psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] [Psidev-pi-dev] Malware in the PSI web site

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

Hi Juanan, we tried to create aliases for all the major formats:

www.psidev.info/traml
 should point to:
http://www.psidev.info/index.php?q=node/405

www.psidev.info/mzml
  should point to:
http://www.psidev.info/index.php?q=node/257

And then we had:

www.psidev.info/mzidentml
www.psidev.info/mzquantml

I don't recall which numbers these pointed to. But Google has all this
information. Look slike mzIdentML was:

www.psidev.info/index.php?q=node/454

and mzQuantML:

www.psidev.info/index.php?q=node/457

And then I think we also has MIAPE:

www.psidev.info/miape
Pointing to:
www.psidev.info/index.php?q=node/91



> -----Original Message-----
> From: Juan Antonio Vizcaino [mailto:ju...@eb...]
> Sent: Tuesday, April 17, 2012 12:02 AM
> To: psi...@li...; Mass spectrometry standard
> development
> Subject: [Psidev-pi-dev] Malware in the PSI web site
>
> Dear all,
>
> Sorry I could not reply to your e-mails individually. Since Sunday, I
> am attending a meeting in Spain and it has been quite busy here.
>
> I received the notification on Friday evening from Google. At the
> moment I am afraid there is not much we can do. The problem is that the
> drupal version in the old site is too old and I don't think it makes
> much sense try to 'fix' the old page.
>
> The alternative is then to move to the new web page that Henning
> introduced briefly in San Diego. However, there are a few issues. One
> of the main ones is how to maintain the links that have been included
> in the related publications. We will do our best but at the moment we
> don't have anyone who can especifically do the work so this will need
> to go on top of everything else for a couple of people. The content
> will not be as updated as in the old site and that means that the
> content will need to be enriched gradually in time. But that should not
> be a problem.
>
> Something that could help is that you send me the links you think have
> been included in your PSI related publications. That way we can try to
> create aliases for them.
>
> Best regards,
>
> Juan Antonio
>
>
>
>
> -----------------------------------------------------------------------
> -------
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[Psidev-ms-dev] Malware in the PSI web site

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

Dear all,

Sorry I could not reply to your e-mails individually. Since Sunday, I am attending a meeting in Spain and it has been quite busy here.

I received the notification on Friday evening from Google. At the moment I am afraid there is not much we can do. The problem is that the drupal version in the old site is too old and I don't think it makes much sense try to 'fix' the old page.

The alternative is then to move to the new web page that Henning introduced briefly in San Diego. However, there are a few issues. One of the main ones is how to maintain the links that have been included in the related publications. We will do our best but at the moment we don't have anyone who can especifically do the work so this will need to go on top of everything else for a couple of people. The content will not be as updated as in the old site and that means that the content will need to be enriched gradually in time. But that should not be a problem. 

Something that could help is that you send me the links you think have been included in your PSI related publications. That way we can try to create aliases for them.

Best regards,

Juan Antonio

[Psidev-ms-dev] Malware on psidev.info

[Matthew C. <mat...@gm...>]

I think someone hacked the site; it's flagged as a malware site by Google and does some redirecting 
to pekawal.ch before loading the site. I emailed web...@ps... but haven't heard a response.

-Matt

[Psidev-ms-dev] Release canditate psi-ms.obo v.3.23.0_rc1

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

Dear proteomics community,

attached there's the the release candidate 3.23.0_rc1 for the psi-ms.obo.
It contains the newly proposed terms concerning mzQuantML validation 
from the San Diego meeting.

Should we use the boolean data type or suffices it to enumerate just the 
values?
Do we need some other terms?

Comments and further proposals are as always welcome.
If there are no objections it's planned to release the next official 
version of the psi-ms.obo friday next week,
so that we can discuss on the terms on the next mzQuantML call on 
thursday (April 19th).


We have already the following terms for mzQuantML validation:
-------------------------------------------------------------
MS:1001833    quantitation analysis summary

MS:1001834    LC-MS label-free quantitation analysis
MS:1001835    SILAC quantitation analysis
MS:1001836    spectral counting quantitation analysis
MS:1001837    iTraq quantitation analysis
MS:1001838    SRM quantitation analysis
MS:1001839    metabolic labeling 14N / 15N quantitation analysis


Newly added CV terms in version 3.23.0_rc1 of psi-ms.obo:
=========================================================
[Term]
id: MS:1002001
name: MS1 Label-based raw feature quantitation
def: "MS1 Label-based raw feature quantitation (FeatureQuantLayer MUST 
be present)." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002002
name: MS1 Label-based peptide level quantitation
def: "MS1 Label-based peptide level quantitation 
(PeptideConsensusQuantLayer MUST be present)." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002003
name: MS1 Label-based protein level quantitation
def: "MS1 Label-based protein level quantitation (ProteinQuantLayer MUST 
be present)." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002004
name: MS1 Label-based proteinGroup level quantitation
def: "MS1 Label-based proteinGroup level quantitation 
(ProteinGroupQuantLayer MUST be present)." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001833 ! quantitation analysis summary

Best regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Report PSI meeting 2012 in San Diego (March 12-14th)

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

Hi all,

First of all, apologies for this big delay in sending my notes about the meeting. I have not managed to finish them till today. 

I am not doing anything very comprehensive here. My idea is to provide the talks and to show some extra ideas that were discussed during the meeting by the people attending the general MS and PI workgroups sessions, apart from the final wrapping session. I am also attaching the list of attendees in a separate excel file. This way, people can have a good overall idea about what happened in the meeting. Of course, please fel free to make additions/ comments, etc. This is not a final version.

The presentations are available to download at:

http://www.psidev.info/SanDiego2012/Presentations_PSI.zip

In addtion, Andy already wrote a couple of e-mails about the progress made in mzIdentML and mzQuantML on March 16th so I will not talk about this in detail.

Content of this e-mail:

- Minutes of the common session (PI and MS groups) on Monday March 12th.
- Minutes on Tuesday March 13th for HUPO Technology/Standards Committee.
- Minutes of the common wrapping session on Wednesday March 14th. 


-> Minutes of the common session (PI and MS groups) on Monday March 12th


** 1. PSI-PI group

Andy Jones gave an introduction about the PSI-PI activities (see 20120312_PSI-ProteomeInformaticsUpdate.pptx in the directory of presentations).


a) mzIdentML

The manuscript corresponding to mzIdentML v1.1 has been recently accepted in MCP (PubMed ID:22375074).

TO DO list for mzIdentML:
- CV terms for protein grouping. Proposal from T. Farrah and S. Seymour to be discussed in detail.
- Issues with fast file parsing? Discuss possibility of an indexed version.
- Plan for improving uptake.

After the talk there was a bit of discussion about the new format mz5, just published in MCP (PMID: 21960719). 
mz5 is a binary representation of a mzML file. Is it the way to move forward? The file is not human readable any more. However, it is useful to control the size (smaller, faster to access, etc.).
P. Mallick: treatment for mz5 mzML files in ProteoWizard is transparent. 
Maybe it would be a trivial work for mzIdentML to do something similar.
Be cautious because we could have the same format problem ahead that the one existing with existing binary vendor formats? The big difference is that mz5 compression is open source.
Sean: we need to move to user adoption and this may help.

b) mzQuantML

Version 1.0 release candidate submitted to the PSI document process on October 2011. 

- Discussion:
Sean: Add groups at two different levels: 'groups of groups'.
Andy: the hierarchy of groups is not supported in the current schema.
The same assay can be assigned to more than one group.

c) mzTab

The presentation was given by Juan A. Vizcaino (20120312_PSI_mzTab.pptx). 

Henning Hermjakob: The main motivation for the format is to get out of the MS proteomics niche.
Andy: There should be support for replicates in the format.
There is a lot of 'summary report type' support needed and it would be good to standardise the way it is done.

d) Standardisation of protein classification in mzIdentML

Standardised way to call protein groups the same way. At the ProteinDetectionHypothesis level, to differentiate protein sequences there.

- Discussion:
Purpose: to have a standard way to report protein identifications in mzIdentML files. 
Andy: the objective is to get something out of a search engine in a clear way, a way to communicate what the data really means.
Sean: Some clear way to say how are you taking into account the protein inference problem: being transparent is the best way.
It is not easy to put together these new potential CV and the passThreshold attribute at mzIdentML. They would need to be consistent. 


** 2. PSI-MS group

Eric Deutsch gave an introduction about the PSI-MS activities (20120312_Deutsch_PSI-MSSWG_Intro). New activities planned for the meeting:

- SRM workflow guidelines.
- Need for a format for SRM data analysis result format (hopefully mzQuantML).
- Data guidelines for the Human Proteome Project (HPP).

a) TraML

Eric gave an overview of the format. The manuscript has just been accepted in MCP (v1.0). No discussion afterwards.

b) mzML

The main open issues for mzML are:

- Ongoing maintenance of CV.
- Cooperative development with imzML (A. Rompp).
- Possible adoption by the metabolomics community (in collaboration with S. Neumann and V. Likic).

Discussion about what is better, to have an index included in the files, or it is better to have it in an external file, or just it is better not to persist it in any way.

Florian Reisinger: The library xxindex very useful for big files. The index is generated and not persisted.

imzML: It does not include support for MS/MS spectra? Full profile spectra to be included in imzML better than mzML?


c) PEFF

Pierre-Alain Binz gave an update about the current status of PEFF (last slides in 20120312_MIAPE-PEFF-update-PAB.ppt). Summary:

- It has gone through the document process: reviewers did not agree on the format.
- Viewer available done by Harald Barsnes.
- Implemented by neXtprot so far.
- Need to evaluate the GPM nomenclature proposed by R. Beavis for protein modifications.


d) Human Proteome Project (HPP) MS Data Guidelines

Information included in the presentation: 20120312_Deutsch_PSI-MSSWG_Intro (Slides 34-36).

Large numbers of heterogeneous datasets will be generated by C-HPP and the B/D-HPP participants. Different data types involved: MS1, MS/MS, SRM, Gel images, imaging MS, molecular interactions, IHC images and characterizations, among others.

What will the guidelines for contribution of proteomics MS data be?

ACTION POINT for the meeting: develop a first fraft of the guidelines for presentation to the HPP Executive Committee for refinement. 


** 3. MIAPE.


a) MIAPE MS and MSI and the new MIAPE Quant

Pierre-Alin reported on this. Information available at: 20120312_MIAPE-PEFF-update-PAB.ppt

MIAPE MS and MSI guidelines are being updating at the moment. One of the major points is to remove quantitative information from MIAPE MS and MSI and to create the new guidelines MIAPE-Quant. The newer versions of the guidelines are:

- MIAPE-MS 2.97.8
- MIAPE MSI 1.2.06
- MIAPE Quant 0.9

Both MIAPE MS and MSI are about to be resubmitted to the PSI document process.

- Discussion:
Eric:  MIAPE-Quant should be adapted for SRM.
MIAPE Ident instead of MIAPE MSI? Change of name? That would involve to do a full resubmission to the PSI document process. Not very practical to do.
Juan asked what people thought about whether it was going to be possible or not to provide full MIAPE compliance of mzML/mzIdentML files through semantic validation and the existing software/ PSI-MS CV.
The consensus was that there will be impossible to have full MIAPE complicance since there are things in the guidelines very difficult to implement in a semantic validator (for instance the taxon filter). However, through the existing software and CV it will be possible to validate properly a high proportion of the existing guidelines. At least, we should provide the way to do it. Implementers may choose not to do it at the end.


