psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] HUPO-PSI: Specification document PSI-MI FeatureTab v1.0 draft 02 - 30-day public review

[Sylvie R. <syl...@un...>]

Dear colleagues, dear members of the HUPO-PSI community,

The HUPO Proteomics Standards Initiative (PSI) develops standards  for 
documentation and storage of proteomics, glycomics and interaction data 
(see http://www.psidev.info for an overview of activities).

Members of the Molecular Interactions Working Group have submitted a new 
recommendation for a PSI standard, *PSI-MI FeatureTab*, *an exchange 
format for molecular interaction features*. The PSI-MI FeatureTab format 
is part of the PSI-MI 2.5 standard. It is related to the tabular format 
provided by PSI MITAB 2.5 and subsequent updates. However, while the PSI 
MITAB 2.5 describes binary interactions, one pair of interactors per 
row, in the PSI-MI FeatureTab each row is feature centric and describes 
in detail a specific feature at the participant level and the effect of 
a feature, if any, on the second participant.

After having passed a 14-day review by two members of the PSI steering 
committee, who suggested minor changes, the proposed specification now 
goes through the 30-day public and external review, which should end on 
August 16th, 2025 but is *extended to August 31st, 2025 *due to  summer 
holidays.

The draft of the specification (version 1.0, draft 02) is attached to 
this e-mail.

This message is to encourage you to contribute to the standards 
development activity by commenting on the document. We invite both 
positive and negative comments on the relevance, correctness, clarity 
and appropriateness of the specification (e.g. is it presented in 
accordance with the templates and clearly written, is it sufficiently 
detailed and comprehensively described and are the examples in agreement 
with the specification?). Comments can be made on the specification as a 
whole or on specific parts.

If you do not feel experienced enough to comment on this document, but 
know colleagues who are, please feel free to forward this message to 
them. There is no requirement that people commenting should have had any 
prior contact with the PSI.

*Please send comments by e-mail directly to 
syl...@un... before August 31st, 2025.*

I thank you very much in advance for your contribution and time.

Kind regards.

Professor Sylvie RICARD-BLUM, HUPO-PSI Editor
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)6 82 02 44 22
E-mail: syl...@un...

Re: [Psidev-ms-dev] Workshop on Digital Data Standards Sustainability in the Chemical Sciences April 3-4, 2025, in Leipzig, Germany

[Randall J. <rkj...@in...>]

Hi Steffen,

I would be keen on attending this meeting, and Indigo would be willing to help be a sponsor if that’s wanted or needed. There is so much more to do than we accomplished with the PSI, but as you say, it’s outside the scope.

Please let me know how I can help with the meeting – it is a terrific idea.

Thanks,
Randall Julian

From: Neumann, Steffen <sne...@ip...>
Date: Thursday, December 5, 2024 at 1:13 PM
To: psi...@li... <psi...@li...>
Subject: [Psidev-ms-dev] Workshop on Digital Data Standards Sustainability in the Chemical Sciences April 3-4, 2025, in Leipzig, Germany
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi,

this is not directly metabolomics (nor proteomics) stuff, but related
to analytical chemistry:

we are currently planning the second community workshop on “Digital
Data Standards Sustainability in the Chemical Sciences” that will take
place from April 3-4, 2025, in Leipzig, Germany.

The workshop will be hosted by the Center for the Transformation of
Chemistry (CTC) in conjunction with the Beilstein-Institut, the InChI
Trust, the IUPAC WorldFAIR Chemistry project and NFDI4Chem.

The primary aim of the workshop is to facilitate adoption of
(chemistry) data standards to enhance interoperability and foster
collaboration for ongoing community resource development.

I see a benefit because it might provide us contacts to stakeholders
beyond instrument vendors and (life-)scientific bioinformatics
community.

Would there be anyone interested to join ? I find PSI a great example
for community-driven standards development. The workshop is invitation
only, but I know where the list is to add invitees :-) Please get in
touch with me if you are interested.

Yours,
Steffen


--
---
IPB Halle                    Bioinformatics and Scientific Data
Dr. Steffen Neumann          http://www.IPB-Halle.DE [1]
Weinberg 3                   Tel. +49 (0) 345 5582 - 1770
06120 Halle                       +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

[1] http://www.IPB-Halle.DE http://www.ipb-halle.de/

_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] Workshop on Digital Data Standards Sustainability in the Chemical Sciences April 3-4, 2025, in Leipzig, Germany

[Neumann, S. <sne...@ip...>]

Hi,

this is not directly metabolomics (nor proteomics) stuff, but related
to analytical chemistry:

we are currently planning the second community workshop on “Digital
Data Standards Sustainability in the Chemical Sciences” that will take
place from April 3-4, 2025, in Leipzig, Germany. 

The workshop will be hosted by the Center for the Transformation of
Chemistry (CTC) in conjunction with the Beilstein-Institut, the InChI
Trust, the IUPAC WorldFAIR Chemistry project and NFDI4Chem.

The primary aim of the workshop is to facilitate adoption of
(chemistry) data standards to enhance interoperability and foster
collaboration for ongoing community resource development.

I see a benefit because it might provide us contacts to stakeholders
beyond instrument vendors and (life-)scientific bioinformatics
community.

Would there be anyone interested to join ? I find PSI a great example
for community-driven standards development. The workshop is invitation
only, but I know where the list is to add invitees :-) Please get in
touch with me if you are interested.

Yours,
Steffen


-- 
---
IPB Halle                    Bioinformatics and Scientific Data
Dr. Steffen Neumann          http://www.IPB-Halle.DE [1]
Weinberg 3                   Tel. +49 (0) 345 5582 - 1770
06120 Halle                       +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

[1] http://www.IPB-Halle.DE http://www.ipb-halle.de/

[Psidev-ms-dev] HUPO-PSI Specification mzIdentML version 1.3.0 + crosslinking extension 45-day public review

[Sylvie R. <syl...@un...>]

Dear colleagues, dear members of the HUPO-PSI community,

The HUPO Proteomics Standards Initiative (PSI) develops standards  for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of activities).

The PSI Proteomics Informatics Working Group has submitted a new 
recommendation for consideration and review as a PSI standard. The 
mzIdentML document, draft of version 1.3.0, defines an XML schema that 
can be used to describe the outputs of proteomics search engines or 
similar software for peptide/protein identification from mass 
spectrometry(MS) data with an extension document for the identification 
of crosslinked peptides.

After having been reviewed by the PSI steering group and revised as 
requested by an internal reviewer, the proposed documents, mzIdentML 
draft of version 1.3.0 and the crosslinking extension document, now go 
through the 45-day public and external review until*April 8^th , 2024*.

The mzIdentML document (draft of version 1.3.0), a word document 
tracking changes from version 1.2.0, the crosslinking extension 
document, and the example files are available on GitHub as detailed below.

*The mzIdentML document version 1.3.0, draft *
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_3-draft/mzIdentML1.3.0-draft_vJuly2023.pdf

*A word document tracking changes from version 1.2.0*
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_3-draft/mzIdentML1.3.0-draft_vJuly2023_CC3%20JAV.docx

*The crosslinking extension document*
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_3-draft/mzIdentML%201.3.0%20Crosslinking%20Extension.pdf

*The example files*
https://github.com/HUPO-PSI/mzIdentML/tree/master/examples/1_3examples/crosslinking

*The pre-print*is available at 
https://www.authorea.com/users/672647/articles/671627-mzidentml 
-1-3-0-essential-progress-on-the-support-of-crosslinking-and-other-identifications-based-on-multiple-spectra

This message is to encourage you to contribute to the standards 
development activity by commenting on the documents. We invite both 
positive and negative comments on the relevance, correctness, clarity 
and appropriateness of the specification (e.g. is it presented in 
accordance with the templates and clearly written, is it sufficiently 
detailed and comprehensively described and are the examples in agreement 
with the specification?). Comments can be made on the specification as a 
whole or on specific parts.

If you do not feel experienced enough to comment on this document, but 
know colleagues who are, please feel free to forward this message to 
them. There is no requirement that people commenting should have had any 
prior contact with the PSI.

Please send your comments by e-mail directly to 
syl...@un... before*April 8th, 2024*.

Thank you very much in advance for your help in improving PSI standards.

Best wishes.

Professor Sylvie RICARD-BLUM - PSI Editor
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...

[Psidev-ms-dev] HUPO-PSI Specification document mzPAF format - 45-day public review

[Sylvie R. <syl...@un...>]

Dear colleagues, dear members of the HUPO-PSI community,

The HUPO Proteomics Standards Initiative (PSI) develops standards for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of activities).

