psidev-pi-dev — General Development List for Proteomics Informatics

Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Multiple search engine encoding (#5)

[Juan A. V. <not...@gi...>]

I also support the change. Life for readers would be much easier, and if needed, people can keep track of all those intermediate results in different mzIdentML files.
Something that has never been discussed in detail, if whether there is the need to create a "wrapper" file that would connect all files belonging to the same experiment together (this is not only applicable to mzidentML, but it could also be applied to link together explicitly identification and quantification results). The most similar thing that there is now is the ProteomeXchange XML format and/or the corresponding tab-delimited file that we use for handling submissions. They would need some extra "tags" to do this, but it would be possible if we think this is needed.

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Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo

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

Yes in fact we did. Gerhard would you mind adding the units back in

From: Eric Deutsch [mailto:ede...@sy...]
Sent: 26 April 2016 16:21
To: Mass spectrometry standard development <psi...@li...>; psi...@li...; psi...@li...
Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo

One little detail: didn’t we want to keep the units on all the terms in this section, and just remove the datatype?

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
..
..


From: Jones, Andy [mailto:And...@li...<mailto:And...@li...>]
Sent: Tuesday, April 26, 2016 6:35 AM
To: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Subject: Re: [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo

Hi Gerhard,
Many thanks for this, looks good.
Best wishes
Andy

From: mayerg97 [mailto:ger...@ru...]
Sent: 26 April 2016 14:23
To: psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Subject: [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo


Dear proteomics community,

attached there's the new version 3.86.0 of the psi-ms.obo file.
It contains all changes agreed on at the HUPO-PSI meeting in Ghent.


New CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ added 11 terms for identifier formats for combined spectra
[Term]
id: MS:1002646
name: native spectrum identifier format, combined spectra
def: "Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated." [PSI:PI]
synonym: "nativeID format, combined spectra" EXACT []
relationship: part_of MS:1000577 ! raw data file

[Term]
id: MS:1002647
name: Thermo nativeID format, combined spectra
def: "Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002648
name: Waters nativeID format, combined spectra
def: "Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002649
name: WIFF nativeID format, combined spectra
def: "WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002650
name: Bruker/Agilent YEP nativeID format, combined spectra
def: "Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002651
name: Bruker BAF nativeID format, combined spectra
def: "Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002652
name: Bruker FID nativeID format, combined spectra
def: "Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002653
name: multiple peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002654
name: single peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002655
name: scan number only nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002656
name: spectrum identifier nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion from mzData. The spectrum id attribute is referenced.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002657
name: mzML unique identifier, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: A unique identifier of a spectrum stored in an mzML file.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002658
name: identification parameter
def: "Identification parameter for the search engine run." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation



Changed CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ Added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ New parent MS:1002657 ! identification parameter
[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications and charge into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

************ Obsoleted the term 'peptide level score'
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in the CV.
is_a: MS:1002358 ! search engine specific score for distinct peptides
is_obsolete: true

************ Changed the definition
[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

************ Added is_a: MS:1001184 ! search statistics
[Term]
id: MS:1002404
name: count of identified proteins
def: "The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details
is_a: MS:1001184 ! search statistics

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity


Best Regards,
Gerhard

--
--
Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER
PhD student
Medizinisches Proteom-Center
DEPARTMENT Medical Bioinformatics
Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554
E-mail ger...@ru...<mailto:ger...@ru...>
www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de>
[cid:image001.jpg@01D1A066.7C96A1D0]

Re: [Psidev-pi-dev] [HUPO-PSI/mzTab] Protein group (#20)

[Juan A. V. <not...@gi...>]

As @jgriss said, when we developed the format we wanted to simplify the reporting of the protein inference. The current encoding was designed from the very beginning and actually it did not change during the process. I am in favour of keeping the concept behind mzTab as it is now. And the idea was never to replace mzIdentML (apart from the protein inference, mzTab is looking more and more a flattened version of mzIdentML) or mzQuantML (in this case, mzTab is not that comprehensive by far).

However, as it usually happens, life for readers is more complex than for writers. I agree in that some guidelines need to be provided, although this will not avoid the issues of people producing "wrong" files. In PRIDE, we need to be able to interpret the information correctly.