** 4. HUPO Technology/Standards Committee

The presentation was given by B. Domon and C. Borchers (20120312_PSI_SanDiego_Domon_Borchers.pptx): "Harmonization of proteomics methods / Quantification methods".

The main idea is to recollect standard experimental protocols in proteomics and centralize them in a way they can be easily accessed. This is essential for the HPP. A lot of similar work has been already done in the small molecule world, but not in proteomics.

- Discussion:

Eric: Is there a concrete aim? How many protocols? Thousands? Limit the numbers? The idea is not to have too many protocols per experimental procedure. 
Andy: How do you get community buying? People will not be getting papers out of this.
Nuno Bandeira: Data analysis protocols should also be included: Reference datasets and reference results of the data analysis. However, to be able to reproduce all the results requires quite some infrastructure (for instance the decoy database).
Christoph/Bruno: Open review process of the protocol. If you review/test it yourself, you put your name there in the protocol.
At the moment, it is a proof of principle: It needs to become a concrete proposal or idea. 


** 5. Miscellaneous.

a) qcML

M. Walzer gave a presentation about a new XML format called qcML (see presentation: 20120312_psi_spring_meeting_qcml.pdf), developed in the context of the PRIME-XS EU grant (http://www.primexs.eu/). 

The idea is to develop a file format that can provide a way to report QC measurements that have been performed. For instance, QC measurements for MS data would be encoded in a qcML file and there could be references in that file to the corresponding mzML. The project is now starting so feedback is very much welcome.


-> Minutes on Tuesday March 13th for HUPO Technology/Standards Committee


The discussion was chaired by C. Vouchers. The concrete idea to move forward  is then:
- Identify a group of people that can do/lead a small pilot project. 
- Do the web page. Very important.
- Editors are also needed. The idea is to mimic the PSI document process (or the journal's peer-review process).

Other ideas that arose during the discussion:

- A possibility would be to join the 'HUPO Tutorials initiative' (organised by Peter James). The four main proteomics journals are already participating. Both the manuscript and a PowerPoint presentation with supporting information are needed for each manuscript to be published. This is a way to encourage people's effort in this initiative.
- Objective: Get a collection of protocols to be used in proteomics. The ideal situation would be to use the protocols in the same sample material. 
- Pierre-Alain: Use the infrastructure provided by ABRF? ProteoRed is also doing experimental validation of protocols somehow. 
- Free access or not? It is something that people could get as an extra for their HUPO membership. Others think that should be completely free as everything done so far by HUPO PSI so far.
- Juan: I cannot see this working in practice since protocols can be quite dynamic. The updating of the protocols would be a problem.
- Juan P. Albar: Core facilities would be interested in this mechanism for sure. Protocols could become SOPs.
- Christoph: Number one priority for the protocols is that they need to be validated.
- Different opinions about the ranking of the protocols:  No protocol should be ranked (Christoph). They should be indeed ranked (Sean and Nuno), especially the data processing ones. It is quite objective to know which ones work better than others.
- First structure to be ready by HUPO 2012 on September in Boston. Be aware that a significant web development is involved. Eric to help at that point.


-> Minutes of the common wrapping session on Wednesday March 14th


I am not reporting on the MI session. However, the presentation made by Sandra Orchard is also available (see presentation: 20120314_mi-windup.ppt).


** 1. PSI-PI group

Presentations: 20120314_PSI-PI summary.pptx and 20120314_Summary_mzTab.pptx (just one slide).

a) mzIdentML

- Current version is stable at version 1.1. No desire to change the format, so feature requests have to be handled by CV terms.
- Protein grouping: We would like to encourage consistency in reporting protein ambiguity from different search engines. S. Seymour and T. Farrah have written an informational document, summarising the issues and making a recommended encoding and the proposal for new CV terms.

 ACTION POINT: Document and CV terms will be sent to main stakeholders for feedback. If there is agreement, CV terms will be circulated for inclusion in PSI-MS.

- Protein modification position scoring. Not currently handled perfectly in the mzIdentML schema. There is no good way of showing that a modification location can be ambiguous (and associating a score to this ambiguity).

 ACTION POINT: Collect examples from the main tools and see if the proposed encoding will work ok (Note: see e-mail from Andy on March 16th for more details).


b) mzQuantML

- Release candidate 1 in the document process. Reviews identified a problem of heterogeneity.
- Another problem is that our own example files are not all consistent with our rules written in the documentation!
- Clear need for validation software to check “recommended” encoding of each type of technique. Semantic validation is a key requisite.
- We have drafted semantic validation rules in the meeting.
- General format rules:
	-iTRAQ, SILAC, label-free, spectral counting rules.
	- SRM encoding rules to follow.

-Liverpool group will make semantic validation software available soon, encoding rules to assign files as valid or invalid.

Proposal for next steps:

- Simplify spec document so it only reports the general framework for mzQuantML (i.e. No example encodings for specific techniques). This fits well with the dates of the deliverables due for the ProteomeXchange grant.
- The semantic validation rules define how specific experimental techniques should be encoded.
- We are unclear about the most appropriate mechanism for releasing this info: Maybe as PSI Informational documents?Appendices to the specification document? Just release software informally...?

Note: see e-mail from Andy on March 16th for more details.

c) mzTab

ACTION POINTS: Robert Chalkley and Nuno to give feedback on the format specification. 
- After that, to be submitted to the PSI document process.
- Replicates should be modeled (Andy).
- Validator for mzTab is worth considering? Something similar is going to be done for MITAB format (PSI-MI workgroup).

d) Minor issue :Ion mobility (IM).

-Minor item – wanting to encode Ion Mobility Mass spectrometry in mzML.
-Also wanting to report IM values about fragments in mzIdentML. Agreed to include proposed CV terms in mzIdentML.

ACTION POINT: Attempt to make a simple example of mzML encoding peak picked IMMS data (Matt Chambers).
Raw IMMS data files are huge (e.g. 50GB), so conversion to mzML will be massive...


** 2. PSI-MS group

See: presentation 20120314_Deutsch_PSI-MSSWG_Closing.pptx


a) TraML

- One subgroup discussed during the meetinghow to enhance small molecule identifier representation in the CV terms. External identifiers to HMDB, KEGG, PubChem, Inchi, SMILES, etc.
- Discussed additional desired implementations such as Skyline, SRMAtlas and OpenMS.
- Problem of old copies on the schema on the PSI web site.
- How do we handle iSRM, TMRM transition list modes?


b) mzML

Nothing new to report.


c) MIAPE Quant

Discussed and improved the existing example from ProteoRed (v0.9).
Example is done except for some open questions where we need to go back to the data producer for clarification.
MIAPE Quant itself is good and captures all the information we wanted to see well.

d) PEFF

- Done so far:
Keep PEFF as «extended» fasta, not XML.
Looked at GPM nomenclature based on HGSV nom.
Introduced ambiguities for sequence positions and modifications.
Add qualifyer/comments : (23|MOD:00045|by similarity).


- Still To Dd:
Finalise/reformat the CV and incorporate in psi-ms CV.
Update FEFF viewer and converter.
Look for implementation options (converter, import in search engines, sequence DB export).
Update documentation, prepare publication.

e) HPP MS Data Guidelines

This is the current status:

- General precepts: All claimed contributions shall be backed by well-annotated raw data and results submitted to an approved data repository at the time of claim. Claims are made either at http://thehpp.org/ and/or in a publication.
- MS/MS Datasets: Must be submitted to PRIDE and accepted by ProteomeXchange, following ProteomeXchange guidelines (to be refined in the next few months), including raw data, results, sufficient study metadata. Contribution claims must be accompanied by a PXD (ProteomeXchange) identifier.
- SRM Datasets: Must be submitted to PeptideAtlas/PASSEL and accepted by ProteomeXchange, following ProteomeXchange guidelines (to be refined in the next few months), including raw data, transition lists, results, and sufficient study metadata. Contribution claims must be accompanied by a PXD identifier.
- Molecular Interactions Datasets: Must be submitted to IMEX, checked by an IMEX curator, and accepted. Contribution claims must be accompanied by an IMEX identifier.



Hope I have not missed anything important. Best regards,

Juan

[Psidev-ms-dev] psi-ms controlled vocabulary v.3.21.0 released

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

Dear proteomics community,

attached there's the new psi-ms.obo version 3.22.0.

I didn't added the matrix solution terms from the release candidate,
since we should use the CV terms from the CHEBI ontology instead.

The following MALDI matrix solution terms are already present in the 
current release (version 90) of the ChEBI ontology:
CHEBI:15714 for 3,5-dimethoxy-4-hydroxycinnamic acid
CHEBI:28747 for picolinic acid
CHEBI:17189 for 2,5-Dihydroxybenzoic acid
CHEBI:17620 for 4-hydroxy-3-methoxycinnamic acid
CHEBI:37510 for anthralin

In addition I submitted the following terms to ChEBI.
They are already fully curated and will be able with the next ChEBI 
release on 7th May 2012:

CHEBI:64340 for alpha-cyano-4-hydroxycinnamic acid
CHEBI:64341 for 2-(4-hydroxyphenylazo)benzoic acid
CHEBI:64342 for 3-hydroxypicolinic acid
CHEBI:64343 for 
trans-2-[3-(4-tert-butylphenyl)-2-methyl-2-propenylidene]malononitrile
CHEBI:64344 for 2',4',6'-trihydroxyacetophenone

Newly added CV terms in version 3.22.0 of psi-ms.obo:
=====================================================
[Term]
id: MS:1001987
name: vacuum drying MALDI sample preparation
def: "Vacuum-drying MALDI sample preparation crystallization method." 
[PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001988
name: crushed crystal MALDI sample preparation
def: "Crushed-crystal MALDI sample preparation method." [PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001989
name: fast evaporation MALDI sample preparation
def: "Fast-evaporation MALDI sample preparation method." 
[DOI:10.1021/ac00091a044]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001990
name: overlayer MALDI sample preparation
def: "Overlayer method combining features of the crushed-crystal method 
and the fast-evaporation method." [PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001991
name: sandwich MALDI sample preparation
def: "Sandwich MALDI sample preparation method." 
[DOI:10.1002/(SICI)1096-9888(199706)32:6<593::AID-JMS511>3.3.CO;2-4]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001992
name: spin coating MALDI sample preparation
def: "Spin coating MALDI sample preparation method." 
[DOI:10.1021/cc0500710, PMID:16283807]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001993
name: quick and dirty MALDI sample preparation
def: "Quick & dirty (Q&D) sample preparation separating matrix handling 
from sample handling." [PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001994
name: top hat baseline reduction
def: "Top-hat morphological filter based on the basic morphological 
operations 'erosion' and 'dilatation'." [PSI:MS]
is_a: MS:1000593 ! baseline reduction

[Term]
id: MS:1001995
name: convex hull baseline reduction
def: "Constructs the baseline by fitting multiple parabolas to the 
spectrum starting with the large scale structures." [PSI:MS]
is_a: MS:1000593 ! baseline reduction

[Term]
id: MS:1001996
name: median baseline reduction
def: "The spectrum that will be baseline subtracted is divided into a 
number of segments." [PSI:MS]
is_a: MS:1000593 ! baseline reduction