The Mass Spectrometry and Proteomics Informatics PSI working groups have 
submitted a new recommendation, the PSI Peak Annotation Format (mzPAF) 
consideration and review as a PSI standard. This document presents a 
specification for a fragment ion peak annotation format for mass 
spectra, focused on peptides. This provides a standardized format for 
describing the origin of fragment ions to be used in spectral libraries, 
other formats that aim to describe fragment ions, and software tools 
that annotate fragment ions.

After having passed a 14-day review of the PSI steering group and having 
been revised as requested by the internal reviewers, the proposed 
document, Draft 10 of Version 1.0, now goes through the 45-day public 
and external review until *April 18th, 2023*. The current draft 
specification (.docx) is attached to this e-mail. Further information, 
including any updates to this document, implementations, and examples is 
available in the GitHub repository: https://github.com/HUPO-PSI/mzPAF 
and at https://psidev.info/mzPAF.

This message is to encourage you to contribute to the standards 
development activity by commenting on the document. We invite both 
positive and negative comments on the relevance, correctness, clarity 
and appropriateness of the specification (e.g. is it presented in 
accordance with the templates and clearly written, is it sufficiently 
detailed and comprehensively described and are the examples in agreement 
with the specification?). Comments can be made on the specification as a 
whole or on specific parts.

If you do not feel experienced enough to comment on this document, but 
know colleagues who are, please feel free to forward this message to 
them. There is no requirement that people commenting should have had any 
prior contact with the PSI.

Please send comments by e-mail directly to 
syl...@un... before*April 18th, 2023*.

Thank you very much in advance for your valuable help.

Best regards.

Professor Sylvie RICARD-BLUM - PSI Editor
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...

[Psidev-ms-dev] HUPO PSI Specification document mzQC format - 60-day public review

[Sylvie R. <syl...@un...>]

Dear colleagues, dear members of the HUPO-PSI community,

The HUPO Proteomics Standards Initiative (PSI) develops standards for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of activities).

The mzQC specification (Reporting and exchange format for mass 
spectrometry quality control data) has been submitted to the PSI 
Document Process for consideration and review as a PSI standard. This 
specification defines the mzQC file format to report and exchange 
quality-related information for a mass spectrometry experiment, 
associated analysis results, or collections thereof.

After having passed a 30-day review of the PSI steering group and having 
been revised as requested by the internal reviewers, the proposed 
document, version 1.0.0 DRAFT v3, now goes through 60-day public 
comments and external review phase until September 8th, 2022. The .docx 
and .pdf files are attached to this e-mail, and more documentation is 
available on the GitHub page (https://github.com/HUPO-PSI/mzQC/) and on 
the corresponding PSI web page ((https://psidev.info/mzqc).

This message is to encourage you to contribute to the standards 
development activity by commenting on the document. We invite both 
positive and negative comments on the relevance, correctness, clarity 
and appropriateness of the specification (e.g. is it presented in 
accordance with the templates and clearly written, is it sufficiently 
detailed and comprehensively described and are the examples in agreement 
with the specification?). Comments can be made on the specification as a 
whole or on specific parts.

If you do not feel experienced enough to comment on this document, but 
know colleagues who are, please feel free to forward this message to 
them. There is no requirement that people commenting should have had any 
prior contact with the PSI.

*Please send comments by e-mail directly to 
syl...@un...* *before September 8th, 2022*.

Thank you very much in advance for your valuable help.

Best regards.

Professor Sylvie RICARD-BLUM - PSI Editor
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...

Re: [Psidev-ms-dev] [Psi-announce] PSI DocProc minor update 1.1.2

[Juan A. V. <ju...@eb...>]

Hi Martin,

Everything fine. Thanks a lot for this.

Cheers,

Juan Antionio



> On 26 Apr 2021, at 15:05, Martin Eisenacher <mar...@ru...> wrote:
> 
> Dear colleagues,
> dear persons interested in the PSI developments,
> 
> a minor update of the PSI DocProc definition has been agreed to by the
> steering committee.
> 
> It mentions "online document editing" systems for public review / removed
> the mentioning of the 
> insecure "comment" function on psidev.info website, changes to shortened
> public and 
> invited review phase from 60 to 45 days; changes the license model from
> "Copyright" to "CC-BY-NC 4.0".
> 
> It has to go through a 14-day public review, after which its status could be
> changed to FINAL.
> I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to
> 1.1.1, so please add or 
> comment until May 10th!
> 
>  Thank you
>       Martin
> --
> PD DR. MARTIN EISENACHER
> Department Leader
> DEPARTMENT Medical Bioinformatics
> Medizinisches Proteom-Center
> Medical Faculty
> &
> Medical Proteome Analysis
> Center for Proteindiagnostics (PRODI)
> 
> Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum
> Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496
> E-mail mar...@ru...
> www.medizinisches-proteom-center.de
> 
> <20210426_PSI_Document_Process_ver_1.1.2_PREFINAL_DIFF.docx>_______________________________________________
> Psi-announce mailing list
> Psi...@eb...
> https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

Re: [Psidev-ms-dev] PSI DocProc minor update 1.1.2

[Eric D. <ede...@sy...>]

This looks good to me, thanks!

-----Original Message-----
From: Martin Eisenacher via Psidev-ms-dev
<psi...@li...>
Sent: Monday, April 26, 2021 7:06 AM
To: psi...@li...;
psi...@li...;
psi...@li...; psi...@eb...
Cc: Martin Eisenacher <mar...@ru...>
Subject: [Psidev-ms-dev] PSI DocProc minor update 1.1.2

Dear colleagues,
dear persons interested in the PSI developments,

a minor update of the PSI DocProc definition has been agreed to by the
steering committee.

It mentions "online document editing" systems for public review / removed
the mentioning of the insecure "comment" function on psidev.info website,
changes to shortened public and invited review phase from 60 to 45 days;
changes the license model from "Copyright" to "CC-BY-NC 4.0".

It has to go through a 14-day public review, after which its status could
be changed to FINAL.
I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to
1.1.1, so please add or comment until May 10th!

  Thank you
       Martin
--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Medical Faculty
&
Medical Proteome Analysis
Center for Proteindiagnostics (PRODI)

Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum Fon +49
(0)234 32-18104 | Fax +49 (0)234 32-14496 E-mail mar...@ru...
www.medizinisches-proteom-center.de

[Psidev-ms-dev] PSI DocProc minor update 1.1.2

[Martin E. <mar...@ru...>]

Dear colleagues,
dear persons interested in the PSI developments,

a minor update of the PSI DocProc definition has been agreed to by the
steering committee.

It mentions "online document editing" systems for public review / removed
the mentioning of the 
insecure "comment" function on psidev.info website, changes to shortened
public and 
invited review phase from 60 to 45 days; changes the license model from
"Copyright" to "CC-BY-NC 4.0".

It has to go through a 14-day public review, after which its status could be
changed to FINAL.
I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to
1.1.1, so please add or 
comment until May 10th!

  Thank you
       Martin
--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Medical Faculty
&
Medical Proteome Analysis
Center for Proteindiagnostics (PRODI)

Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum
Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496
E-mail mar...@ru...
www.medizinisches-proteom-center.de

[Psidev-ms-dev] HUPO PSI specification: MAGETAB and SDRF for Proteomics - 60-day public review

[Sylvie R. <syl...@un...>]

Dear colleague, dear member of the Proteomics community,

The HUPO Proteomics Standards Initiative (PSI) develops standards for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of PSI activities).

The PSI Mass Spectrometry and Proteomics Informatics Working Groups have 
submitted to the PSI document process a document presenting a 
specification for a sample metadata annotation of proteomics 
experiments. The document is entitled “MAGE-TAB Proteomics: Sample and 
Data Relationship Format (SDRF) for Proteomics” version 1.0.
After having passed a 30-day review of the PSI steering group and being 
revised, the proposed document now goes through 60-day public comments 
and external review phase until June 30, 2021.

- The .docx file " is attached to this e-mail.
- Further detailed information, including any updates to this document, 
implementations, and examples is available at 
https://github.com/bigbio/proteomics-metadata-standard.
- The PSI web page for the document is 
https://www.psidev.info/magetab-and-sdrf-proteomics

This message is to encourage you to contribute to the standards 
development activity by commenting on the document. We invite both 
positive and negative comments on the relevance, correctness, clarity 
and appropriateness of the specification (e.g. is it presented in 
accordance with the templates and clearly written, is it sufficiently 
detailed and comprehensively described and are the examples in agreement 
with the specification?). Comments can be made on the specification as a 
whole or on specific parts.

