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

[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #93 on issue 42 by javizca74: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

I sent my comments to Andreas. I am not including here minor typo errors. I  
am also
attaching Andreas comments (### lines).

1) These 2 terms are somehow redundant. The def of MS:1001013 should be  
changed
(remove the examples, I guess):

[Term]
id: MS:1001011
name: search database details
def: "Details about the database searched." [PSI:PI]
is_a: MS:1001249 ! search input details


[Term]
id: MS:1001013
name: database name
def: "The name of the search database (nr, SwissProt or est_human)."  
[PSI:PI]
is_a: MS:1001011 ! search database details

##### the 1001013 term is used for mapping to
#####  
/mzIdentML/DataCollection/Inputs/SearchDatabase/DatabaseName/cvParam/@accession
##### all the child term of the 1013 are allowed here, but not the term  
itself
##### the first term is mapped to
/mzIdentML/DataCollection/Inputs/SearchDatabase/cvParam/@accession
##### and contains a large collection of terms
##### however, some of the child terms of 1001011 should not be used.
##### maybe we should restructure the CV, to only allow term that make  
sense?

2) Perhaps the def should be changed in the definition? (range:-3, +3, not  
zero,
instead of 1-6).

[Term]
id: MS:1001024
name: translation frame
def: "The translated open reading frames from a nucleotide database  
considered in the
search (range: 1-6)." [PSI:PI]
is_a: MS:1001011 ! search database details


3) Perhaps change term name DB filter on sequences” to “DB filter on amino  
acid
sequence pattern”?


[Term]
id: MS:1001027
name: DB filter on sequences
def: "Filtering applied specifically by amino acid sequence pattern."  
[PSI:PI]
is_a: MS:1001019 ! database filtering

##### maybe "DB filter on sequence pattern"? The phrase amino acid would  
restrict it
to protein databases

4)Change term name to quality estimation method details?

[Term]
id: MS:1001060
name: quality estimation details
def: "Method for quality estimation (manually or wih decoy database)."  
[PSI:PI]
is_a: MS:1001249 ! search input details

#### accepted and done

5) Delete this one?

[Term]
id: MS:1001060
name: quality estimation details
def: "Method for quality estimation (manually or wih decoy database)."  
[PSI:PI]
is_a: MS:1001249 ! search input details

#### same as above?

6) Updated def. I would change the name to “database type nucleotide”:

[Term]
id: MS:1001079
name: database type NA
def: "Database contains nucleic acid sequences." [PSI:PI]
is_a: MS:1001018 ! database type

#### accepted and done

7) I would update the term to “sequence coverage”.

[Term]
id: MS:1001093
name: coverage
def: "The percent coverage for the protein based upon the matched peptide  
sequences
(can be calculated)." [PSI:PI]
xref: value-type:xsd\:decimal "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details

#### accepted and done

8)  Update def:

[Term]
id: MS:1001115
name: scan number(s)
def: "Take from mzData. TODO: What does this mean?" [PSI:PI]
is_a: MS:1001105 ! peptide result details

9) Change this term: this is not a name for any database. It could be  
changed to
“database type EST”. Or if you are referring to the EST database from NCBI,  
it should
be called: dbEST.


[Term]
id: MS:1001178
name: database EST
is_a: MS:1001013 ! database name

10) Add synonyms to all terms containing “product ion” (fragment ion).

[Term]
id: MS:1001225
name: product ion m/z
def: "The m/z of the product ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of the product ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001227
name: product ion m/z error
def: "The product ion m/z error (ADD more docu here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

#### accepted and done

11) This term name is wrong. There is no database called EST (dbEST is the  
one from
the NCBI, for instance).

[Term]
id: MS:1001295
name: decoy DB from EST
is_a: MS:1001284 ! decoy DB derived from

#### see 9) above

12) Is it pending to add more mascot related terms?