[Term]
id: MS:1001997
name: wavelet transformation smoothing
def: "The random noise is removed by using the undecimated wavelet 
transform." [DOI:10.1093/bioinformatics/btl355, PMID:16820428]
is_a: MS:1000592 ! smoothing

[Term]
id: MS:1001998
name: sophisticated numerical annotation procedure
def: "It searches for known patterns in the measured spectrum." 
[DOI:10.1021/ac951158i, PMID:21619291]
synonym: "SNAP" EXACT []
is_a: MS:1000801 ! area peak picking

[Term]
id: MS:1001999
name: area normalization
def: "Normalization of areas below the curves." [PSI:MS]
is_a: MS:1001484 ! intensity normalization

[Term]
id: MS:1002000
name: LIFT
def: "A Bruker’s proprietary technique where molecular ions are 
initially accelerated at lower energy, then collide with inert gas in a 
collision cell that is then “lifted” to high potential. The use of inert 
gas is optional, as it could lift also fragments provided by LID." 
[DOI:10.1007/s00216-003-2057-0 , PMID:12830354]
is_a: MS:1000044 ! dissociation method

Best Regards and Happy Easter,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.22.0_rc1 of psi-ms.obo

[Bhat, T. N. <tal...@ni...>]

Hi,
In the context of ontology involving chemical compounds, I would like to mention a different (complementary) ontology that is not covered by ChEBI.
I am enclosing a recent paper and URL to illustrate its use to organize, related and query millions of compounds from PubChem and PDB using visual tools.
http://xpdb.nist.gov/chemblast/pdb.pl
http://xpdb.nist.gov/hiv2_d/download.cgi?ID=JSWIS_2010_reprint.pdf&file_location=../hiv2_d
Thanks

T N Bhat

-----Original Message-----
From: Steffen Neumann [mailto:sne...@ip...] 
Sent: Tuesday, April 03, 2012 3:14 AM
To: pierre-alain binz
Cc: psi...@li...; Mass spectrometry standard development; Eric Deutsch; psi...@li...
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.22.0_rc1 of psi-ms.obo

Hi,

On Tue, 2012-04-03 at 08:41 +0200, pierre-alain binz wrote:
...
> About the chemical compounds: do we really want to have them in the 
> PSI-MS CV?
> This opens the door for a ton of new terms
Approx. 30 million I'd say ...

> or if we want an obo formatted CV for them ask to put them in chebi. 
> BTW, how reactive is chebi in this?
ChEBI is quite open to this from my experience, especially since Christ Steinbeck is also into Standardisation.

There is already an OBO formatted version of ChEBI at ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/

Maybe there could also be an equivalent http URL, that might make live easier e.g. for people behind firewalls.

Yours,
Steffen

> >> [Term]
> >> id: MS:1001996
> >> name: 2-(4-Hydroxyphenylazo)benzoic acid
> >> def: "2-(4-Hydroxyphenylazo)benzoic acid MALDI matrix."
> >> [PubChem_Compound:5357439]
> >> synonym: "HABA" EXACT []
> >> is_a: MS:1000834 ! matrix solution
> >>
> >> [Term]
> >> id: MS:1001997
> >> name: 3-Hydroxypicolinic acid
> >> def: "3-Hydroxypicolinic acid MALDI matrix." 
> >> [PubChem_Compound:13401]
> >> is_a: MS:1000834 ! matrix solution

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409



------------------------------------------------------------------------------
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Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.22.0_rc1 of psi-ms.obo

[pierre-alain b. <pie...@is...>]

Hi,

yes, chebi can be accessed via the EBI website either directly:
http://www.ebi.ac.uk/chebi/

or via the OLS system
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CHEBI

besides the obo. file that you can get from the ftp

Pierre-Alain

On 03.04.2012 09:14, Steffen Neumann wrote:
> Hi,
>
> On Tue, 2012-04-03 at 08:41 +0200, pierre-alain binz wrote:
> ...
>> About the chemical compounds: do we really want to have them in the
>> PSI-MS CV?
>> This opens the door for a ton of new terms
> Approx. 30 million I'd say ...
>
>> or if we want an obo formatted CV for them ask to put them in chebi.
>> BTW, how reactive is chebi in this?
> ChEBI is quite open to this from my experience,
> especially since Christ Steinbeck is also into Standardisation.
>
> There is already an OBO formatted version of ChEBI
> at ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/
>
> Maybe there could also be an equivalent http URL,
> that might make live easier e.g. for people behind firewalls.
>
> Yours,
> Steffen
>
>>>> [Term]
>>>> id: MS:1001996
>>>> name: 2-(4-Hydroxyphenylazo)benzoic acid
>>>> def: "2-(4-Hydroxyphenylazo)benzoic acid MALDI matrix."
>>>> [PubChem_Compound:5357439]
>>>> synonym: "HABA" EXACT []
>>>> is_a: MS:1000834 ! matrix solution
>>>>
>>>> [Term]
>>>> id: MS:1001997
>>>> name: 3-Hydroxypicolinic acid
>>>> def: "3-Hydroxypicolinic acid MALDI matrix." [PubChem_Compound:13401]
>>>> is_a: MS:1000834 ! matrix solution

Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.22.0_rc1 of psi-ms.obo

[Steffen N. <sne...@ip...>]

Hi,

On Tue, 2012-04-03 at 08:41 +0200, pierre-alain binz wrote:
> They should be as explicit 
> and precise as possible. We should avoid too much simplification in the 
> naming, this to avoid ambiguities.
I'd also suggest to put in references or links outside this. 
I was not aware that "Quick&  dirty (Q&D) sample preparation"
has a protocol associated to it. 

I'd also see a better LinkOut for e.g. 
"sophisticated numerical annotation procedure"

> About the chemical compounds: do we really want to have them in the 
> PSI-MS CV?
> This opens the door for a ton of new terms, for which we need to agree 
> on the nomenclature, the choce of the synonyms, the definition, the 
> xrefs, the classification etc. I'm here just wondering if we should use 
> another mechanism for them, such as providing the pubchem ID, or if we 
> want an obo formatted CV for them ask to put them in chebi. 
An alternative to ChEBI is to use the EDAM Ontology, 
which is able to encode PubChem (or whatever) chemical stuff.

We'd need to represent that (CHEBI:15714) is_a "matrix solution".


Yours,
Steffen


Yours,
Steffen


[Term]
id: MS:1001995
name: 3,5-dimethoxy-4-hydroxycinnamic acid
def: "3,5-dimethoxy-4-hydroxycinnamic acid MALDI matrix." 
[PubChem_Compound:637775]
synonym: "sinapic acid" EXACT []
synonym: "sinapinicc acid" EXACT []
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1001996
name: 2-(4-Hydroxyphenylazo)benzoic acid
def: "2-(4-Hydroxyphenylazo)benzoic acid MALDI matrix." 
[PubChem_Compound:5357439]
synonym: "HABA" EXACT []
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1001997
name: 3-Hydroxypicolinic acid
def: "3-Hydroxypicolinic acid MALDI matrix." [PubChem_Compound:13401]
is_a: MS:1000834 ! matrix solution


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.22.0_rc1 of psi-ms.obo

[Steffen N. <sne...@ip...>]

Hi,

On Tue, 2012-04-03 at 08:41 +0200, pierre-alain binz wrote:
...
> About the chemical compounds: do we really want to have them in the 
> PSI-MS CV?
> This opens the door for a ton of new terms
Approx. 30 million I'd say ...

> or if we want an obo formatted CV for them ask to put them in chebi. 
> BTW, how reactive is chebi in this?
ChEBI is quite open to this from my experience, 
especially since Christ Steinbeck is also into Standardisation.

There is already an OBO formatted version of ChEBI 
at ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/

Maybe there could also be an equivalent http URL, 
that might make live easier e.g. for people behind firewalls.

Yours,
Steffen

> >> [Term]
> >> id: MS:1001996
> >> name: 2-(4-Hydroxyphenylazo)benzoic acid
> >> def: "2-(4-Hydroxyphenylazo)benzoic acid MALDI matrix."
> >> [PubChem_Compound:5357439]
> >> synonym: "HABA" EXACT []
> >> is_a: MS:1000834 ! matrix solution
> >>
> >> [Term]
> >> id: MS:1001997
> >> name: 3-Hydroxypicolinic acid
> >> def: "3-Hydroxypicolinic acid MALDI matrix." [PubChem_Compound:13401]
> >> is_a: MS:1000834 ! matrix solution

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.22.0_rc1 of psi-ms.obo

[pierre-alain b. <pie...@is...>]

Hi Gerhard,
I fully agree with Eric on the terms names. They should be as explicit 
and precise as possible. We should avoid too much simplification in the 
naming, this to avoid ambiguities.

About the chemical compounds: do we really want to have them in the 
PSI-MS CV?
This opens the door for a ton of new terms, for which we need to agree 
on the nomenclature, the choce of the synonyms, the definition, the 
xrefs, the classification etc. I'm here just wondering if we should use 
another mechanism for them, such as providing the pubchem ID, or if we 
want an obo formatted CV for them ask to put them in chebi. BTW, how 
reactive is chebi in this?

