <eri...@is...>; Robert Chalkley < cha...@cg...>; Jones, Andy <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go... *Cc:* nj...@ge... *Subject:* RE: [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save the Date I have been in touch with Nathan Edwards (Georgetown University, copied). He expressed interest in attending the session to discuss supporting glycoproteomics data. Best regards, Joe *From:* Eric Deutsch <eri...@is...> *Sent:* Tuesday, November 26, 2019 7:40 PM *To:* Robert Chalkley <cha...@cg...>; Zaia, Joseph <jz...@bu...>; Jones, Andy <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development < psi...@li...>; psi...@li...; Co...@go... *Subject:* Re: [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save the Date 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 _______________________________________________ Psi-announce mailing list Psi...@eb... https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce -- 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 -- You received this message because you are subscribed to the Google Groups "CompMS" group. To unsubscribe from this group and stop receiving emails from it, send an email to com...@go.... To view this discussion on the web visit https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu <https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu?utm_medium=email&utm_source=footer> . |
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