So, basically, in the context of protein groups we have two options:
- Keep things like they are now. There is one mechanism to "avoid" the fact that the protein accession is unique, by adding [1], [2], .... after the accession number, if this is needed. This was added for quantification purposes mainly (the case explained by @mvaudel but also if different proteoforms were reported), but it can only be applied to identification. Make clear in the guidelines that only one anchor protein and the corresponding ambiguity members need to be reported per row, and avoid the rest of the complexity. The format is lossy in that respect.
There is not the need to change the specification, but maybe create a version 1.0.1, amending that paragraph highlighted by Yasset, and adding a new section to clarify this in detail. Of course, there is no way to enforce this in practise, but as not too many people are writing the files yet, I think that we could probably manage that most people would write it in the right way.
- If after some time, we see that this is not enough, and there is the need to support Protein Groups, as Andy mentioned before, a new section just for Protein Groups could be added. That extra section would solve properly the problems related to the modelling of protein inference, but the changes would need to be agreed, it would take some time, etc etc.

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Re: [Psidev-pi-dev] [HUPO-PSI/qcML-development] Created README.md (#19)

[Mathias W. <not...@gi...>]

Will just merge this so that all contributors have a welcoming landing page/readme of the repository as soon as the PR for restructuring the repository layout is ready.

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Re: [Psidev-pi-dev] [HUPO-PSI/qcML-development] No read me, no wiki (#18)

[Mathias W. <not...@gi...>]

wiki is being built

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[Psidev-pi-dev] [HUPO-PSI/qcML-development] Created README.md (#19)

[Mathias W. <not...@gi...>]

addresses #18
You can view, comment on, or merge this pull request online at:

  https://github.com/HUPO-PSI/qcML-development/pull/19

-- Commit Summary --

  * Created README.md

-- File Changes --

    A README.md (33)

-- Patch Links --

https://github.com/HUPO-PSI/qcML-development/pull/19.patch
https://github.com/HUPO-PSI/qcML-development/pull/19.diff

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[Psidev-pi-dev] [HUPO-PSI/qcML-development] No read me, no wiki (#18)

[Mathias W. <not...@gi...>]

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Re: [Psidev-pi-dev] [HUPO-PSI/mzTab] Protein group (#20)

[Yasset Perez-R. <not...@gi...>]

@andrewrobertjones @jgriss I agree to remove the complexity of Protein Inference from the mztab. However, we should make that clear in the specification. Probably we MUST change the specification in this paragraph:

<img width="914" alt="screen shot 2016-04-26 at 20 00 16" src="https://cloud.githubusercontent.com/assets/52113/14830664/a710408a-0be9-11e6-9981-146f726b0866.png">

Instead of **SHOULD** we can use **MUST**. The problem @jgriss @andrewrobertjones is that we already have some examples where the writers try to model the protein inference using CVterms, annotation of the proteins inside the proteins groups etc. That is the reason why I'm making this clear here. 

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Re: [Psidev-pi-dev] [HUPO-PSI/mzTab] Protein group (#20)

[andrewrobertjones <not...@gi...>]

I'm in agreement with @jgriss on this one. Would be good to rule out the group being reported on multiple lines. Difficult to enforce but at least the spec doc should be written very clearly.  I think there is a way to encode extra info about group members in optional columns

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Re: [Psidev-pi-dev] [HUPO-PSI/mzTab] Protein group (#20)

[Johannes G. <not...@gi...>]

@ypriverol First of all, I want to stress that even though your example is valid according to the schema, it is **not** the way the format should be used.

I personally do not think that it is a good idea to add a mechanism that essentially breaks the main concept of mzTab. Every parser would then have to evaluate these additional cvParams to be sure to know what the _reporter_ protein stands for.

I therefore prefer to adapt the schema specification and explicitly rule these cases out (ie. proteins mentioned as ambiguity members **MUST NOT** be reported as individual entries - actually, I was under the impression that this was already part of the specification)

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Re: [Psidev-pi-dev] [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo

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

One little detail: didn’t we want to keep the units on all the terms in
this section, and just remove the datatype?



************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
..

..





*From:* Jones, Andy [mailto:And...@li...]
*Sent:* Tuesday, April 26, 2016 6:35 AM
*To:* Mass spectrometry standard development;
psi...@li...; psi...@li...
*Subject:* Re: [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo



Hi Gerhard,

Many thanks for this, looks good.

Best wishes

Andy



*From:* mayerg97 [mailto:ger...@ru... <ger...@ru...>]
*Sent:* 26 April 2016 14:23
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo



Dear proteomics community,

attached there's the new version 3.86.0 of the psi-ms.obo file.
It contains all changes agreed on at the HUPO-PSI meeting in Ghent.


New CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ added 11 terms for identifier formats for combined spectra
[Term]
id: MS:1002646
name: native spectrum identifier format, combined spectra
def: "Describes how the native spectrum identifiers that have been combined
prior to searching or interpretation are formated." [PSI:PI]
synonym: "nativeID format, combined spectra" EXACT []
relationship: part_of MS:1000577 ! raw data file

[Term]
id: MS:1002647
name: Thermo nativeID format, combined spectra
def: "Thermo comma separated list of spectra that have been combined prior
to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002648
name: Waters nativeID format, combined spectra
def: "Waters comma separated list of spectra that have been combined prior
to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002649
name: WIFF nativeID format, combined spectra
def: "WIFF comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002650
name: Bruker/Agilent YEP nativeID format, combined spectra
def: "Bruker/Agilent comma separated list of spectra that have been
combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002651
name: Bruker BAF nativeID format, combined spectra
def: "Bruker BAF comma separated list of spectra that have been combined
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002652
name: Bruker FID nativeID format, combined spectra
def: "Bruker FID comma separated list of spectra that have been combined
prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002653
name: multiple peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
comment: Used for conversion of peak list files with multiple spectra, i.e.
MGF, PKL, merged DTA files. Index is the spectrum number in the file,
starting from 0.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002654
name: single peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID. Used for
conversion of peak list files with one spectrum per file, typically folder
of PKL or DTAs, each sourceFileRef is different.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002655
name: scan number only nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
comment: Used for conversion from mzXML, or DTA folder where native scan
numbers can be derived.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002656
name: spectrum identifier nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
comment: Used for conversion from mzData. The spectrum id attribute is
referenced.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002657
name: mzML unique identifier, combined spectra
def: "Comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
comment: A unique identifier of a spectrum stored in an mzML file.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002658
name: identification parameter
def: "Identification parameter for the search engine run." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation



Changed CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ Added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ New parent MS:1002657 ! identification parameter
[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications."
[PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications
into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications and
charge into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

************ Obsoleted the term 'peptide level score'
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in the
CV.
is_a: MS:1002358 ! search engine specific score for distinct peptides
is_obsolete: true

************ Changed the definition
[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which the
peptide has been mapped, relative to peptide-chromosome start, assuming a
zero-based counting system. The first value MUST match the value in peptide
start on chromosome." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

************ Added is_a: MS:1001184 ! search statistics
[Term]
id: MS:1002404
name: count of identified proteins
def: "The number of proteins that have been identified, which must match
the number of groups that pass the threshold in the file." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details
is_a: MS:1001184 ! search statistics

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of identified
spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity


Best Regards,
Gerhard



-- 

*--*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail *ger...@ru...

www.medizinisches-proteom-center.de

Re: [Psidev-pi-dev] [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo

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

Hi Gerhard,
Many thanks for this, looks good.
Best wishes
Andy

From: mayerg97 [mailto:ger...@ru...]
Sent: 26 April 2016 14:23
To: psi...@li...; psi...@li...; psi...@li...
Subject: [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo


Dear proteomics community,

attached there's the new version 3.86.0 of the psi-ms.obo file.
It contains all changes agreed on at the HUPO-PSI meeting in Ghent.


New CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ added 11 terms for identifier formats for combined spectra
[Term]
id: MS:1002646
name: native spectrum identifier format, combined spectra
def: "Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated." [PSI:PI]
synonym: "nativeID format, combined spectra" EXACT []
relationship: part_of MS:1000577 ! raw data file

[Term]
id: MS:1002647
name: Thermo nativeID format, combined spectra
def: "Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002648
name: Waters nativeID format, combined spectra
def: "Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002649
name: WIFF nativeID format, combined spectra
def: "WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002650
name: Bruker/Agilent YEP nativeID format, combined spectra
def: "Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002651
name: Bruker BAF nativeID format, combined spectra
def: "Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002652
name: Bruker FID nativeID format, combined spectra
def: "Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002653
name: multiple peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002654
name: single peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002655
name: scan number only nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002656
name: spectrum identifier nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion from mzData. The spectrum id attribute is referenced.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002657
name: mzML unique identifier, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: A unique identifier of a spectrum stored in an mzML file.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002658
name: identification parameter
def: "Identification parameter for the search engine run." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation



Changed CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ Added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ New parent MS:1002657 ! identification parameter
[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications and charge into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

************ Obsoleted the term 'peptide level score'
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in the CV.
is_a: MS:1002358 ! search engine specific score for distinct peptides
is_obsolete: true