Pierre-Alain


On 03.04.2012 07:22, Eric Deutsch wrote:
> Hi Gerhard, I do not know the status of these. I would say that it would be
> nice to make some of these term names more complete on their own. In many
> cases, the definition probably should be the term name. For example, I think
> I would suggest "sandwich MALDI sample preparation" instead of just
> "sandwich". The definition should then describe what this really is.
>
>
>> -----Original Message-----
>> From: Gerhard Mayer [mailto:Ger...@ru...]
>> Sent: Sunday, April 01, 2012 11:56 PM
>> To: psi...@li...; psidev-pi-
>> de...@li...; Mass spectrometry standard development
>> Subject: [Psidev-ms-dev] Release candidate 3.22.0_rc1 of psi-ms.obo
>>
>> Dear proteomics community,
>>
>> attached there's a list of pending proposed new CV terms mainly about
>> MALDI sample
>> preparation methods, MALDI matrix solutions and baseline reduction
>> methods, which
>> were requested in February 2011, but were until now not integrated into
>> the CV. I don't
>> know the details about the current discussion status of these terms.
>> Does someone know more details about the status of these terms?
>>
>> Comments and suggestions are as always welcome.
>>
>> Newly added CV terms in 3.22.0_rc1:
>> ===================================
>> [Term]
>> id: MS:1001987
>> name: vacuum drying
>> def: "Vacuum-drying MALDI sample preparation crystallization method."
>> [PSI:MS]
>> is_a: MS:1000833 ! matrix application type
>>
>> [Term]
>> id: MS:1001988
>> name: crushed crystal
>> def: "Crushed-crystal MALDI sample preparation method." [PSI:MS]
>> is_a: MS:1000833 ! matrix application type
>>
>> [Term]
>> id: MS:1001989
>> name: fast evaporation
>> def: "Fast-evaporation MALDI sample preparation method." [PSI:MS]
>> is_a: MS:1000833 ! matrix application type
>>
>> [Term]
>> id: MS:1001990
>> name: overlayer
>> def: "Overlayer method combining features of the crushed-crystal method
>> and the fast-evaporation method." [PSI:MS]
>> is_a: MS:1000833 ! matrix application type
>>
>> [Term]
>> id: MS:1001991
>> name: sandwich
>> def: "Sandwich MALDI sample preparation method." [PSI:MS]
>> is_a: MS:1000833 ! matrix application type
>>
>> [Term]
>> id: MS:1001992
>> name: spin coating
>> def: "Spin coating MALDI sample preparation method." [PSI:MS]
>> is_a: MS:1000833 ! matrix application type
>>
>> [Term]
>> id: MS:1001993
>> name: quick and dirty
>> def: "Quick&  dirty (Q&D) sample preparation separating matrix handling
>> from sample handling." [PSI:MS]
>> is_a: MS:1000833 ! matrix application type
>>
>> [Term]
>> id: MS:1001994
>> name: alpha-cyano-4-hydroxycinnamic acid
>> def: "Alpha-cyano-4-hydroxycinnamic acid MALDI matrix."
>> [PubChem_Compound:5328791]
>> synonym: "CHCA" EXACT []
>> synonym: "alpha-Cyano" EXACT []
>> is_a: MS:1000834 ! matrix solution
>>
>> [Term]
>> id: MS:1001995
>> name: 3,5-dimethoxy-4-hydroxycinnamic acid
>> def: "3,5-dimethoxy-4-hydroxycinnamic acid MALDI matrix."
>> [PubChem_Compound:637775]
>> synonym: "sinapic acid" EXACT []
>> synonym: "sinapinicc acid" EXACT []
>> is_a: MS:1000834 ! matrix solution
>>
>> [Term]
>> id: MS:1001996
>> name: 2-(4-Hydroxyphenylazo)benzoic acid
>> def: "2-(4-Hydroxyphenylazo)benzoic acid MALDI matrix."
>> [PubChem_Compound:5357439]
>> synonym: "HABA" EXACT []
>> is_a: MS:1000834 ! matrix solution
>>
>> [Term]
>> id: MS:1001997
>> name: 3-Hydroxypicolinic acid
>> def: "3-Hydroxypicolinic acid MALDI matrix." [PubChem_Compound:13401]
>> is_a: MS:1000834 ! matrix solution
>>
>> [Term]
>> id: MS:1001998
>> name: picolinic acid
>> def: "Picolinic acid MALDI matrix." [PubChem_Compound:1018]
>> is_a: MS:1000834 ! matrix solution
>>
>> [Term]
>> id: MS:1001999
>> name: 2,5-Dihydroxybenzoic acid
>> def: "2,5-Dihydroxybenzoic acid MALDI matrix." [PubChem_Compound:7424]
>> synonym: "gentisic acid" EXACT []
>> synonym: "DHB" EXACT []
>> is_a: MS:1000834 ! matrix solution
>>
>> [Term]
>> id: MS:1002000
>> name: 4-hydroxy-3-methoxycinnamic acid
>> def: "4-hydroxy-3-methoxycinnamic acid MALDI matrix."
>> [PubChem_Compound:736186]
>> synonym: "ferulic acid" EXACT []
>> is_a: MS:1000834 ! matrix solution
>>
>> [Term]
>> id: MS:1002001
>> name: anthralin
>> def: "Anthralin MALDI matrix." [PubChem_Compound:2202]
>> synonym: "dithranol" EXACT []
>> is_a: MS:1000834 ! matrix solution
>>
>> [Term]
>> id: MS:1002002
>> name: T-2-(3-(4-t-Butyl-phenyl)-2-methyl-2-propenylidene) malonitrile
>> def: "T-2-(3-(4-t-Butyl-phenyl)-2-methyl-2-propenylidene) malonitrile
>> MALDI matrix." [PubChem_Compound:6382826]
>> synonym: "DCTB" EXACT []
>> is_a: MS:1000834 ! matrix solution
>>
>> [Term]
>> id: MS:1002003
>> name: 2,4,6-Trihydroxyacetophenone
>> def: "2,4,6-Trihydroxyacetophenone MALDI matrix."
>> [PubChem_Compound:68073]
>> synonym: "THAP" EXACT []
>> is_a: MS:1000834 ! matrix solution
>>
>> [Term]
>> id: MS:1002004
>> name: top hat
>> def: "Top-hat morphological filter based on the basic morphological
>> operations 'erosion' and 'dilatation'." [PSI:MS]
>> is_a: MS:1000593 ! baseline reduction
>>
>> [Term]
>> id: MS:1002005
>> name: convex hull
>> def: "Constructs the baseline by fitting multiple parabolas to the
>> spectrum starting with the large scale structures." [PSI:MS]
>> is_a: MS:1000593 ! baseline reduction
>>
>> [Term]
>> id: MS:1002006
>> name: median
>> def: "The spectrum that will be baseline subtracted is divided into a
>> number of segments." [PSI:MS]
>> is_a: MS:1000593 ! baseline reduction
>>
>> [Term]
>> id: MS:1002007
>> name: wavelet transformation smoothing
>> def: "The random noise is removed by using the undecimated wavelet
>> transform." [PSI:MS]
>> is_a: MS:1000592 ! smoothing
>>
>> [Term]
>> id: MS:1002008
>> name: sophisticated numerical annotation procedure
>> def: "It searches for known patterns in the measured spectrum."
>> [PSI:MS]
>> synonym: "SNAP" EXACT []
>> is_a: MS:1000801 ! area peak picking
>>
>> [Term]
>> id: MS:1002009
>> name: area normalization
>> def: "Normalization of areas below the curves." [PSI:MS]
>> is_a: MS:1001484 ! intensity normalization
>>
>> [Term]
>> id: MS:1002010
>> name: LIFT
>> def: "A Bruker’s proprietary technique where molecular ions are
>> initially accelerated at lower energy, then collide with inert gas in a
>> collision cell that is then “lifted” to high potential. The use of
>> inert
>> gas is optional, as it could lift also fragments provided by LID."
>> [DOI:10.1007/s00216-003-2057-0 , PMID:12830354]
>> is_a: MS:1000044 ! dissociation method
>>
>> Best regards,
>> Gerhard
>>
>> --
>> ---
>> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
>> BioInformatik
>> Medizinisches-Proteom-Center (MPC)
>> Ruhr-Universität Bochum
>> Zentrum für klinische Forschung I (ZKF I)
>> E.042
>> Universitätsstrasse 150
>> D-44801 Bochum
>>
>> Phone:	+49(0)234/32-29836
>> Fax:	+49(0)234/32-14554
>> Email:	Ger...@ru...
>> Web:	http://www.medizinisches-proteom-center.de
> ------------------------------------------------------------------------------
> Better than sec? Nothing is better than sec when it comes to
> monitoring Big Data applications. Try Boundary one-second
> resolution app monitoring today. Free.
> http://p.sf.net/sfu/Boundary-dev2dev
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

Re: [Psidev-ms-dev] Release candidate 3.22.0_rc1 of psi-ms.obo

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

Hi Gerhard, I do not know the status of these. I would say that it would be
nice to make some of these term names more complete on their own. In many
cases, the definition probably should be the term name. For example, I think
I would suggest "sandwich MALDI sample preparation" instead of just
"sandwich". The definition should then describe what this really is.


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Sunday, April 01, 2012 11:56 PM
> To: psi...@li...; psidev-pi-
> de...@li...; Mass spectrometry standard development
> Subject: [Psidev-ms-dev] Release candidate 3.22.0_rc1 of psi-ms.obo
>
> Dear proteomics community,
>
> attached there's a list of pending proposed new CV terms mainly about
> MALDI sample
> preparation methods, MALDI matrix solutions and baseline reduction
> methods, which
> were requested in February 2011, but were until now not integrated into
> the CV. I don't
> know the details about the current discussion status of these terms.
> Does someone know more details about the status of these terms?
>
> Comments and suggestions are as always welcome.
>
> Newly added CV terms in 3.22.0_rc1:
> ===================================
> [Term]
> id: MS:1001987
> name: vacuum drying
> def: "Vacuum-drying MALDI sample preparation crystallization method."
> [PSI:MS]
> is_a: MS:1000833 ! matrix application type
>
> [Term]
> id: MS:1001988
> name: crushed crystal
> def: "Crushed-crystal MALDI sample preparation method." [PSI:MS]
> is_a: MS:1000833 ! matrix application type
>
> [Term]
> id: MS:1001989
> name: fast evaporation
> def: "Fast-evaporation MALDI sample preparation method." [PSI:MS]
> is_a: MS:1000833 ! matrix application type
>
> [Term]
> id: MS:1001990
> name: overlayer
> def: "Overlayer method combining features of the crushed-crystal method
> and the fast-evaporation method." [PSI:MS]
> is_a: MS:1000833 ! matrix application type
>
> [Term]
> id: MS:1001991
> name: sandwich
> def: "Sandwich MALDI sample preparation method." [PSI:MS]
> is_a: MS:1000833 ! matrix application type
>
> [Term]
> id: MS:1001992
> name: spin coating
> def: "Spin coating MALDI sample preparation method." [PSI:MS]
> is_a: MS:1000833 ! matrix application type
>
> [Term]
> id: MS:1001993
> name: quick and dirty
> def: "Quick & dirty (Q&D) sample preparation separating matrix handling
> from sample handling." [PSI:MS]
> is_a: MS:1000833 ! matrix application type
>
> [Term]
> id: MS:1001994
> name: alpha-cyano-4-hydroxycinnamic acid
> def: "Alpha-cyano-4-hydroxycinnamic acid MALDI matrix."
> [PubChem_Compound:5328791]
> synonym: "CHCA" EXACT []
> synonym: "alpha-Cyano" EXACT []
> is_a: MS:1000834 ! matrix solution
>
> [Term]
> id: MS:1001995
> name: 3,5-dimethoxy-4-hydroxycinnamic acid
> def: "3,5-dimethoxy-4-hydroxycinnamic acid MALDI matrix."
> [PubChem_Compound:637775]
> synonym: "sinapic acid" EXACT []
> synonym: "sinapinicc acid" EXACT []
> is_a: MS:1000834 ! matrix solution
>
> [Term]
> id: MS:1001996
> name: 2-(4-Hydroxyphenylazo)benzoic acid
> def: "2-(4-Hydroxyphenylazo)benzoic acid MALDI matrix."
> [PubChem_Compound:5357439]
> synonym: "HABA" EXACT []
> is_a: MS:1000834 ! matrix solution
>
> [Term]
> id: MS:1001997
> name: 3-Hydroxypicolinic acid
> def: "3-Hydroxypicolinic acid MALDI matrix." [PubChem_Compound:13401]
> is_a: MS:1000834 ! matrix solution
>
> [Term]
> id: MS:1001998
> name: picolinic acid
> def: "Picolinic acid MALDI matrix." [PubChem_Compound:1018]
> is_a: MS:1000834 ! matrix solution
>
> [Term]
> id: MS:1001999
> name: 2,5-Dihydroxybenzoic acid
> def: "2,5-Dihydroxybenzoic acid MALDI matrix." [PubChem_Compound:7424]
> synonym: "gentisic acid" EXACT []
> synonym: "DHB" EXACT []
> is_a: MS:1000834 ! matrix solution
>
> [Term]
> id: MS:1002000
> name: 4-hydroxy-3-methoxycinnamic acid
> def: "4-hydroxy-3-methoxycinnamic acid MALDI matrix."
> [PubChem_Compound:736186]
> synonym: "ferulic acid" EXACT []
> is_a: MS:1000834 ! matrix solution
>
> [Term]
> id: MS:1002001
> name: anthralin
> def: "Anthralin MALDI matrix." [PubChem_Compound:2202]
> synonym: "dithranol" EXACT []
> is_a: MS:1000834 ! matrix solution
>
> [Term]
> id: MS:1002002
> name: T-2-(3-(4-t-Butyl-phenyl)-2-methyl-2-propenylidene) malonitrile
> def: "T-2-(3-(4-t-Butyl-phenyl)-2-methyl-2-propenylidene) malonitrile
> MALDI matrix." [PubChem_Compound:6382826]
> synonym: "DCTB" EXACT []
> is_a: MS:1000834 ! matrix solution
>
> [Term]
> id: MS:1002003
> name: 2,4,6-Trihydroxyacetophenone
> def: "2,4,6-Trihydroxyacetophenone MALDI matrix."
> [PubChem_Compound:68073]
> synonym: "THAP" EXACT []
> is_a: MS:1000834 ! matrix solution
>
> [Term]
> id: MS:1002004
> name: top hat
> def: "Top-hat morphological filter based on the basic morphological
> operations 'erosion' and 'dilatation'." [PSI:MS]
> is_a: MS:1000593 ! baseline reduction
>
> [Term]
> id: MS:1002005
> name: convex hull
> def: "Constructs the baseline by fitting multiple parabolas to the
> spectrum starting with the large scale structures." [PSI:MS]
> is_a: MS:1000593 ! baseline reduction
>
> [Term]
> id: MS:1002006
> name: median
> def: "The spectrum that will be baseline subtracted is divided into a
> number of segments." [PSI:MS]
> is_a: MS:1000593 ! baseline reduction
>
> [Term]
> id: MS:1002007
> name: wavelet transformation smoothing
> def: "The random noise is removed by using the undecimated wavelet
> transform." [PSI:MS]
> is_a: MS:1000592 ! smoothing
>
> [Term]
> id: MS:1002008
> name: sophisticated numerical annotation procedure
> def: "It searches for known patterns in the measured spectrum."
> [PSI:MS]
> synonym: "SNAP" EXACT []
> is_a: MS:1000801 ! area peak picking
>
> [Term]
> id: MS:1002009
> name: area normalization
> def: "Normalization of areas below the curves." [PSI:MS]
> is_a: MS:1001484 ! intensity normalization
>
> [Term]
> id: MS:1002010
> name: LIFT
> def: "A Bruker’s proprietary technique where molecular ions are
> initially accelerated at lower energy, then collide with inert gas in a
> collision cell that is then “lifted” to high potential. The use of
> inert
> gas is optional, as it could lift also fragments provided by LID."
> [DOI:10.1007/s00216-003-2057-0 , PMID:12830354]
> is_a: MS:1000044 ! dissociation method
>
> Best regards,
> Gerhard
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> BioInformatik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.042
> Universitätsstrasse 150
> D-44801 Bochum
>
> Phone:	+49(0)234/32-29836
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.22.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's a list of pending proposed new CV terms mainly about 
MALDI sample
preparation methods, MALDI matrix solutions and baseline reduction 
methods, which
were requested in February 2011, but were until now not integrated into 
the CV. I don't
know the details about the current discussion status of these terms.
Does someone know more details about the status of these terms?