If you do not feel experienced enough to comment on this document, but 
know colleagues who are, please feel free to forward this message to 
them. There is no requirement that people commenting should have had any 
prior contact with the PSI.

*Please send comments by e-mail directly to 
syl...@un... before June 30, 2021.*

Thank you very much in advance for your valuable help.

Kind regards.

Professor Sylvie RICARD-BLUM, *HUPO-PSI Editor*
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...

[Psidev-ms-dev] HUPO PSI specification update MI-TAB 2.8 - 30-days public review

[Martin E. <mar...@ru...>]

Dear colleagues,



Please forward this request for public review into interested communities!



The HUPO Proteomics Standards Initiative (PSI) develops standards  for

documentation and storage of Proteomics data (see  http://www.psidev.info

for an overview of activities).



An updated specification document of PSI-MI TAB (version 2.8) has been

submitted to the PSI document process.

Aims of format and update: The ability to display molecular interactions in

a single, unified PSI-MI XML format represented a milestone in the field

of molecular interactions. A tab-delimited format, MITAB, has proven more

suitable for users requiring a simple, human-readable configuration.

Implementation of these standards by all leading molecular interaction

databases has considerably contributed to data exchange, representation

and comparison. PSI-MI TAB format and PSI-MI controlled vocabulary have been

extended to include additional terms representing aspects of causal 
interactions

for the representation and dissemination of signalling information. PSI-MITAB 
2.7

has been extended by adding four more columns allowing the description of

signalling data and, therefore, updated to the new PSI-MITAB 2.8 version



Specification document, CV terms and use case example:

attached to https://psidev.info/mi-tab-28-in-docproc



The proposed document version 2.8.0 DRAFT now goes

through a 30-day public comments and external review phase until May 30th, 
2021.



This message is to encourage you to contribute to the standards development 
activity by commenting

on the document. We invite both positive and negative comments on the 
relevance, correctness,

clarity and appropriateness of the specification (e.g. is it presented in 
accordance with the

templates and clearly written, is it sufficiently detailed and comprehensively 
described and

are the examples in agreement with the specification?).

Comments can be made on the specification as a whole or on specific parts.



If you do not feel experienced enough to comment on this document, but know 
colleagues

who are, please feel free to forward this message to them. There is no 
requirement that

people commenting should have had any prior contact with the PSI.



Please send comments by e-mail directly to me until May 30th, 2021.



Thank you very much in advance for your valuable help!



  Best regards

      Martin Eisenacher (PSI Editor)



--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Medical Faculty

&

Medical Proteome Analysis

Center for Proteindiagnostics (PRODI)



Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum

Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496

E-mail mar...@ru... <mailto:mar...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] HUPO PSI Specification document Proforma v2 - 60-days public review

[Sylvie R. <syl...@un...>]

Dear colleagues, dear members of the Proteomics community,

The HUPO Proteomics Standards Initiative (PSI) develops standards for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of activities).

The *specification document* *ProForma, Proteoform and Peptidoform 
Notation* (version 2, draft 12) has been submitted to the PSI document 
process. It aims to standardise the representation of 
proteoforms/peptidoforms supporting the main proteomics approaches, 
including both bottom-up (focused on peptides/peptidoforms) and top down 
(focused on proteins/proteoforms) approaches.

*Specification document*: http://www.psidev.info/proforma-v2
*Use case examples*: https://github.com/HUPO-PSI/ProForma/)
*Development background*: https://github.com/HUPO-PSI/ProForma

After having passed a 30-day review of the PSI steering group with minor 
changes, the proposed document version 2.0.0 DRAFT now goes through 
*60-day public comments and external review phase until February 27th, 
2021*.

This message is to encourage you to contribute to the standards 
development activity by commenting on the document. We invite both 
positive and negative comments on the relevance, correctness, clarity 
and appropriateness of the specification (e.g. is it presented in 
accordance with the templates and clearly written, is it sufficiently 
detailed and comprehensively described and are the examples in agreement 
with the specification?). Comments can be made on the specification as a 
whole or on specific parts.

If you do not feel experienced enough to comment on this document, but 
know colleagues who are, please feel free to forward this message to 
them. There is no requirement that people commenting should have had any 
prior contact with the PSI.

*Please send comments by e-mail directly to 
syl...@un... *before *February 27th, 2021.*

Thank you very much in advance for your valuable help.

Best regards.

Professor Sylvie RICARD-BLUM - *PSI Editor*
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...
http://www.icbms.fr
The French Society for Matrix Biology http://www.sfbmec.fr
The International Society for Matrix Biology http://ismb.org

[Psidev-ms-dev] HUPO PSI recommendation document (Universal Spectrum Identifier), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Mass Spectrometry community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

 <http://www.psidev.info> http://www.psidev.info for an overview of
activities).

 

A recommendation document specifying
the Universal Spectrum Identifier (USI)

has been submitted to the PSI document process.

 

Because it is not a file format, there is neither a Schema definition
nor XML / tab example files, but some practical examples of USIs from 

ProteomeXchange member DBs and others (included in the document).

 

Specification document:
https://github.com/HUPO-PSI/usi/blob/master/Specification/USI_SpecDoc_1.0.dr
aft07_2020-09-29.docx?raw=true

Use case examples: http://www.psidev.info/usi

(USIs used in repository URLs).

Development background:  <https://github.com/HUPO-PSI/usi>
https://github.com/HUPO-PSI/usi

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 7

now goes through 60-days public comments and external 

review phase (end: 18th December 2020).

 

Purpose of the standard (excerpt from the spec. doc.):
"This document presents a specification for a multi-part identifier 

of the form mzspec:<collection>:<msRun>:<indexType>:<indexNumber>:<optional
interpretation> 

for mass spectra so that they may be easily and universally referenced for 

subsequent access. The Universal Spectrum Identifier (USI) describes a 

virtual path to locate a spectrum plus a possible interpretation of that 

spectrum. The USI is being implemented at most ProteomeXchange partner 

repositories and can be freely used by any other software. While initially

implemented for the field of proteomics, its design is amenable to other 

fields that use mass spectrometers for analyte detection."

 

PLEASE SEND COMMENTS directly to mar...@ru...

for example regarding the following criteria:

 

- That it is well formed - that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is attached 

as well as available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Medical Faculty

&

Medical Proteome Analysis

Center for Proteindiagnostics (PRODI)

 

Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum

Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de

 



 

 

Re: [Psidev-ms-dev] webmaster@psidev.info? 550 No Such User Here

[Walzer <wa...@eb...>]

Hi Colin,

it is good you mailed here. I am not the admin, but I just checked and 
seems I can edit the 'Tools that implement mzIdentML' page. Just pass me 
the details for the two new entries and I'll add them.

cheers,

   mths

On 13/07/2020 09:45, Colin Combe wrote:
> Hi,
>
> I emailed web...@ps... to ask to have two pieces of software
> added to the list of tools that implement mzIdentML at
> http://www.psidev.info/tools-implementing-mzidentml.
>
> The email was returned with the message 'No Such User Here'. Who should
> I ask about this or what's the correct place to bring it up?
>
> Thanks for your help,
>
> Colin
>
> The University of Edinburgh is a charitable body, registered in 
> Scotland, with registration number SC005336.
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

-- 
Mathias Walzer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Office: +44 (0)1223 494 2610
E-mail: wa...@eb...

[Psidev-ms-dev] webmaster@psidev.info? 550 No Such User Here

[Colin C. <col...@ed...>]

Hi,

I emailed web...@ps... to ask to have two pieces of software
added to the list of tools that implement mzIdentML at
http://www.psidev.info/tools-implementing-mzidentml.

The email was returned with the message 'No Such User Here'. Who should
I ask about this or what's the correct place to bring it up?

Thanks for your help,

Colin

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

Re: [Psidev-ms-dev] [EXT] RE: mzML - additional terms for ion mobility data

[Susan S. <Sus...@wa...>]

Thanks Eric, I know Hans and Ian well.  Hans is currently on leave and back next week when I’m on leave, hence my email to you.  He’s my usual source on these matters.  I have weekly meetings that both Ian and I attend on different projects, but I didn’t know that he was also involved in this, so now I have two go-to sources.  Thanks for the documentation I haven’t seen it previously but it is very useful, particularly as a follow up to the conversation I had yesterday with Matt Chambers on this topic.

Best wishes,

Sue.