************ Changed the definition
[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

************ Added is_a: MS:1001184 ! search statistics
[Term]
id: MS:1002404
name: count of identified proteins
def: "The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details
is_a: MS:1001184 ! search statistics

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity


Best Regards,
Gerhard

--

--
Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER
PhD student
Medizinisches Proteom-Center
DEPARTMENT Medical Bioinformatics
Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554
E-mail ger...@ru...<mailto:ger...@ru...>
www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de>
[cid:ima...@01...5838F0]

Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] MS:1002404 (count of identified proteins) ought to be a child of MS:1001184 (search statistics)? (#8)

[Gerhard M. <not...@gi...>]

Done in version 3.86.0 of psi-ms.obo

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] MS:1002404 (count of identified proteins) ought to be a child of MS:1001184 (search statistics)? (#8)

[Gerhard M. <not...@gi...>]

Closed #8.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Remove the value requirement for CV terms used to indicate data type for a list (#7)

[Gerhard M. <not...@gi...>]

Closed #7.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Remove the value requirement for CV terms used to indicate data type for a list (#7)

[Gerhard M. <not...@gi...>]

Done in version 3.86.0 of psi-ms.obo

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[Psidev-pi-dev] New version 3.86.0 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 3.86.0 of the psi-ms.obo file.
It contains all changes agreed on at the HUPO-PSI meeting in Ghent.


New CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ added 11 terms for identifier formats for combined spectra
[Term]
id: MS:1002646
name: native spectrum identifier format, combined spectra
def: "Describes how the native spectrum identifiers that have been 
combined prior to searching or interpretation are formated." [PSI:PI]
synonym: "nativeID format, combined spectra" EXACT []
relationship: part_of MS:1000577 ! raw data file

[Term]
id: MS:1002647
name: Thermo nativeID format, combined spectra
def: "Thermo comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002648
name: Waters nativeID format, combined spectra
def: "Waters comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002649
name: WIFF nativeID format, combined spectra
def: "WIFF comma separated list of spectra that have been combined prior 
to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002650
name: Bruker/Agilent YEP nativeID format, combined spectra
def: "Bruker/Agilent comma separated list of spectra that have been 
combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002651
name: Bruker BAF nativeID format, combined spectra
def: "Bruker BAF comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002652
name: Bruker FID nativeID format, combined spectra
def: "Bruker FID comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002653
name: multiple peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: Used for conversion of peak list files with multiple spectra, 
i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the 
file, starting from 0.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002654
name: single peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID. Used for 
conversion of peak list files with one spectrum per file, typically 
folder of PKL or DTAs, each sourceFileRef is different.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002655
name: scan number only nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: Used for conversion from mzXML, or DTA folder where native scan 
numbers can be derived.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002656
name: spectrum identifier nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: Used for conversion from mzData. The spectrum id attribute is 
referenced.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002657
name: mzML unique identifier, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: A unique identifier of a spectrum stored in an mzML file.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002658
name: identification parameter
def: "Identification parameter for the search engine run." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation



Changed CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ Added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ New parent MS:1002657 ! identification parameter
[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications." 
[PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications 
into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications 
and charge into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

************ Obsoleted the term 'peptide level score'
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in 
the CV.
is_a: MS:1002358 ! search engine specific score for distinct peptides
is_obsolete: true

************ Changed the definition
[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which 
the peptide has been mapped, relative to peptide-chromosome start, 
assuming a zero-based counting system. The first value MUST match the 
value in peptide start on chromosome." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

************ Added is_a: MS:1001184 ! search statistics
[Term]
id: MS:1002404
name: count of identified proteins
def: "The number of proteins that have been identified, which must match 
the number of groups that pass the threshold in the file." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details
is_a: MS:1001184 ! search statistics

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned 
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of 
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of 
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity


Best Regards,
Gerhard


-- 

*--*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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

Re: [Psidev-pi-dev] [HUPO-PSI/mzTab] Protein group (#20)

[Yasset Perez-R. <not...@gi...>]

@jgriss @andrewrobertjones I FULLY agree with this. However, the RECOMNDATIONS in the mztab specification should be encoded in the file with at least CVTerms to make clear for the users/readers and consumers of the files about the content of the file. For example:

Protein Accession .... Ambiguity members              opt_global_cv_MS:1001301_protein_rank
Protein 1 ....                 Protein 2, Protein 3                                             1
Protein 2 ....                          NULL                                                          2
Protein 3 ....                          NULL                                                          3

This example is schema compliant but not the recommended way of reporting the results. Then if a reader arrive and as @andrewrobertjones pointed take the list of proteins as the number of identified proteins, then the results are wrong. My vote is to keep it now as simple as possible AS IT IS, but include some CVTERMs in the header how the user implemented our RECOMENDATIONS. 