Comments and suggestions are as always welcome.

Newly added CV terms in 3.22.0_rc1:
===================================
[Term]
id: MS:1001987
name: vacuum drying
def: "Vacuum-drying MALDI sample preparation crystallization method." 
[PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001988
name: crushed crystal
def: "Crushed-crystal MALDI sample preparation method." [PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001989
name: fast evaporation
def: "Fast-evaporation MALDI sample preparation method." [PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001990
name: overlayer
def: "Overlayer method combining features of the crushed-crystal method 
and the fast-evaporation method." [PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001991
name: sandwich
def: "Sandwich MALDI sample preparation method." [PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001992
name: spin coating
def: "Spin coating MALDI sample preparation method." [PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001993
name: quick and dirty
def: "Quick & dirty (Q&D) sample preparation separating matrix handling 
from sample handling." [PSI:MS]
is_a: MS:1000833 ! matrix application type

[Term]
id: MS:1001994
name: alpha-cyano-4-hydroxycinnamic acid
def: "Alpha-cyano-4-hydroxycinnamic acid MALDI matrix." 
[PubChem_Compound:5328791]
synonym: "CHCA" EXACT []
synonym: "alpha-Cyano" EXACT []
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1001995
name: 3,5-dimethoxy-4-hydroxycinnamic acid
def: "3,5-dimethoxy-4-hydroxycinnamic acid MALDI matrix." 
[PubChem_Compound:637775]
synonym: "sinapic acid" EXACT []
synonym: "sinapinicc acid" EXACT []
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1001996
name: 2-(4-Hydroxyphenylazo)benzoic acid
def: "2-(4-Hydroxyphenylazo)benzoic acid MALDI matrix." 
[PubChem_Compound:5357439]
synonym: "HABA" EXACT []
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1001997
name: 3-Hydroxypicolinic acid
def: "3-Hydroxypicolinic acid MALDI matrix." [PubChem_Compound:13401]
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1001998
name: picolinic acid
def: "Picolinic acid MALDI matrix." [PubChem_Compound:1018]
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1001999
name: 2,5-Dihydroxybenzoic acid
def: "2,5-Dihydroxybenzoic acid MALDI matrix." [PubChem_Compound:7424]
synonym: "gentisic acid" EXACT []
synonym: "DHB" EXACT []
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1002000
name: 4-hydroxy-3-methoxycinnamic acid
def: "4-hydroxy-3-methoxycinnamic acid MALDI matrix." 
[PubChem_Compound:736186]
synonym: "ferulic acid" EXACT []
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1002001
name: anthralin
def: "Anthralin MALDI matrix." [PubChem_Compound:2202]
synonym: "dithranol" EXACT []
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1002002
name: T-2-(3-(4-t-Butyl-phenyl)-2-methyl-2-propenylidene) malonitrile
def: "T-2-(3-(4-t-Butyl-phenyl)-2-methyl-2-propenylidene) malonitrile 
MALDI matrix." [PubChem_Compound:6382826]
synonym: "DCTB" EXACT []
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1002003
name: 2,4,6-Trihydroxyacetophenone
def: "2,4,6-Trihydroxyacetophenone MALDI matrix." [PubChem_Compound:68073]
synonym: "THAP" EXACT []
is_a: MS:1000834 ! matrix solution

[Term]
id: MS:1002004
name: top hat
def: "Top-hat morphological filter based on the basic morphological 
operations 'erosion' and 'dilatation'." [PSI:MS]
is_a: MS:1000593 ! baseline reduction

[Term]
id: MS:1002005
name: convex hull
def: "Constructs the baseline by fitting multiple parabolas to the 
spectrum starting with the large scale structures." [PSI:MS]
is_a: MS:1000593 ! baseline reduction

[Term]
id: MS:1002006
name: median
def: "The spectrum that will be baseline subtracted is divided into a 
number of segments." [PSI:MS]
is_a: MS:1000593 ! baseline reduction

[Term]
id: MS:1002007
name: wavelet transformation smoothing
def: "The random noise is removed by using the undecimated wavelet 
transform." [PSI:MS]
is_a: MS:1000592 ! smoothing

[Term]
id: MS:1002008
name: sophisticated numerical annotation procedure
def: "It searches for known patterns in the measured spectrum." [PSI:MS]
synonym: "SNAP" EXACT []
is_a: MS:1000801 ! area peak picking

[Term]
id: MS:1002009
name: area normalization
def: "Normalization of areas below the curves." [PSI:MS]
is_a: MS:1001484 ! intensity normalization

[Term]
id: MS:1002010
name: LIFT
def: "A Bruker’s proprietary technique where molecular ions are 
initially accelerated at lower energy, then collide with inert gas in a 
collision cell that is then “lifted” to high potential. The use of inert 
gas is optional, as it could lift also fragments provided by LID." 
[DOI:10.1007/s00216-003-2057-0 , PMID:12830354]
is_a: MS:1000044 ! dissociation method

Best regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] psi-ms controlled vocabulary v.3.21.0 released

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

Dear proteomics community,

attached there's the new psi-ms.obo version 3.21.0.

1. Changed CV terms:
====================
The use of web links is now unified by specifying web links always in 
the dbxref lists following the definition of the def tag.

Wherever possible the "GO database abbreviations" as defined in 
http://www.geneontology.org/cgi-bin/xrefs.cgi
were used:
     BRENDA            for links to the BRENDA enzyme database
     DOI                    for Digital Object Identifier links
     PMID                for PubMed links
     PubChem_Compound    for links to PubChem

The affected terms are:
-----------------------
[Term]
id: MS:1000872
name: MaRiMba
def: "Software used to predict transitions for selected reaction 
monitoring experiments based on observed spectrum libraries developed 
and distributed by the Institute for Systems Biology." 
[http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba 
""]
is_a: MS:1000871 ! SRM software

[Term]
id: MS:1000874
name: SSRCalc
def: "Sequence Specific Retention Calculator esimates the retention time 
of peptides based on their sequence." 
[http://hs2.proteome.ca/SSRCalc/SSRCalc.html ""]
is_a: MS:1000873 ! peptide attribute calculation software

[Term]
id: MS:1000902
name: H-PINS retention time normalization standard
def: "The de facto standard providing the retention times at which a set 
of halogenated reference peptides exit the reference chromatographic 
column." [DOI:10.1074/mcp.M800569-MCP200, PMID:19411281]
is_a: MS:1000901 ! retention time normalization standard

[Term]
id: MS:1000922
name: Skyline
def: "Software used to predict, select, and optimize transitions as well 
as analyze the results of selected reaction monitoring runs developed 
and distributed by the MacCoss lab at the University of Washington. 
https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default." 
[PSI:MS]
is_a: MS:1000871 ! SRM software

[Term]
id: MS:1000923
name: TIQAM
def: "Software used to predict, select, and optimize transitions for 
selected reaction monitoring experiments developed and distributed by 
the Institute for Systems Biology." 
[http://tools.proteomecenter.org/TIQAM/TIQAM.html ""]
is_a: MS:1000871 ! SRM software

[Term]
id: MS:1000924
name: MaRiMba
def: "OBSOLETE Software used to predict transitions for selected 
reaction monitoring experiments based on observed spectrum libraries 
developed and distributed by the Institute for Systems Biology." 
[http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba 
""]
comment: This term was made obsolete because it was redundant with an 
existing term (MS:1000872)
is_obsolete: true
replaced_by: MS:1000872

[Term]
id: MS:1001874
name: FDRScore
def: "Quality measurement score." [PMID:19253293]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001915
name: leukocyte elastase
def: "Enzyme leukocyte elastase (EC 3.4.21.37)." [BRENDA:3.4.21.37]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001957 ! (?<=[ALIV])(?!P)

[Term]
id: MS:1001916
name: proline endopeptidase
def: "Enzyme proline endopeptidase (EC 3.4.21.26)." [BRENDA:3.4.21.26]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001958 ! (?<=[HKR]P)(?!P)