Dr. Susan E. Slade
Principal Applications Chemist
Waters Corporation

phone +44 (0) 161 435 4302   mobile +44 (0) 7736 865448
web www.waters.com<http://www.waters.com/>     email sus...@wa...<mailto:sus...@wa...>

Micromass UK Limited is registered in England under No 3162904
Registered Office: Stamford Avenue,
Altrincham Road,
Wilmslow, SK9 4AX



From: Eric Deutsch <eri...@is...>
Sent: 22 May 2020 05:33
To: Mass spectrometry standard development <psi...@li...>; Susan Slade <Sus...@wa...>
Cc: Eric Deutsch <ede...@sy...>
Subject: [EXT] RE: [Psidev-ms-dev] mzML - additional terms for ion mobility data

ATTENTION: This email originated from outside of the organization. Please do not open any attachments or click any links unless you recognize the sender and know the content is safe.

Hi Sue, have you seen this draft document, attached? It has recently been shared with your colleagues Ian Reah and Hans Vissers, and they may be good sources of background information. If the contents do not answer all your questions, please do follow up.

Regards,
Eric


From: Susan Slade <Sus...@wa...<mailto:Sus...@wa...>>
Sent: Thursday, May 21, 2020 12:51 AM
To: psi...@li...<mailto:psi...@li...>
Subject: [Psidev-ms-dev] mzML - additional terms for ion mobility data

Good morning I am trying to find out details on the additional terms that are used in the current mzML schema to describe ion mobility information.  Could you please provide any documentation relating to this and if there are any differences between vendor outputs?

Thank you!

Best wishes,

Sue.


Dr. Susan E. Slade
Principal Applications Chemist
Waters Corporation

phone +44 (0) 161 435 4302   mobile +44 (0) 7736 865448
web www.waters.com<http://www.waters.com/>     email sus...@wa...<mailto:sus...@wa...>

Micromass UK Limited is registered in England under No 3162904
Registered Office: Stamford Avenue,
Altrincham Road,
Wilmslow, SK9 4AX



________________________________
The information in this email is confidential, and is intended solely for the addressee(s). Access to this email by anyone else is unauthorized and therefore prohibited. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and may be unlawful.

Re: [Psidev-ms-dev] mzML - additional terms for ion mobility data

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

Hi Sue, have you seen this draft document, attached? It has recently been
shared with your colleagues Ian Reah and Hans Vissers, and they may be good
sources of background information. If the contents do not answer all your
questions, please do follow up.



Regards,

Eric





*From:* Susan Slade <Sus...@wa...>
*Sent:* Thursday, May 21, 2020 12:51 AM
*To:* psi...@li...
*Subject:* [Psidev-ms-dev] mzML - additional terms for ion mobility data



Good morning I am trying to find out details on the additional terms that
are used in the current mzML schema to describe ion mobility information.
Could you please provide any documentation relating to this and if there
are any differences between vendor outputs?



Thank you!



Best wishes,



Sue.





*Dr. Susan E. Slade*

Principal Applications Chemist

*Waters Corporation*



*phone* +44 (0) 161 435 4302   *mobile *+44 (0) 7736 865448

*web* www.waters.com     *email* sus...@wa...



Micromass UK Limited is registered in England under No 3162904

Registered Office: Stamford Avenue,

Altrincham Road,

Wilmslow, SK9 4AX






------------------------------

The information in this email is confidential, and is intended solely for
the addressee(s). Access to this email by anyone else is unauthorized and
therefore prohibited. If you are not the intended recipient you are
notified that disclosing, copying, distributing or taking any action in
reliance on the contents of this information is strictly prohibited and may
be unlawful.

[Psidev-ms-dev] mzML - additional terms for ion mobility data

[Susan S. <Sus...@wa...>]

Good morning I am trying to find out details on the additional terms that are used in the current mzML schema to describe ion mobility information.  Could you please provide any documentation relating to this and if there are any differences between vendor outputs?

Thank you!

Best wishes,

Sue.


Dr. Susan E. Slade
Principal Applications Chemist
Waters Corporation

phone +44 (0) 161 435 4302   mobile +44 (0) 7736 865448
web www.waters.com<http://www.waters.com/>     email sus...@wa...<mailto:sus...@wa...>

Micromass UK Limited is registered in England under No 3162904
Registered Office: Stamford Avenue,
Altrincham Road,
Wilmslow, SK9 4AX



======================================================================
The information in this email is confidential, and is intended solely for the addressee(s). Access to this email by anyone else is unauthorized and therefore prohibited. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and may be unlawful.

Re: [Psidev-ms-dev] New term needed for timsTOF Flex instrument

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

I don’t know much about this instrument itself, but seems reasonable to me.



My only suggested change is to remove the apostrophe. It is incorrectly
used and unnecessary. But I also notice that all Bruker instruments have
this (so Juan was just following the pattern, okay). But I vote that we fix
this everywhere in the CV. i.e. s/Daltonics’/Daltonics/g



Thermo doesn’t have apostrophes, Waters doesn’t have apostrophes. I assume
the intent was to imply a possessive, but I propose we strip that for all
Bruker models. It’s only in the definition anyway, so should not affect
software.



Thanks,

Eric





*From:* Juan Antonio Vizcaino <ju...@eb...>
*Sent:* Thursday, March 5, 2020 3:46 AM
*To:* psi...@li...
*Cc:* psi...@li...; Mass spectrometry standard
development <psi...@li...>; Deepti Jaiswal Kundu <
ja...@eb...>
*Subject:* [Psidev-ms-dev] New term needed for timsTOF Flex instrument



Dear all,



We have a submitter that has generated data coming from an timsTOF fleX
instrument.



This term is not yet in the PSI MS CV. The one that is there is for the
timsTOF Pro (MS:1003005). So I am proposing to add it to the CV.



[Term]
id: MS:1xxxxx
name: timsTOF fleX
def: "Bruker Daltonics' timsTOF fleX." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model





Thanks in advance,



Juan

[Psidev-ms-dev] New term needed for timsTOF Flex instrument

[Juan A. V. <ju...@eb...>]

Dear all,

We have a submitter that has generated data coming from an timsTOF fleX instrument. 

This term is not yet in the PSI MS CV. The one that is there is for the timsTOF Pro (MS:1003005). So I am proposing to add it to the CV.

[Term]
id: MS:1xxxxx
name: timsTOF fleX
def: "Bruker Daltonics' timsTOF fleX." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model


Thanks in advance,

Juan

[Psidev-ms-dev] New version 4.1.35 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new and changed terms for the
version 4.1.35 of the psi-ms.obo file,
which can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.35 of psi-ms.obo:
=============================================
[Term]
id: MS:1003083
name: raw data file
def: "Data file that contains original data as generated by an 
instrument, although not necessarily in the original data format (i.e. 
an original raw file converted to a different format is still a raw data 
file)." [PSI:MS]
is_a: MS:1000577 ! source data file

[Term]
id: MS:1003084
name: processed data file
def: "File that contains data that has been substantially processed or 
transformed from what was originally acquired by an instrument." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000577 ! source data file

[Term]
id: MS:1003085
name: previous MSn-1 scan precursor intensity
def: "Intensity of the precursor ion in the previous MSn-1 scan (prior 
in time to the referencing MSn scan). For an MS2 scan, this means the 
MS1 precursor intensity. It is unspecified on whether this is an apex 
(across m/z) intensity, integrated (across m/z) intensity, a centroided 
peak intensity of unknown origin, or even summed across several 
isotopes." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001141 ! intensity of precursor ion
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003086
name: precursor apex intensity
def: "Intensity of the precursor ion current as measured by its apex 
point over time and m/z. It is unspecified whether this is the intensity 
of the selected isotope or the most intense isotope." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001141 ! intensity of precursor ion
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003087
name: supported by repository but incomplete data and/or metadata
def: "Dataset for which the identifications and/or spectra/traces are in 
formats that can be parsed by the hosting data repository such that 
internal references between identifications and spectra/traces are 
preserved and browsable at the repository. However, some metadata is not 
properly described due to lack of CV terms or some auxiliary data, such 
as data used to create a spectral library or a sequence search database 
crucial to the analysis, is not available." [PSI:PI]
is_a: MS:1002844 ! Experiment additional parameter

[Term]
id: MS:1003088
name: truncation and zlib compression
def: "Compression using truncation and zlib." 
[https://github.com/biospi/pwiz]
xref: value-type:xsd\:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1003089
name: truncation, delta prediction and zlib compression
def: "Compression using truncation, delta prediction and zlib." 
[https://github.com/biospi/pwiz]
xref: value-type:xsd\:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1003090
name: truncation, linear prediction and zlib compression
def: "Compression using truncation, linear prediction and zlib." 
[https://github.com/biospi/pwiz]
xref: value-type:xsd\:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type