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Re: [Psidev-pi-dev] [HUPO-PSI/mzTab] Protein group (#20)

[Johannes G. <not...@gi...>]

Hi all,
When we created mzTab we deliberately did not encode the complete information. mzTab was always only intended to encode final _results_.

Protein groups can be loosely recorded using the main (reporter) accession column in combination with the ambiguitiy_member column. As pointed out by @andrewrobertjones in down-stream analysis pipelines, you don't really care about anything else.

I therefore strongly suggest to keep mzTab as simple as possible and use mzIdentML / mzQuantML for the complex cases. That's how it's always meant to be. Otherwise, mzTab will become even more complicated to process and will neither contain a correct modelling of all use cases nor will it be easy to parse. 

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Mod re-scoring (#3)

[Harald B. <not...@gi...>]

@andrewrobertjones I decided to add the them as separate issues instead as I think this is clearer and easier to maintain. So please add more if there is something I forgot.

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[Psidev-pi-dev] [HUPO-PSI/mzIdentML] Update list of anticipated CV terms during validation (#12)

[Harald B. <not...@gi...>]

The following terms ought to be anticipated when running the validator (and thus remove the warning messages):

- MS:1002567 (phosphoRS score threshold) and MS:1002557 (D-Score threshold) ought to be anticipated terms under Threshold under SpectrumIdentificationProtocol?

- MS:1002497 (group PSMs by sequence with modifications) (and the other new related terms) ought to be anticipated terms under AdditionalSearchParams?

- MS:1000894 (retention time) ought to be anticipated terms under SpectrumIdentificationResult?

- MS:1002471, MS:1002470 and MS:1002542 ought to be anticipated terms under ProteinAmbiguityGroup?

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[Psidev-pi-dev] [HUPO-PSI/mzIdentML] Incorrect CV term requirement for PTM localization scoring? (#11)

[Harald B. <not...@gi...>]

It seems to be mandatory to add MS:1002507 (modification rescoring:false localization rate) (or any of its child terms, of which there are none btw) when including MS:1002491 (modification localization scoring) in the AdditionalSearchParams list.

This means that terms such as MS:1001969 (phosphoRS score), MS:1002536 (D-Score), MS:1002550 (peptide:phosphoRS score and MS:1002553 (peptide:D-Score) (and others) cannot be used for the PTM rescoring.

I think that either these terms have to be children of MS:1002507 (modification rescoring:false localization rate) or the mandatory term when using modification rescoring ought to be MS:1002505 (regular expression for modification localization scoring) or one of its children?

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[Psidev-pi-dev] [HUPO-PSI/mzIdentML] Scientific notation not allowed in PTM localization scores? (#10)

[Harald B. <not...@gi...>]

Why is the following not allowed?

"MS:1001969" name="phosphoRS score" value="1:1.0468246849444967E-8:4:false"

Is scientific annotation not supported?

Full error:
"The regular expression in SpectrumIdentificationItem (id='SII_4070_1') element at /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem/cvParam ('phosphoRS score') is not valid."

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[Psidev-pi-dev] [HUPO-PSI/mzIdentML] How to use MS:1001239 (frag: immonium ion) to annotate immonium ions on specific amino acids? (#9)

[Harald B. <not...@gi...>]

What is the intended use of MS:1001239 (frag: immonium ion) and how can this be used to annotate immonium ions on specific amino acids?

Here's what we currently do in the PeptideShaker mzIdentML export using the outdated PRIDE CV terms:

<IonType charge="1" index="4 5">
   <FragmentArray measure_ref="Measure_MZ" values="120.0808411"/>
   <FragmentArray measure_ref="Measure_Int" values="14483.125"/>
   <FragmentArray measure_ref="Measure_Error" values="6.53397579810644E-5"/>
   <cvParam cvRef="PRIDE" accession="PRIDE:0000244" name="immonium F"/>
</IonType>

How would the same be done with MS:1001239 (frag: immonium ion)?

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[Psidev-pi-dev] [HUPO-PSI/mzIdentML] MS:1002404 (count of identified proteins) ought to be a child of MS:1001184 (search statistics)? (#8)

[Harald B. <not...@gi...>]

MS:1002404 (count of identified proteins) is _not_ a child of MS:1001184 (search statistics)? Should it not be? Will remove warning messages when running the validator.

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