[Term]
id: MS:1001917
name: glutamyl endopeptidase
def: "Enzyme glutamyl endopeptidase (EC 3.4.21.19)." [BRENDA:3.4.21.19]
synonym: "staphylococcal protease" EXACT []
synonym: "Glu-C" EXACT []
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001959 ! (?<=[^E]E)

[Term]
id: MS:1001918
name: 2-iodobenzoate
def: "Chemical iodobenzoate. Cleaves after W." [PubChem_Compound:4739928]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001960 ! (?<=W)



For MS:1000889 the definition was proposed to change
from
def: "A sequence of letter symbols denoting the order of amino acids 
that compose the peptide plus the encoding any amino acid mass 
modifications that are present using the notation where the total mass 
of the modified amino acid is specified in square bracketed numbers 
following the letter (e.g. R[162.10111] indicates an arginine whose 
final modified mass is 162.10111 amu)." [PSI:MS]
to
def: "A sequence of letter symbols denoting the order of amino acids 
that compose the peptide plus the encoding any amino acid modifications 
that are present." [PSI:MS]

[Term]
id: MS:1000889
name: modified peptide sequence
def: "A sequence of letter symbols denoting the order of amino acids 
that compose the peptide plus the encoding any amino acid modifications 
that are present." [PSI:MS]
comment: Make it more general as there are actually many other ways to 
display a modified peptide sequence.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000887 ! peptide attribute


2. Newly added CV terms:
========================
Here also the official "GO database abbreviations" DOI and PMID are now 
used in the dbxref lists for the new terms
MS:1001969
MS:1001970
MS:1001971
MS:1001978
MS:1001985
MS:1001986

2.1 terms for ion mobility:
---------------------------
[Term]
id: MS:1001966
name: product ion mobility
def: "The mobility of an MS2 product ion, as measured by ion mobility 
mass spectrometry." [PSI:MS]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001967
name: product ion drift time
def: "The ion drift time of an MS2 product ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000028 ! millisecond


2.2 terms for phosphorylation site localization:
------------------------------------------------
[Term]
id: MS:1001968
name: PTM localization score
def: "A score that assign confidence to the localization of an amino 
acid modification on a peptide sequence." [PSI:MS]
is_a: MS:1001143 ! search engine specific score for peptides

[Term]
id: MS:1001969
name: ProteomeDiscoverer:phosphoRS score
def: "Peptide score based on the cumulative binomial probability that 
the observed match is a random event." [DOI:10.1021/pr200611n, 
PMID:22073976]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001970
name: ProteomeDiscoverer:phosphoRS sequence probability
def: "Probability that the respective isoform is correct." 
[DOI:10.1021/pr200611n, PMID:22073976]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001971
name: ProteomeDiscoverer:phosphoRS site probability
def: "Estimate of the probability that the respective site is truly 
phosphorylated." [DOI:10.1021/pr200611n, PMID:22073976]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001972
name: PTM scoring algorithm version
def: "Version of the post-translational modification scoring algorithm." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1001973
name: DeBunker
def: "DeBunker software." [PSI:MS]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001974
name: DeBunker:score
def: "Score specific to DeBunker." [PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001975
name: delta m/z
def: "The difference between a theoretically calculated m/z and the 
corresponding experimentally measured m/z. It can be expressed as 
absolute or relative value." [PSI:MS]
synonym: "m/z difference" EXACT []
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1001976
name: delta M
def: "The difference between a theoretically calculated molecular mass M 
and the corresponding experimentally measured M. It can be expressed as 
absolute or relative value." [PSI:MS]
synonym: "mass difference" EXACT []
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1001977
name: MSQuant
def: "MSQuant software." [PSI:MS]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001978
name: MSQuant:PTM-score
def: "The PTM score from MSQuant software." [DOI:10.1021/pr900721e, 
PMID:19888749]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001979
name: MaxQuant:PTM Score
def: "The PTM score from MaxQuant software." [PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001980
name: MaxQuant:Phospho (STY) Probabilities
def: "The Phospho (STY) Probabilities from MaxQuant software." [PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001981
name: MaxQuant:Phospho (STY) Score Diffs
def: "The Phospho (STY) Score Diffs from MaxQuant software." [PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001982
name: MaxQuant:P-site localization probability
def: "The P-site localization probability value from MaxQuant software." 
[PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001983
name: MaxQuant:PTM Delta Score
def: "The PTM Delta Score value from MaxQuant software (Difference 
between highest scoring site and second highest)." [PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001984
name: Ascore
def: "Ascore software." [PSI:MS]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001985
name: Ascore:Ascore
def: "The Ascore score value from Ascore software." 
[DOI:10.1038/nbt1240, PMID:16964243]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001986
name: H-Score
def: "H-Score for peptide phosphorylation site location." 
[DOI:10.1021/pr1006813, PMID:20836569]
is_a: MS:1001968 ! PTM localization score

Best regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.21.0_rc3 of psi-ms.obo

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

Dear proteomics community,

attached there's the psi-ms.obo release candidate 3.21.0_rc3.

It contains the terms proposed by Andy Jones concerning the ion mobility,
and terms requested by Henk van den Toorn resp. Pierre-Alain Binz concerning
post translational modification scoring and site localization algorithms.

Comments and suggestions are as always welcome. If there are no
objections it's planned to release this new version 3.21.0 next friday.

1. Changed CV terms:
====================
For MS:1000889 the definition was proposed to change
from
def: "A sequence of letter symbols denoting the order of amino acids 
that compose the peptide plus the encoding any amino acid mass 
modifications that are present using the notation where the total mass 
of the modified amino acid is specified in square bracketed numbers 
following the letter (e.g. R[162.10111] indicates an arginine whose 
final modified mass is 162.10111 amu)." [PSI:MS]
to
def: "A sequence of letter symbols denoting the order of amino acids 
that compose the peptide plus the encoding any amino acid modifications 
that are present." [PSI:MS]

[Term]
id: MS:1000889
name: modified peptide sequence
def: "A sequence of letter symbols denoting the order of amino acids 
that compose the peptide plus the encoding any amino acid modifications 
that are present." [PSI:MS]
comment: Make it more general as there are actually many other ways to 
display a modified peptide sequence.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000887 ! peptide attribute


2. Newly added CV terms:
========================
2.1 terms for ion mobility:
---------------------------

[Term]
id: MS:1001966
name: product ion mobility
def: "The mobility of an MS2 product ion, as measured by ion mobility 
mass spectrometry." [PSI:MS]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001967
name: product ion drift time
def: "The ion drift time of an MS2 product ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000028 ! millisecond


2.2 terms for phosphorylation site localization:
------------------------------------------------
[Term]
id: MS:1001968
name: PTM localization score
def: "A score that assign confidence to the localization of an amino 
acid modification on a peptide sequence." [PSI:MS]
is_a: MS:1001143 ! search engine specific score for peptides

[Term]
id: MS:1001969
name: ProteomeDiscoverer:phosphoRS score
def: "Peptide score based on the cumulative binomial probability that 
the observed match is a random event." [doi:10.1021/pr200611n "DOI", 
http://www.ncbi.nlm.nih.gov/pubmed/22073976 "PubMed", 
http://pubs.acs.org/doi/abs/10.1021/pr200611n ""]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001970
name: ProteomeDiscoverer:phosphoRS sequence probability
def: "Probability that the respective isoform is correct." 
[doi:10.1021/pr200611n "DOI", 
http://www.ncbi.nlm.nih.gov/pubmed/22073976 "PubMed", 
http://pubs.acs.org/doi/abs/10.1021/pr200611n ""]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001971
name: ProteomeDiscoverer:phosphoRS site probability
def: "Estimate of the probability that the respective site is truly 
phosphorylated." [doi:10.1021/pr200611n "DOI", 
http://www.ncbi.nlm.nih.gov/pubmed/22073976 "PubMed", 
http://pubs.acs.org/doi/abs/10.1021/pr200611n ""]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001972
name: PTM scoring algorithm version
def: "Version of the post-translational modification scoring algorithm." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1001973
name: DeBunker
def: "DeBunker software." [PSI:MS]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001974
name: DeBunker:score
def: "Score specific to DeBunker." [PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001975
name: delta m/z
def: "The difference between a theoretically calculated m/z and the 
corresponding experimentally measured m/z. It can be expressed as 
absolute or relative value." [PSI:MS]
synonym: "m/z difference" EXACT []
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1001976
name: delta M
def: "The difference between a theoretically calculated molecular mass M 
and the corresponding experimentally measured M. It can be expressed as 
absolute or relative value." [PSI:MS]
synonym: "mass difference" EXACT []
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1001977
name: MSQuant
def: "MSQuant software." [PSI:MS]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001978
name: MSQuant:PTM-score
def: "The PTM score from MSQuant software." [doi:10.1021/pr900721e 
"DOI", http://www.ncbi.nlm.nih.gov/pubmed/19888749 "PubMed", 
http://pubs.acs.org/doi/pdfplus/10.1021/pr900721e ""]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001979
name: MaxQuant:PTM Score
def: "The PTM score from MaxQuant software." [PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001980
name: MaxQuant:Phospho (STY) Probabilities
def: "The Phospho (STY) Probabilities from MaxQuant software." [PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001981
name: MaxQuant:Phospho (STY) Score Diffs
def: "The Phospho (STY) Score Diffs from MaxQuant software." [PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001982
name: MaxQuant:P-site localization probability
def: "The P-site localization probability value from MaxQuant software." 
[PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001983
name: MaxQuant:PTM Delta Score
def: "The PTM Delta Score value from MaxQuant software (Difference 
between highest scoring site and second highest)." [PSI:MS]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001984
name: Ascore
def: "Ascore software." [PSI:MS]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001985
name: Ascore:Ascore
def: "The Ascore score value from Ascore software." [doi:10.1038/nbt1240 
"DOI", http://www.ncbi.nlm.nih.gov/pubmed/16964243 "PubMed", 
http://www.nature.com/nbt/journal/v24/n10/full/nbt1240.html ""]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001986
name: H-Score
def: "H-Score for peptide phosphorylation site location." 
[doi:10.1021/pr1006813 "DOI", 
http://www.ncbi.nlm.nih.gov/pubmed/20836569 "PubMed", 
http://pubs.acs.org/doi/pdf/10.1021/pr1006813 ""]
is_a: MS:1001968 ! PTM localization score


Best regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] TraML: Polarity in wrong position ?

[Steffen N. <sne...@ip...>]

Hi,

our spec doc says http://www.peptideatlas.org/schemas/TraML/1.0.0/TraML1.0.0.html#Instrument
that <cvParam value="Positive" accession="MS:1000037" name="polarity" cvRef="MS"/>
goes under <Instrument>.


1) "MS:1000037" is in purgatory. Is that a problem ? Or just cosmetics ?

2) The polarity cvParam in the example of the spec doc is probably 
   not covered by the MappingFile, because the only rule is 
   "MUST supply a *child* term of MS:1000031 (instrument model)",
   but no "MAY ...". 

3) Isn't that rather stuff for the <Configuration> 
   used under <Target> and <Transition> ?
   Because those will be converted to the instrument methods,
   where the polarity matters, and the instrument may
   switch polarities during the run (at least for the <Target> lists.

Comments ?