Changed CV terms in version 4.1.35 of psi-ms.obo:
=================================================
************ Added is_a relation
[Term]
id: MS:1000224
name: molecular mass
def: "Mass of a molecule measured in unified atomic mass units (u or 
Da)." [https://en.wikipedia.org/wiki/Molecular_mass]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000861 ! molecular entity property
relationship: has_units UO:0000002 ! mass unit

************ renamed and added relationship: part_of MS:1002806 ! ion
[Term]
id: MS:1000507
name: ion property
def: "Nonphysical characteristic attributed to an ion." [PSI:MS]
relationship: part_of MS:1002806 ! ion

************ Added is_a relation
[Term]
id: MS:1002959
name: isomer
def: "One of several species (or molecular entities) that have the same 
atomic composition (molecular formula) but different line formulae or 
different stereochemical formulae." 
[https://goldbook.iupac.org/html/I/I03289.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000859 ! molecule

************ renamed and added is_a relation
[Term]
id: MS:1000577
name: source data file
def: "Data file from which an entity is sourced." [PSI:MS]
synonym: "source file" EXACT []
relationship: part_of MS:1001458 ! spectrum generation information
is_a: MS:1000499 ! spectrum attribute

************ changed the definition
[Term]
id: MS:1002856
name: Supported dataset by repository
def: "Dataset for which the identifications and/or spectra/traces are in 
formats that can be parsed by the hosting data repository such that 
internal references between identifications and spectra/traces are 
preserved and browsable at the repository. This is usually called a 
complete submission." [PSI:PI]
is_a: MS:1002844 ! Experiment additional parameter

[Term]
id: MS:1002857
name: Unsupported dataset by repository
def: "Dataset for which the identifications and/or spectra/traces are in 
formats that cannot be parsed by the hosting data repository and thus 
internal references between identifications and spectra/traces are not 
browsable at the repository. This is usually called a partial 
submission." [PSI:PI]
is_a: MS:1002844 ! Experiment additional parameter

Best Regards,
Gerhard

-- 

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

*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>

[Psidev-ms-dev] New version 4.1.33 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new terms for the version 4.1.33 of the psi-ms.obo file,
which can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains new terms for spectral libraries and a term for the MS-DIAL 
software.

We also reorganized part of the CV, renamed some terms,
reactivated some obsolete terms and made some definitions more clear.


New CV terms in version 4.1.33 of psi-ms.obo:
=============================================
[Term]
id: MS:1003033
name: molecular entity attribute
def: "Non-inherent characteristic attributed to a molecular entity." 
[PSI:PI]
relationship: part_of MS:1000881 ! molecular entity

[Term]
id: MS:1003034
name: atom
def: "Smallest constituent unit of ordinary matter that constitutes a 
chemical element." [https://en.wikipedia.org/wiki/Atom]
is_a: MS:1000881 ! molecular entity

[Term]
id: MS:1003035
name: small molecule
def: "Low molecular weight (< 900 daltons) organic compound that may 
regulate a biological process." 
[https://en.wikipedia.org/wiki/Small_molecule]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003036
name: metabolite
def: "Small molecule that is the intermediate end product of 
metabolism." [https://en.wikipedia.org/wiki/Metabolite]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003037
name: ribonucleotide
def: "Nucleotide containing ribose as its pentose component." 
[https://en.wikipedia.org/wiki/Ribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003038
name: deoxyribonucleotide
def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." 
[https://en.wikipedia.org/wiki/Deoxyribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003039
name: amino acid
def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) 
functional groups, along with a side chain (R group) that is specific to 
each amino acid." [https://en.wikipedia.org/wiki/Amino_acid]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003040
name: monosaccharide
def: "Simplest form of sugar and the most basic units of carbohydrate 
that cannot be further hydrolyzed to a simpler molecule." 
[https://en.wikipedia.org/wiki/Monosaccharide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003041
name: nucleic acid
def: "Molecule composed of a chain of nucleotides." 
[https://en.wikipedia.org/wiki/Nucleic_acid]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003042
name: polysaccharide
def: "Polymeric carbohydrate molecules composed of long chains of 
monosaccharide units bound together by glycosidic linkages." 
[https://en.wikipedia.org/wiki/Polysaccharide]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003043
name: number of residues
def: "Number of amino acid residues in a peptide, commonly referred to 
as the peptide length." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003044
name: number of missed cleavages
def: "Number of amino acid residue bonds that should have been cleaved 
by the cleavage agent used, but were not." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003045
name: peptide-to-protein mapping
def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003046
name: peptide-to-protein mapping attribute
def: "Nonphysical characteristic attributed to the result of 
peptide-to-protein mapping." [PSI:PI]
is_a: MS:1003045 ! peptide-to-protein mapping

[Term]
id: MS:1003047
name: protein sequence offset
def: "Offset in number of residues from the n terminus of the protein at 
which the peptide begins. Use 1 when the first residue of the peptide 
sequence is the first residue of the protein sequence." [PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003048
name: number of enzymatic termini
def: "Total number of termini that match standard rules for the cleavage 
agent, 2 when both termini match cleavage agent rules, 1 when only one 
terminus does, and 0 if neither terminus matches cleavage agent rules." 
[PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003049
name: peptidoform
def: "Peptide that contains zero or more mass modifications on the 
termini or side chains of its amino acid residues, and may be 
differentiated from other peptidoforms with the same peptide sequence 
but different mass modification configurations." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003050
name: peptidoform attribute
def: "Non-inherent characteristic attributed to a peptidoform." [PSI:PI]
relationship: part_of MS:1003049 ! peptidoform

[Term]
id: MS:1003051
name: peptidoform ion
def: "Peptidoform that has formed an adduct with an ion, thereby 
rendering it potentially detectable with a mass spectrometer. Commonly 
called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI]
is_a: MS:1003049 ! peptidoform
synonym: "precursor" RELATED []
synonym: "precursor ion" RELATED []
synonym: "parent ion" RELATED []

[Term]
id: MS:1003052
name: peptidoform ion property
def: "Inherent or measurable characteristic of a peptidoform ion." [PSI:PI]
relationship: part_of MS:1003051 ! peptidoform ion

[Term]
id: MS:1003053
name: theoretical monoisotopic m/z
def: "Mass-to-charge ratio of a peptidoform ion composed of the most 
common isotope of each atom computed from the putative knowledge of its 
molecular constituents." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003054
name: theoretical average m/z
def: "Mass-to-charge ratio of a peptidoform ion computed from the 
putative knowledge of its molecular constituents, averaged over the 
distribution of naturally occurring isotopes." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003055
name: adduct
def: "Product of a direct addition of two or more distinct molecules, 
resulting in a single reaction product containing all atoms of all 
components. The resultant is considered a distinct molecular species." 
[https://en.wikipedia.org/wiki/Adduct]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003056
name: adduct ion property
def: "Physical measurable characteristic of an adduct ion." [PSI:PI]
relationship: part_of MS:1000353 ! adduct ion

[Term]
id: MS:1003057
name: scan number
def: "Ordinal number of the scan indicating its order of acquisition 
within a mass spectrometry acquisition run." [PSI:PI]
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1003058
name: spectrum property
def: "Inherent or measurable characteristic of a spectrum." [PSI:PI]
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1003059
name: number of peaks
def: "Number of peaks or features in a spectrum. For a peak-picked 
spectrum, this will correspond to the number of data points. For a 
non-peak-picked spectrum, this corresponds to the number of features 
discernable in the spectrum, which will be fewer than the number of data 
points." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003060
name: number of data points
def: "Number of data points in a spectrum. For a peak-picked spectrum, 
this will correspond to the number of peaks. For a non-peak-picked 
spectrum, this corresponds to the number of values in the data array, 
which are not all peaks." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003061
name: spectrum name
def: "Label attached to a spectrum uniquely naming it within a 
collection of spectra, often in a spectral library. It is often a string 
combination of peptide sequence, charge, mass modifications, collision 
energy, but will obviously be different for small molecules or 
unidentified spectra. It must be unique within a collection." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003062
name: spectrum index
def: "Integer index value associated with a spectrum within a collection 
of spectra, often in a spectral library. By custom, index counters 
should begin with 0." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003063
name: universal spectrum identifier
def: "PSI universal spectrum identifier (USI) multipart key that 
uniquely identifies a spectrum available in a ProteomeXchange datasets 
or spectral library." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003064
name: spectrum aggregation attribute
def: "Non-inherent characteristic attributed to spectrum aggregation." 
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003065
name: spectrum aggregation type
def: "Categorization of a spectrum based on its type of aggregation 
(e.g., individual spectrum, consensus spectrum, best replicate spectrum, 
etc.)." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003066
name: singleton spectrum
def: "Spectrum that is not the result of some aggregation process." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003067
name: consensus spectrum
def: "Spectrum that is the result of merging several replicate spectra 
to form a spectrum that is more representative of its class and ideally 
less noisy that any of its source replicates." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003068
name: best replicate spectrum
def: "Spectrum that is considered the most representative from a pool of 
replicate spectra." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003069
name: number of replicate spectra available
def: "Number of replicate spectra available for use during the 
aggregation process." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003070
name: number of replicate spectra used
def: "Number of replicate spectra used during the aggregation process. 
This is generally applicable when there are many replicates available, 
but some are discarded as being low S/N, blended, or otherwise 
unsuitable, and the remaining set is then used for merging via a 
consensus algorithm." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003071
name: spectrum origin attribute
def: "Non-inherent characteristic attributed to spectrum aggregation." 
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003072
name: spectrum origin type
def: "Categorization of a spectrum based on its origin (e.g., observed 
spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI:PI]
is_a: MS:1003071 ! spectrum origin attribute

[Term]
id: MS:1003073
name: observed spectrum
def: "Spectrum that originates from an analysis attempt of a single 
analyte species on an instrument." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003074
name: predicted spectrum
def: "Spectrum that originates from a compututational algorithm that 
attempts to predict spectra." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003075
name: demultiplexed spectrum
def: "Spectrum that originates from an attempted extraction of a single 
ion spieces from a multiplexed spectrum that contains multiple ion 
species." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003076
name: uninterpreted spectrum
def: "Spectrum provided in the form of plain numerical values without 
any information pertaining to the interpretation of features." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003077
name: interpreted spectrum
def: "Spectrum provided in a form where specific features of the 
spectrum are interpreted to provide putative explanations for some 
feature." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003078
name: interpreted spectrum attribute
def: "Non-inherent characteristic attributed to an interpreted 
spectrum." [PSI:PI]
relationship: part_of MS:1003077 ! interpreted spectrum

[Term]
id: MS:1003079
name: total unassigned intensity fraction
def: "Fraction of intensity summed from all unassigned peaks divided by 
the intensity summed from all peaks in the spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003080
name: top 20 peak unassigned intensity fraction
def: "Fraction of intensity summed from unassigned peaks among the top 
20 divided by the intensity summed from all top 20 peaks in the 
spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003081
name: unidentified modification monoisotopic mass delta
def: "Monoisotopic mass delta in Daltons of an amino acid residue 
modification whose atomic composition or molecular identity has not been 
determined. This term should not be used for modifications of known 
molecular identity such as those available in Unimod, RESID or PSI-MOD. 
This term MUST NOT be used inside the <Modification> element in 
mzIdentML." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
xref: value-type:xsd\:double "The allowed value-type for this CV term."
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1003082
name: MS-DIAL
def: "Data processing software for untargeted metabolomics and 
lipidomics that supports multiple instruments and MS vendors." 
[PMID:25938372]
is_a: MS:1002878 ! small molecule software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 

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

*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>

Re: [Psidev-ms-dev] Release candidate 4.1.33_rc1 of psi-ms.obo

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

Many thanks for putting this together, Gerhard. Here are some suggested
refinements or corrections:



[Term]

id: MS:1003065

name: spectrum aggregation type

def: "Categorization of a spectrum based on its type of aggregation (e.g.,
individual spectrum, consensus spectrum, best replicate spectrum, etc.)."
[PSI:PI]

is_a: MS:1003064 ! spectrum aggregation attribute



[Term]

id: MS:1003072

name: spectrum origin type

def: "Categorization of a spectrum based on its origin (e.g., observed
spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI-PI]

is_a: MS:1003071 ! spectrum origin attribute



[Term]

id: MS:1003033

name: molecular entity attribute

def: "Non-inherent characteristic attributed to a molecular entity."
[PSI:PI]

relationship: part_of MS:1000881 ! molecular entity



[Term]

id: MS:1003050

name: peptidoform attribute

def: "Non-inherent characteristic attributed to a peptidoform." [PSI:PI]

relationship: part_of MS:1003049 ! peptidoform





[Term]

id: MS:1003052

name: peptidoform ion property

def: "Inherent or measurable characteristic of a peptidoform ion." [PSI:PI]

relationship: part_of MS:1003051 ! peptidoform ion



[Term]

id: MS:1003058

name: spectrum property

def: " Inherent or measurable characteristic of a spectrum." [PSI:PI]

relationship: part_of MS:1000442 ! spectrum



[Term]

id: MS:1003064

name: spectrum aggregation attribute

def: "Non-inherent characteristic attributed to spectrum aggregation."
[PSI:PI]

is_a: MS:1000499 ! spectrum attribute



[Term]

id: MS:1003071

name: spectrum origin attribute

def: "Non-inherent characteristic attributed to spectrum aggregation."
[PSI:PI]

is_a: MS:1000499 ! spectrum attribute



[Term]

id: MS:1003078

name: interpreted spectrum attribute

def: "Non-inherent characteristic attributed to an interpreted spectrum."
[PSI:PI]

relationship: part_of MS:1003077 ! interpreted spectrum



[Term]

id: MS:1003082

name: MS-DIAL

def: "Data processing software for untargeted metabolomics and lipidomics
that supports multiple instruments and MS vendors." [PMID:25938372]

is_a: MS:1002878 ! small molecule software

is_a: MS:1001457 ! data processing software







*From:* Gerhard Mayer via Psidev-ms-dev <psi...@li...>

*Sent:* Thursday, January 16, 2020 12:10 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Cc:* Gerhard Mayer <may...@ru...>
*Subject:* [Psidev-ms-dev] Release candidate 4.1.33_rc1 of psi-ms.obo



Dear proteomics/metabolomics community,

following are the new terms for the release version 4.1.33_rc1 of
the psi-ms.obo file.

It contains new terms for spectral libraries
and a term for the MS-DIAL software.

We also reorganized part of the CV, renamed some terms,
reactivated some obsolete terms and made some definitions more clear.
Please unpack and diff the two files to see the detailed changes.


New CV terms in version 4.1.33_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003033
name: molecular entity attribute
def: "A nonphysical characteristic attributed to a molecular entity."
[PSI:PI]
relationship: part_of MS:1000881 ! molecular entity

[Term]
id: MS:1003034
name: atom
def: "Smallest constituent unit of ordinary matter that constitutes a
chemical element." [https://en.wikipedia.org/wiki/Atom]
is_a: MS:1000881 ! molecular entity

[Term]
id: MS:1003035
name: small molecule
def: "Low molecular weight (< 900 daltons) organic compound that may
regulate a biological process." [
https://en.wikipedia.org/wiki/Small_molecule]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003036
name: metabolite
def: "Small molecule that is the intermediate end product of metabolism." [
https://en.wikipedia.org/wiki/Metabolite]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003037
name: ribonucleotide
def: "Nucleotide containing ribose as its pentose component." [
https://en.wikipedia.org/wiki/Ribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003038
name: deoxyribonucleotide
def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." [
https://en.wikipedia.org/wiki/Deoxyribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003039
name: amino acid
def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH)
functional groups, along with a side chain (R group) that is specific to
each amino acid." [https://en.wikipedia.org/wiki/Amino_acid]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003040
name: monosaccharide
def: "Simplest form of sugar and the most basic units of carbohydrate that
cannot be further hydrolyzed to a simpler molecule." [
https://en.wikipedia.org/wiki/Monosaccharide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003041
name: nucleic acid
def: "Molecule composed of a chain of nucleotides." [
https://en.wikipedia.org/wiki/Nucleic_acid]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003042
name: polysaccharide
def: "Polymeric carbohydrate molecules composed of long chains of
monosaccharide units bound together by glycosidic linkages." [
https://en.wikipedia.org/wiki/Polysaccharide]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003043
name: number of residues
def: "Number of amino acid residues in a peptide, commonly referred to as
the peptide length." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003044
name: number of missed cleavages
def: "Number of amino acid residue bonds that should have been cleaved by
the cleavage agent used, but were not." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003045
name: peptide-to-protein mapping
def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003046
name: peptide-to-protein mapping attribute
def: "Nonphysical characteristic attributed to the result of
peptide-to-protein mapping." [PSI:PI]
is_a: MS:1003045 ! peptide-to-protein mapping