Yours,
Steffen


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

[Psidev-ms-dev] mzQuantML update from San Diego

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

Hi all,

I've written up my notes on mzQuantML and circulated for comment and amendment. I've included the PSI-MS list as well, since I would like comments from this group as well, especially with regards to SRM support,
cheers
Andy

Summary of mzQuantML outcomes of PSI meeting
**********************************************

1. No major problems with general schema, but very challenging to implement consistently for different techniques.
2. Some minor changes to the schema seem sensible, some we discussed, some I am proposing now:
    - Move all metadata-type elements up to the top of the hierarchy
    - Enforce a reference from PeptideConsensus to one or more Features (a feature is minimally just a m/z and charge value), no reason not to provide this
    - I would like to propose a simplication in the reference system from PeptideConsensus to Feature

    We currently have parallel arrays within PeptideConsensus:
        <PeptideConsensus id="PEPTIDER" charge="2">
            <PeptideSequence>PEPTIDER</PeptideSequence>
            <Fe_refs>ft_13768 ft_137629 ft_137630 ft_137631 ft_137632 ft_137633 ft_137634 ft_137635 ft_137636 ft_137637 ft_137638 ft_137639 ft_573540 ft_573541 ft_573542 ft_573543 ft_573544 ft_573545 ft_573546 ft_573547 ft_573548 ft_573549 ft_573550 ft_573551</Fe_refs>
            <Assay_refs>ass_0 ass_1 ass_2 ass_3 ass_4 ass_5 ass_6 ass_7 ass_8 ass_9 ass_10 ass_11</Assay_refs>
        </PeptideConsensus>

        In our example files, the parallel arrays contain lots of errors. These could be checked by the semantic validator but I prefer the long-hand way of doing this that explicitly ties every feature to an assay:

        <PeptideConsensus id="PEPTIDER" charge="2">
            <PeptideSequence>PEPTIDER</PeptideSequence>
            <FeatureRef feature_ref="featureB_1" assay_ref="B1"/>
            <FeatureRef feature_ref="featureB_1" assay_ref="B1"/>
            <FeatureRef feature_ref="featureB_1" assay_ref="B1"/>
            <FeatureRef feature_ref="featureB_1" assay_ref="C1"/>
            <FeatureRef feature_ref="featureE_1" assay_ref="E1"/>
            ....
        </PeptideConsensus>

    - Some minor changes to the case of elements
    - Added optional chromatogram_id and spectrum_id to feature. The former is required for SRM, the latter seems like it would be useful for approaches that are not based on rt maps.
    - Made charge mandatory on Feature - is this ever not known?

3. The major new proposal at the meeting was that we need to build (very soon) semantic validation software to enforce rules beyond XML schema checking and mapping file validation. This is because mzQuantML is a general specification and different types of quant method need to be represented consistently. As such, we have created a set of rules which will be formalised in semantic validation software.

The semantic validator will perform the following steps (to be coded in Java):

- XML Schema validation
- First check the type of method (in level 1 we support MS1 label free, MS1 label, MS2 tag and spectral count)
- Load the appropriate module encoding the rules defined in Rule Files in the schema directory for this technique
- Provide warnings or error messages for each rule broken by the file
- Perform CV validation by loading the general mzq Mapping file and a specific mapping file for the technique (can we re-use any of the EBI's validator for this?)

ACTION: Da to start work on the software, release for beta testing by the end of the month.

4. The plan is to get the core specifications for mzQuantML back into the PSI document process very soon with the semantic validation software encoding the specific types of example soon after or at the same time - still to discuss. The core documentation needs to describe only the basic format. The mechanism for describing the technique-specific encodings may be:
    - Appendices to the main spec doc
    - PSI Informational documents
    - Some other mechanism?

5. We will resume weekly conference calls when possible for the next 2-3 months to get everything finalised, proposal is to resume at 4pm UK time on Thursdays?

6. SRM support - This was identified by a reviewer as an important need. Eric has started an example document and we should see this through to completion before submitting the core specifications, since there may be further minor schema changes. My current feeling is to leave SRM out of the level 1 technique support, since we still do not have sufficient experience of what is currenty produced by SRM tools. If anyone from the MS community is willing to help with this, we can try to include it in level 1, else it will have to wait for the level 2 release, due at the end of the year.

ACTION: Andy to add further schema changes for SRM support including method files  for referencing TraML etc.

7. We would like to get mzQuantML support into ProteoWizard soon to sanity check the schema e.g. exporting from TPP tools.
ACTION: Andy to liaise with Parag to find a suitable person to code this up - someone could be employed on a short term basis to do this, any volunteers?

Did I miss anything else...?

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Open psi-ms.obo term proposals to discuss at HUPO-PSI meeting in San Diego next week

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

Hi Gerhard, many thanks for putting this together. It will be great to
finalize this next week. One suggestion I'll make is to include the
original publication of each of the scoring algorithm definitions. I think
each one probably derives from an original single publication. It would
also be good to use the same punctuation/capitalization as the original
paper as the term name.

Thanks!
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Friday, March 09, 2012 5:19 AM
> To: psi...@li...; psidev-pi-
> de...@li...; Mass spectrometry standard development
> Subject: [Psidev-ms-vocab] Open psi-ms.obo term proposals to discuss at
> HUPO-PSI meeting in San Diego next week
>
> Dear proteomics community,
>
> attached there's the psi-ms.obo release candidate 3.21.0_rc2 as a basis
> for
> discussion on the HUPO PSI meeting next week in San Diego.
>
> It contains some new terms proposed by Andy Jones concerning the ion
> mobility
> resp. Henk van den Toorn concerning post translational modification
> scoring.
>
> In addition Terry Farah and Sean L. Seymour will make a proposal of
> some
> CV terms
> belonging to protein grouping to us (see also the attached Powerpoint
> and Excel files).
>
>
> Newly added CV terms:
> =====================
> [Term]
> id: MS:1001966
> name: product ion mobility
> def: "The mobility of an MS2 product ion, as measured by ion mobility
> mass spectrometry." [PSI:MS]
> is_a: MS:1001221 ! fragmentation information
>
> [Term]
> id: MS:1001967
> name: product ion drift time
> def: "The ion drift time of an MS2 product ion." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> relationship: has_units UO:0000028 ! millisecond
>
> [Term]
> id: MS:1001968
> name: PTM scoring algorithm name
> def: "Name of the algorithm used for post-translational modification
> scoring." [PSI:MS]
> is_a: MS:1001471 ! peptide modification details
>
> [Term]
> id: MS:1001969
> name: pRS score
> def: "Peptide score based on the cumulative binomial probability that
> the observed match is a random event." [PSI:MS]
> is_a: MS:1001968 ! PTM scoring algorithm name
>
> [Term]
> id: MS:1001970
> name: pRS sequence probability
> def: "Probability that the isoform is correct." [PSI:MS]
> is_a: MS:1001968 ! PTM scoring algorithm name
>
> [Term]
> id: MS:1001971
> name: pRS site probability
> def: "For each phosphorylation site, this value is an estimate of the
> probability that the site is truly phosphorylated." [PSI:MS]
> is_a: MS:1001968 ! PTM scoring algorithm name
>
> [Term]
> id: MS:1001972
> name: PTM score
> def: "Posttranslational modification score." [PSI:MS]
> is_a: MS:1001968 ! PTM scoring algorithm name
>
> [Term]
> id: MS:1001973
> name: a-score
> def: "A-Score for peptide phosphorylation site location." [PSI:MS]
> is_a: MS:1001968 ! PTM scoring algorithm name
>
> [Term]
> id: MS:1001974
> name: h-score
> def: "H-Score for peptide phosphorylation site location." [PSI:MS]
> is_a: MS:1001968 ! PTM scoring algorithm name
>
> [Term]
> id: MS:1001975
> name: delta score
> def: "Phosphorylation site localization delta score." [PSI:MS]
> is_a: MS:1001968 ! PTM scoring algorithm name
>
> [Term]
> id: MS:1001976
> name: PTM scoring algorithm version
> def: "Version of the post-translational modification scoring
> algorithm."
> [PSI:MS]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001471 ! peptide modification details
>
> [Term]
> id: MS:1001977
> name: PTM scoring value
> def: "Score value for post-translational modification." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
>
> Best regards,
> Gerhard
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> BioInformatik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.042
> Universitätsstrasse 150
> D-44801 Bochum
>
> Phone:	+49(0)234/32-29836
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Open psi-ms.obo term proposals to discuss at HUPO-PSI meeting in San Diego next week

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

Dear proteomics community,

attached there's the psi-ms.obo release candidate 3.21.0_rc2 as a basis for
discussion on the HUPO PSI meeting next week in San Diego.

It contains some new terms proposed by Andy Jones concerning the ion 
mobility
resp. Henk van den Toorn concerning post translational modification scoring.

In addition Terry Farah and Sean L. Seymour will make a proposal of some 
CV terms
belonging to protein grouping to us (see also the attached Powerpoint 
and Excel files).


Newly added CV terms:
=====================
[Term]
id: MS:1001966
name: product ion mobility
def: "The mobility of an MS2 product ion, as measured by ion mobility 
mass spectrometry." [PSI:MS]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001967
name: product ion drift time
def: "The ion drift time of an MS2 product ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000028 ! millisecond

[Term]
id: MS:1001968
name: PTM scoring algorithm name
def: "Name of the algorithm used for post-translational modification 
scoring." [PSI:MS]
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1001969
name: pRS score
def: "Peptide score based on the cumulative binomial probability that 
the observed match is a random event." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001970
name: pRS sequence probability
def: "Probability that the isoform is correct." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001971
name: pRS site probability
def: "For each phosphorylation site, this value is an estimate of the 
probability that the site is truly phosphorylated." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001972
name: PTM score
def: "Posttranslational modification score." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001973
name: a-score
def: "A-Score for peptide phosphorylation site location." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001974
name: h-score
def: "H-Score for peptide phosphorylation site location." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001975
name: delta score
def: "Phosphorylation site localization delta score." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001976
name: PTM scoring algorithm version
def: "Version of the post-translational modification scoring algorithm." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1001977
name: PTM scoring value
def: "Score value for post-translational modification." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

Best regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] PSI MSS WG call notes

[Henk v. d. T. <h.w...@uu...>]

Dear workgroup,

I missed Gerhard's proposal, or else I would have tried to join the WG 
call. I'm happy to see the quick response!

I fully agree we should have an enumeration for the PTM-score name. On 
the other hand, if I look at the PSM scores, I see a flat list (e.g. 
Mascot:score). Would this be the naming convention of choice (like 
ProteomeDiscoverer:pRS site probability) or would the enumeration be a 
better way?

Moreover, different scores exist (at least in Proteome Discoverer) for 
different things:
pRS score
pRS probability
pRS sequence probability
Site probability

pRS score and pRS probability are the same thing, but site probability 
is specific to a modification. Can this be captured in the proposed 
scheme? Could this be applied to proteins as well?