[Term]
id: MS:1003047
name: protein sequence offset
def: "Offset in number of residues from the n terminus of the protein at
which the peptide begins. Use 1 when the first residue of the peptide
sequence is the first residue of the protein sequence." [PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003048
name: number of enzymatic termini
def: "Total number of termini that match standard rules for the cleavage
agent, 2 when both termini match cleavage agent rules, 1 when only one
terminus does, and 0 if neither terminus matches cleavage agent rules."
[PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003049
name: peptidoform
def: "Peptide that contains zero or more mass modifications on the termini
or side chains of its amino acid residues, and may be differentiated from
other peptidoforms with the same peptide sequence but different mass
modification configurations." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003050
name: peptidoform attribute
def: "Nonphysical characteristic attributed to a peptidoform." [PSI:PI]
relationship: part_of MS:1003049 ! peptidoform

[Term]
id: MS:1003051
name: peptidoform ion
def: "Peptidoform that has formed an adduct with an ion, thereby rendering
it potentially detectable with a mass spectrometer. Commonly called a
'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI]
is_a: MS:1003049 ! peptidoform
synonym: "precursor" RELATED []
synonym: "precursor ion" RELATED []
synonym: "parent ion" RELATED []

[Term]
id: MS:1003052
name: peptidoform ion property
def: "A physical characteristic of a peptidoform ion." [PSI:PI]
relationship: part_of MS:1003051 ! peptidoform ion

[Term]
id: MS:1003053
name: theoretical monoisotopic m/z
def: "Mass-to-charge ratio of a peptidoform ion composed of the most common
isotope of each atom computed from the putative knowledge of its molecular
constituents." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003054
name: theoretical average m/z
def: "Mass-to-charge ratio of a peptidoform ion computed from the putative
knowledge of its molecular constituents, averaged over the distribution of
naturally occurring isotopes." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003055
name: adduct
def: "Product of a direct addition of two or more distinct molecules,
resulting in a single reaction product containing all atoms of all
components. The resultant is considered a distinct molecular species." [
https://en.wikipedia.org/wiki/Adduct]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003056
name: adduct ion property
def: "Physical measurable characteristic of an adduct ion." [PSI:PI]
relationship: part_of MS:1000353 ! adduct ion

[Term]
id: MS:1003057
name: scan number
def: "Ordinal number of the scan indicating its order of acquisition within
a mass spectrometry acquisition run." [PSI:PI]
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1003058
name: spectrum property
def: "Physical measurable characteristic of a spectrum." [PSI:PI]
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1003059
name: number of peaks
def: "Number of peaks or features in a spectrum. For a peak-picked
spectrum, this will correspond to the number of data points. For a
non-peak-picked spectrum, this corresponds to the number of features
discernable in the spectrum, which will be fewer than the number of data
points." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003060
name: number of data points
def: "Number of data points in a spectrum. For a peak-picked spectrum, this
will correspond to the number of peaks. For a non-peak-picked spectrum,
this corresponds to the number of values in the data array, which are not
all peaks." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003061
name: spectrum name
def: "Label attached to a spectrum uniquely naming it within a collection
of spectra, often in a spectral library. It is often a string combination
of peptide sequence, charge, mass modifications, collision energy, but will
obviously be different for small molecules or unidentified spectra. It must
be unique within a collection." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003062
name: spectrum index
def: "Integer index value associated with a spectrum within a collection of
spectra, often in a spectral library. By custom, index counters should
begin with 0." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003063
name: universal spectrum identifier
def: "PSI universal spectrum identifier (USI) multipart key that uniquely
identifies a spectrum available in a ProteomeXchange datasets or spectral
library." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003064
name: spectrum aggregation attribute
def: "Nonphysical characteristic attributed to spectrum aggregation."
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003065
name: spectrum aggregation type
def: "Categorization of a spectrum based on the type of aggregation it is
based on (e.g., an individual spectrum, a consensus spectrum, best
replicate spectrum, etc.)." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003066
name: singleton spectrum
def: "Spectrum that is not the result of some aggregation process." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003067
name: consensus spectrum
def: "Spectrum that is the result of merging several replicate spectra to
form a spectrum that is more representative of its class and ideally less
noisy that any of its source replicates." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003068
name: best replicate spectrum
def: "Spectrum that is considered the most representative from a pool of
replicate spectra." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003069
name: number of replicate spectra available
def: "Number of replicate spectra available for use during the aggregation
process." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003070
name: number of replicate spectra used
def: "Number of replicate spectra used during the aggregation process. This
is generally applicable when there are many replicates available, but some
are discarded as being low S/N, blended, or otherwise unsuitable, and the
remaining set is then used for merging via a consensus algorithm." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003071
name: spectrum origin attribute
def: "Nonphysical characteristic attributed to spectrum aggregation."
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003072
name: spectrum origin type
def: "Categorization of a spectrum based on its type of aggregation (e.g.,
an individual spectrum, a consensus spectrum, best replicate spectrum,
etc.)." [PSI:PI]
is_a: MS:1003071 ! spectrum origin attribute

[Term]
id: MS:1003073
name: observed spectrum
def: "Spectrum that originates from an analysis attempt of a single analyte
species on an instrument." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003074
name: predicted spectrum
def: "Spectrum that originates from a compututational algorithm that
attempts to predict spectra." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003075
name: demultiplexed spectrum
def: "Spectrum that originates from an attempted extraction of a single ion
spieces from a multiplexed spectrum that contains multiple ion species."
[PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003076
name: uninterpreted spectrum
def: "Spectrum provided in the form of plain numerical values without any
information pertaining to the interpretation of features." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003077
name: interpreted spectrum
def: "Spectrum provided in a form where specific features of the spectrum
are interpreted to provide putative explanations for some feature." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003078
name: interpreted spectrum attribute
def: "Nonphysical characteristic attributed to an interpreted spectrum."
[PSI:PI]
relationship: part_of MS:1003077 ! interpreted spectrum

[Term]
id: MS:1003079
name: total unassigned intensity fraction
def: "Fraction of intensity summed from all unassigned peaks divided by the
intensity summed from all peaks in the spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003080
name: top 20 peak unassigned intensity fraction
def: "Fraction of intensity summed from unassigned peaks among the top 20
divided by the intensity summed from all top 20 peaks in the spectrum."
[PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003081
name: unidentified modification monoisotopic mass delta
def: "Monoisotopic mass delta in Daltons of an amino acid residue
modification whose atomic composition or molecular identity has not been
determined. This term should not be used for modifications of known
molecular identity such as those available in Unimod, RESID or PSI-MOD.
This term MUST NOT be used inside the <Modification> element in mzIdentML."
[PSI:PI]
is_a: MS:1001471 ! peptide modification details
xref: value-type:xsd\:double "The allowed value-type for this CV term."
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1003082
name: MS-DIAL
def: "MS-DIAL is a universal program for untargeted metabolomics and
lipidomics that supports multiple instruments and MS vendors."
[PMID:25938372]
is_a: MS:1002878 ! small molecule software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 

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

*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...

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

[Psidev-ms-dev] Release candidate 4.1.33_rc1 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new terms for the release version 4.1.33_rc1 of
the psi-ms.obo file.

It contains new terms for spectral libraries
and a term for the MS-DIAL software.

We also reorganized part of the CV, renamed some terms,
reactivated some obsolete terms and made some definitions more clear.
Please unpack and diff the two files to see the detailed changes.


New CV terms in version 4.1.33_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003033
name: molecular entity attribute
def: "A nonphysical characteristic attributed to a molecular entity." 
[PSI:PI]
relationship: part_of MS:1000881 ! molecular entity

[Term]
id: MS:1003034
name: atom
def: "Smallest constituent unit of ordinary matter that constitutes a 
chemical element." [https://en.wikipedia.org/wiki/Atom]
is_a: MS:1000881 ! molecular entity

[Term]
id: MS:1003035
name: small molecule
def: "Low molecular weight (< 900 daltons) organic compound that may 
regulate a biological process." 
[https://en.wikipedia.org/wiki/Small_molecule]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003036
name: metabolite
def: "Small molecule that is the intermediate end product of 
metabolism." [https://en.wikipedia.org/wiki/Metabolite]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003037
name: ribonucleotide
def: "Nucleotide containing ribose as its pentose component." 
[https://en.wikipedia.org/wiki/Ribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003038
name: deoxyribonucleotide
def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." 
[https://en.wikipedia.org/wiki/Deoxyribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003039
name: amino acid
def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) 
functional groups, along with a side chain (R group) that is specific to 
each amino acid." [https://en.wikipedia.org/wiki/Amino_acid]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003040
name: monosaccharide
def: "Simplest form of sugar and the most basic units of carbohydrate 
that cannot be further hydrolyzed to a simpler molecule." 
[https://en.wikipedia.org/wiki/Monosaccharide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003041
name: nucleic acid
def: "Molecule composed of a chain of nucleotides." 
[https://en.wikipedia.org/wiki/Nucleic_acid]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003042
name: polysaccharide
def: "Polymeric carbohydrate molecules composed of long chains of 
monosaccharide units bound together by glycosidic linkages." 
[https://en.wikipedia.org/wiki/Polysaccharide]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003043
name: number of residues
def: "Number of amino acid residues in a peptide, commonly referred to 
as the peptide length." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003044
name: number of missed cleavages
def: "Number of amino acid residue bonds that should have been cleaved 
by the cleavage agent used, but were not." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003045
name: peptide-to-protein mapping
def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003046
name: peptide-to-protein mapping attribute
def: "Nonphysical characteristic attributed to the result of 
peptide-to-protein mapping." [PSI:PI]
is_a: MS:1003045 ! peptide-to-protein mapping

[Term]
id: MS:1003047
name: protein sequence offset
def: "Offset in number of residues from the n terminus of the protein at 
which the peptide begins. Use 1 when the first residue of the peptide 
sequence is the first residue of the protein sequence." [PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003048
name: number of enzymatic termini
def: "Total number of termini that match standard rules for the cleavage 
agent, 2 when both termini match cleavage agent rules, 1 when only one 
terminus does, and 0 if neither terminus matches cleavage agent rules." 
[PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003049
name: peptidoform
def: "Peptide that contains zero or more mass modifications on the 
termini or side chains of its amino acid residues, and may be 
differentiated from other peptidoforms with the same peptide sequence 
but different mass modification configurations." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003050
name: peptidoform attribute
def: "Nonphysical characteristic attributed to a peptidoform." [PSI:PI]
relationship: part_of MS:1003049 ! peptidoform

[Term]
id: MS:1003051
name: peptidoform ion
def: "Peptidoform that has formed an adduct with an ion, thereby 
rendering it potentially detectable with a mass spectrometer. Commonly 
called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI]
is_a: MS:1003049 ! peptidoform
synonym: "precursor" RELATED []
synonym: "precursor ion" RELATED []
synonym: "parent ion" RELATED []

[Term]
id: MS:1003052
name: peptidoform ion property
def: "A physical characteristic of a peptidoform ion." [PSI:PI]
relationship: part_of MS:1003051 ! peptidoform ion

[Term]
id: MS:1003053
name: theoretical monoisotopic m/z
def: "Mass-to-charge ratio of a peptidoform ion composed of the most 
common isotope of each atom computed from the putative knowledge of its 
molecular constituents." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003054
name: theoretical average m/z
def: "Mass-to-charge ratio of a peptidoform ion computed from the 
putative knowledge of its molecular constituents, averaged over the 
distribution of naturally occurring isotopes." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003055
name: adduct
def: "Product of a direct addition of two or more distinct molecules, 
resulting in a single reaction product containing all atoms of all 
components. The resultant is considered a distinct molecular species." 
[https://en.wikipedia.org/wiki/Adduct]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003056
name: adduct ion property
def: "Physical measurable characteristic of an adduct ion." [PSI:PI]
relationship: part_of MS:1000353 ! adduct ion

[Term]
id: MS:1003057
name: scan number
def: "Ordinal number of the scan indicating its order of acquisition 
within a mass spectrometry acquisition run." [PSI:PI]
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1003058
name: spectrum property
def: "Physical measurable characteristic of a spectrum." [PSI:PI]
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1003059
name: number of peaks
def: "Number of peaks or features in a spectrum. For a peak-picked 
spectrum, this will correspond to the number of data points. For a 
non-peak-picked spectrum, this corresponds to the number of features 
discernable in the spectrum, which will be fewer than the number of data 
points." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003060
name: number of data points
def: "Number of data points in a spectrum. For a peak-picked spectrum, 
this will correspond to the number of peaks. For a non-peak-picked 
spectrum, this corresponds to the number of values in the data array, 
which are not all peaks." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003061
name: spectrum name
def: "Label attached to a spectrum uniquely naming it within a 
collection of spectra, often in a spectral library. It is often a string 
combination of peptide sequence, charge, mass modifications, collision 
energy, but will obviously be different for small molecules or 
unidentified spectra. It must be unique within a collection." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003062
name: spectrum index
def: "Integer index value associated with a spectrum within a collection 
of spectra, often in a spectral library. By custom, index counters 
should begin with 0." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003063
name: universal spectrum identifier
def: "PSI universal spectrum identifier (USI) multipart key that 
uniquely identifies a spectrum available in a ProteomeXchange datasets 
or spectral library." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003064
name: spectrum aggregation attribute
def: "Nonphysical characteristic attributed to spectrum aggregation." 
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003065
name: spectrum aggregation type
def: "Categorization of a spectrum based on the type of aggregation it 
is based on (e.g., an individual spectrum, a consensus spectrum, best 
replicate spectrum, etc.)." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003066
name: singleton spectrum
def: "Spectrum that is not the result of some aggregation process." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003067
name: consensus spectrum
def: "Spectrum that is the result of merging several replicate spectra 
to form a spectrum that is more representative of its class and ideally 
less noisy that any of its source replicates." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003068
name: best replicate spectrum
def: "Spectrum that is considered the most representative from a pool of 
replicate spectra." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003069
name: number of replicate spectra available
def: "Number of replicate spectra available for use during the 
aggregation process." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003070
name: number of replicate spectra used
def: "Number of replicate spectra used during the aggregation process. 
This is generally applicable when there are many replicates available, 
but some are discarded as being low S/N, blended, or otherwise 
unsuitable, and the remaining set is then used for merging via a 
consensus algorithm." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003071
name: spectrum origin attribute
def: "Nonphysical characteristic attributed to spectrum aggregation." 
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003072
name: spectrum origin type
def: "Categorization of a spectrum based on its type of aggregation 
(e.g., an individual spectrum, a consensus spectrum, best replicate 
spectrum, etc.)." [PSI:PI]
is_a: MS:1003071 ! spectrum origin attribute

[Term]
id: MS:1003073
name: observed spectrum
def: "Spectrum that originates from an analysis attempt of a single 
analyte species on an instrument." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003074
name: predicted spectrum
def: "Spectrum that originates from a compututational algorithm that 
attempts to predict spectra." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003075
name: demultiplexed spectrum
def: "Spectrum that originates from an attempted extraction of a single 
ion spieces from a multiplexed spectrum that contains multiple ion 
species." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003076
name: uninterpreted spectrum
def: "Spectrum provided in the form of plain numerical values without 
any information pertaining to the interpretation of features." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003077
name: interpreted spectrum
def: "Spectrum provided in a form where specific features of the 
spectrum are interpreted to provide putative explanations for some 
feature." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003078
name: interpreted spectrum attribute
def: "Nonphysical characteristic attributed to an interpreted spectrum." 
[PSI:PI]
relationship: part_of MS:1003077 ! interpreted spectrum

[Term]
id: MS:1003079
name: total unassigned intensity fraction
def: "Fraction of intensity summed from all unassigned peaks divided by 
the intensity summed from all peaks in the spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003080
name: top 20 peak unassigned intensity fraction
def: "Fraction of intensity summed from unassigned peaks among the top 
20 divided by the intensity summed from all top 20 peaks in the 
spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003081
name: unidentified modification monoisotopic mass delta
def: "Monoisotopic mass delta in Daltons of an amino acid residue 
modification whose atomic composition or molecular identity has not been 
determined. This term should not be used for modifications of known 
molecular identity such as those available in Unimod, RESID or PSI-MOD. 
This term MUST NOT be used inside the <Modification> element in 
mzIdentML." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
xref: value-type:xsd\:double "The allowed value-type for this CV term."
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1003082
name: MS-DIAL
def: "MS-DIAL is a universal program for untargeted metabolomics and 
lipidomics that supports multiple instruments and MS vendors." 
[PMID:25938372]
is_a: MS:1002878 ! small molecule software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 

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

*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>

[Psidev-ms-dev] PSI202 Registration open

[Jones, A. <And...@li...>]

Dear 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, and registration is now open: http://www.psidev.info/hupo-psi-meeting-2020
There is no cost to attend the workshop, with lunches, coffee/tea and a workshop dinner included. You will have to cover your own costs for travel and hotels.
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 on the molecular interactions side on mapping standards to Cytoscape.
We will be welcoming the new PSI work group - Intrinsically Disordered Proteins (IDP). We are also planning a new session related to standards for glycoproteomics, to scope out the community need in this area.
The PSI is always keen to recruit new members, so please join if you think you may be interested in data sharing and standards for proteomics. Please also get in touch, if you are interested to join PSI activities in general but cannot travel to San Diego.
Best wishes
Andy Jones (PSI Chair)