Thanks, Henk

On 2/28/2012 5:39 PM, Eric Deutsch wrote:
>
> Notes from the MSS WG call 2012-02-28
>
> + Present: Florian, Eric, Matt, Pierre-Alain
>
> Agenda:
>
> 1) Plans and agenda for spring PSI workshop in San Diego March 12-14
>
> - Evaluate MIAPE -- Quant for SRM specifically
>
> - Evaluate mzQuantML for SRM specifically and generate examples
>
> - Assemble  guideline recommendations for the HPP
>
> + We will work together with Christoph's track on this
>
> - TraML implementations
>
> - Other
>
> 2) mzML status
>
> - No critical issues
> + Need to add an ion mobility array?
>
> + It would be good to discuss at the SD meeting how to encode ion 
> mobility data in mzML (Wed?)
>
> + There seem to be several possible ways to do it. Can we settle on one?
>
> 3) TraML status
>
> - No critical issues
>
> - Propose TraML examples for encode small molecules using BRENDA or 
> SMILES or other?
>
> 4) Discuss controlled vocabulary items
>
> - Only currently open issues appear to be PI/MSI related
>
> - Any additional terms needed to support metabolomics
>
> - CV Terms from Gerhard:
>
> [Term]
>
> id: MS:1001966
>
> name: product ion mobility
>
> def: "The mobility of an MS2 product ion, as measured by ion mobility
>
> mass spectrometry." [PSI:MS]
>
> is_a: MS:1001221 ! fragmentation information
>
> [Term]
>
> id: MS:1001967
>
> name: product ion drift time
>
> def: "The ion drift time of an MS2 product ion." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> relationship: has_units UO:0000028 ! millisecond
>
> is_a: ???????
>
> + Maybe not necessary???
>
> [Term]
>
> id: MS:1001968
>
> name: PTM scoring algorithm name
>
> def: "Name of the algorithm used for post-translational modification
>
> scoring." [PSI:MS]
>
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
>
> is_a: MS:1001471 ! peptide modification details
>
> + Instead of a free text string, this should be a parent term with 
> enumerated children.
>
> [Term]
>
> id: MS:1001969
>
> name: PTM scoring algorithm version
>
> def: "Version of the post-translational modification scoring algorithm."
>
> [PSI:MS]
>
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
>
> is_a: MS:1001471 ! peptide modification details
>
> [Term]
>
> id: MS:1001970
>
> name: PTM scoring value
>
> def: "Score value for post-translational modification." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> is_a: MS:1001143 ! search engine specific score for peptides
>
> is_a: MS:1001153 ! search engine specific score
>
> + This needs a lot more discussion
>
> 5) MIAPE -- MS
>
> - Trying to collect some final example files from Matt and Salva
>
> + We now have all the example documents for MIAPE -- MS
>
> + MIAPE -- MSI is now nearly ready
>
> + MIAPE -- MS is ready. Will be submitted by the end of the week.
>
> 6) MIAPE -- Quant
>
> - In doc process
>
> - Needs review with SRM in mind
>
> - Needs an SRM example document
>
> + Work on this in San Diego
>
> Next meeting: in person in San Diego March 12^th
>
> *From:*Eric Deutsch [mailto:Eri...@sy... 
> <mailto:Eri...@sy...>]
> *Sent:* Monday, February 27, 2012 11:47 PM
> *To:* Mass spectrometry standard development
> *Cc:* Eric Deutsch
> *Subject:* PSI MSS WG call reminder
>
> Hi everyone, this is a reminder about the PSI MSS WG teleconference 
> call tomorrow, Tuesday, at the usual time.
>
> 08:00 San Francisco
>
> 11:00 New York
>
> 16:00 London
>
> 17:00 Geneva
>
> + Germany: 08001012079
>
> + Switzerland: 0800000860
>
> + Finland: 080011569
>
> + UK: 08081095644
>
> + USA:1-866-832-8490
>
> Generic international: +44 2083222500 (UK number)
>
> access code: 297427 #
>
> Agenda:
>
> 1) Plans and agenda for spring PSI workshop in San Diego March 12-14
>
> 2) mzML status
>
> 3) TraML status
>
> 4) Discuss controlled vocabulary items
>
> 5) MIAPE -- MS
>
> 6) MIAPE -- Quant
>
> Next meeting:
>
> - in San Diego March 12
>


-- 
-------------------------------------------------------------------------------------------------------
*Henk van den Toorn, bioinformatician*
Biomolecular Mass Spectrometry and Proteomics Group
Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences
Utrecht University
Padualaan, 8
3584 CH Utrecht
The Netherlands

E-mail: h.w...@uu...
Tel: +31 30 253 6758
Fax: +31 30 253 6919
--------------------------------------------------------------------------------------------------

[Psidev-ms-dev] PSI MSS WG call notes

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

Notes from the MSS WG call 2012-02-28



+ Present: Florian, Eric, Matt, Pierre-Alain



Agenda:



1) Plans and agenda for spring PSI workshop in San Diego March 12-14

- Evaluate MIAPE – Quant for SRM specifically

- Evaluate mzQuantML for SRM specifically and generate examples

- Assemble  guideline recommendations for the HPP

+ We will work together with Christoph’s track on this

- TraML implementations

- Other

2) mzML status

- No critical issues
+ Need to add an ion mobility array?

+ It would be good to discuss at the SD meeting how to encode ion mobility
data in mzML (Wed?)

+ There seem to be several possible ways to do it. Can we settle on one?

3) TraML status

- No critical issues

- Propose TraML examples for encode small molecules using BRENDA or SMILES
or other?

4) Discuss controlled vocabulary items

- Only currently open issues appear to be PI/MSI related

- Any additional terms needed to support metabolomics

- CV Terms from Gerhard:

[Term]

id: MS:1001966

name: product ion mobility

def: "The mobility of an MS2 product ion, as measured by ion mobility

mass spectrometry." [PSI:MS]

is_a: MS:1001221 ! fragmentation information



[Term]

id: MS:1001967

name: product ion drift time

def: "The ion drift time of an MS2 product ion." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

relationship: has_units UO:0000028 ! millisecond

is_a: ???????

+ Maybe not necessary???



[Term]

id: MS:1001968

name: PTM scoring algorithm name

def: "Name of the algorithm used for post-translational modification

scoring." [PSI:MS]

xref: value-type:xsd\:string "The allowed value-type for this CV term."

is_a: MS:1001471 ! peptide modification details

+ Instead of a free text string, this should be a parent term with
enumerated children.



[Term]

id: MS:1001969

name: PTM scoring algorithm version

def: "Version of the post-translational modification scoring algorithm."

[PSI:MS]

xref: value-type:xsd\:string "The allowed value-type for this CV term."

is_a: MS:1001471 ! peptide modification details



[Term]

id: MS:1001970

name: PTM scoring value

def: "Score value for post-translational modification." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1001143 ! search engine specific score for peptides

is_a: MS:1001153 ! search engine specific score

+ This needs a lot more discussion



5) MIAPE – MS

- Trying to collect some final example files from Matt and Salva

+ We now have all the example documents for MIAPE – MS

+ MIAPE – MSI is now nearly ready

+ MIAPE – MS is ready. Will be submitted by the end of the week.

6) MIAPE – Quant

- In doc process

- Needs review with SRM in mind

- Needs an SRM example document

+ Work on this in San Diego



Next meeting: in person in San Diego March 12th











*From:* Eric Deutsch [mailto:Eri...@sy...]
*Sent:* Monday, February 27, 2012 11:47 PM
*To:* Mass spectrometry standard development
*Cc:* Eric Deutsch
*Subject:* PSI MSS WG call reminder



Hi everyone, this is a reminder about the PSI MSS WG teleconference call
tomorrow, Tuesday, at the usual time.



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ Finland: 080011569

+ UK: 08081095644

+ USA: 1-866-832-8490

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) Plans and agenda for spring PSI workshop in San Diego March 12-14

2) mzML status

3) TraML status

4) Discuss controlled vocabulary items

5) MIAPE – MS

6) MIAPE – Quant



Next meeting:

- in San Diego March 12

[Psidev-ms-dev] psi-ms.obo release candidate

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

Dear community,

attached there's the psi-ms.obo release candidate 3.21.0_rc1.
It contains some new terms proposed by Andy resp. Henk.
We can discuss them at today's PSI MSS WG teleconference.

Newly added CV terms:
=====================
[Term]
id: MS:1001966
name: product ion mobility
def: "The mobility of an MS2 product ion, as measured by ion mobility 
mass spectrometry." [PSI:MS]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001967
name: product ion drift time
def: "The ion drift time of an MS2 product ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000028 ! millisecond

[Term]
id: MS:1001968
name: PTM scoring algorithm name
def: "Name of the algorithm used for post-translational modification 
scoring." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1001969
name: PTM scoring algorithm version
def: "Version of the post-translational modification scoring algorithm." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1001970
name: PTM scoring value
def: "Score value for post-translational modification." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

Best regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] PSI MSS WG call reminder

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

Hi everyone, this is a reminder about the PSI MSS WG teleconference call
tomorrow, Tuesday, at the usual time.



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ Finland: 080011569

+ UK: 08081095644

+ USA: 1-866-832-8490

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) Plans and agenda for spring PSI workshop in San Diego March 12-14

2) mzML status

3) TraML status

4) Discuss controlled vocabulary items

5) MIAPE – MS

6) MIAPE – Quant



Next meeting:

- in San Diego March 12

Re: [Psidev-ms-dev] psi-ms controlled vocabulary v.3.20.0 released

[Henk v. d. T. <h.w...@uu...>]

Dear community,

I'd like to discuss some CV parameters for the annotation of 
post-translational modification (PTM) scores. I'm working on a Proteome 
Discoverer plugin for Pride converter 2 (a DAO) for which I need these 
parameters. I couldn't find any appropriate terms for this, so I'm 
interested if something should be created.

The things I think should be stored are:
- The name of the algorithm (maybe with a version number). i.e. PTM 
score, a-score, h-score, pRS score, delta score, ...
- The score itself for each PTM

If I look at the psi-ms obo file, I was expecting this, score would be 
under 'peptide modification details' (MS:1001471), although I also found 
the 'peptide attribute' (MS:1000887) that also refers to modifications. 
Possibly somebody can shed some light on this?
Moreover, I would suggest the possibility to add PTM scores at the 
protein level (under 'protein modifications' MS:1000933) so future 
'compounded' scores can be addressed.

Does anybody have any thoughts on this?

Thanks, Henk

-- 
-------------------------------------------------------------------------------------------------------
*Henk van den Toorn, bioinformatician*
Biomolecular Mass Spectrometry and Proteomics Group
Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences
Utrecht University
Padualaan, 8
3584 CH Utrecht
The Netherlands

E-mail: h.w...@uu...
Tel: +31 30 253 6758
Fax: +31 30 253 6919
--------------------------------------------------------------------------------------------------

[Psidev-ms-dev] psi-ms controlled vocabulary v.3.20.0 released

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

Dear community,

I updated the psi-ms.obo file to the version 3.20.0 in the SourceForge CVS.
It contains the following changes and new terms:

1. Changes to existing CV terms:
================================
[Term]
id: MS:1001667
name: Mascot:use MudPIT scoring
def: "Determines whether to use MudPIT or normal scoring." [PSI:MS]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

2. Newly added CV terms:
========================
[Term]
id: MS:1001963
name: ProteinExtractor:Weighting
def: "Weighting factor for protein list compilation by ProteinExtractor." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001964
name: ProteinScape:second round Mascot
def: "Flag indicating a second round search with Mascot." [PSI:MS]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001965
name: ProteinScape:second round Phenyx
def: "Flag indicating a second round search with Phenyx." [PSI:MS]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

Best regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de