[Term]
id: MS:1001326
name: TODO_add_others
is_a: MS:1001302 ! search engine specific input parameter

13) These terms are redundant:

[Term]
id: MS:1001343
name: NA sequence
def: "The sequence is a nucleic acid sequence." [PSI:PI]
is_a: MS:1001342 ! database sequence details

[Term]
id: MS:1001344
name: AA sequence
def: "The sequence is a amino acid sequence." [PSI:PI]
is_a: MS:1001342 ! database sequence details


There are those ones:

[Term]
id: MS:1001073
name: database type AA
def: "Database contains amino acid sequences." [PSI:PI]
is_a: MS:1001018 ! database type

[Term]
id: MS:1001079
name: database type NA
def: "Database contains nucleic acid sequences." [PSI:PI]
is_a: MS:1001018 ! database type

#### right these are redundant. However, they can be used in different  
locations
#### I would suggest to keep them



--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings

[Psidev-pi-dev] Issue 44 in psi-pi: Issues with all instance docs

[<cod...@go...>]

Comment #22 on issue 44 by andrewrobertjones: Issues with all instance docs
http://code.google.com/p/psi-pi/issues/detail?id=44

My preference would be to treat a neutral loss as any other modification  
and go with
option 1. Is there some information that would be lost by encoding it in  
this way?



--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings

[Psidev-pi-dev] Issue 44 in psi-pi: Issues with all instance docs

[<cod...@go...>]

Comment #21 on issue 44 by dcreasy: Issues with all instance docs
http://code.google.com/p/psi-pi/issues/detail?id=44

Regarding comment 19: Could we have an example with a modification with a  
neutral
loss defined?

The Mascot 15N example specifies Oxidation, and this can have a neutral  
loss of:
<umod:NeutralLoss avge_mass="64.1069" composition="H(4) C O S" flag="false"
mono_mass="63.998285">

Unfortunately, this seems to get lost in the conversion of the unimod.xml to
unimod.obo file, so this needs to be fixed. (Please, Martin!)

We should probably also specify, for each peptide match, which neutral  
loss, if any,
was 'dominant' and/or used for scoring.
Two pieces of information are required: The position and the loss, and  
there can of
course be multiple neutral losses.
For an example sequence of ALNVMESK, we'd want to specify that it is  
residue 5, and
the loss is 63.998285

There are 3 possible places for CV terms for this:
1.
     <Peptide id="peptide_21_1">
       <peptideSequence>ALNVMESK</peptideSequence>
       <Modification location="5" residues="M"  
monoisotopicMassDelta="15.994919">
         <cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD" />
--->    <cpParam accession="MS:1001xxx" name="neutral loss" cvRef="PSI-MS"
value="63.998285" />
       </Modification>
     </Peptide>


2. Or, it could be with other cv terms directly under:
     <SpectrumIdentificationItem id="SII_21_1"
But to cope with multiple pairs of values, this would require a structure  
similar to
the one under <Peptide> and therefore a change to the schema

3. In the fragment arrays (remember it's the 5th residue that is  
methionine):

     <SpectrumIdentificationItem id="SII_21_1"
       <Fragmentation>
         <IonType index="1 2 3 4 5" charge="1">
           <cvParam cvRef="PSI-MS" accession="MS:1001224" name="frag: b  
ion"/>
           <FragmentArray values="72.09201 185.11602 299.24156 398.31937  
481.32147 "
Measure_ref="m_mz"/>
           <FragmentArray values="1.217 0.5765 0.9995 0.3048 0.6491"
Measure_ref="m_intensity"/>
           <FragmentArray values="0.0476 -0.0124 0.0702 0.0796 0.0446"
Measure_ref="m_error"/>
--->      <FragmentArray values="0, 0, 0, 0, 63.998285"  
Measure_ref="m_neutral_loss"/>
         </IonType>


And we'd also need to define m_neutral_loss:

     <AnalysisData>
       <SpectrumIdentificationList id="SIL_1" numSequencesSearched="4944">
         <FragmentationTable>
           <Measure id="m_m_neutral_loss">
--->        <cvParam cvRef="PSI-MS" accession="MS:100xxxx" name="product  
ion neutral
loss"/>
           </Measure>


I propose #3 - anyone disagree? Perhaps we can discuss at the telecon.


--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings

Re: [Psidev-pi-dev] Non-OBO files in the cvList element

[Darren K. <da...@pr...>]

Hi David,

Thanks for the clarification on this.  Perhaps the cvList entry (in
the example files) should point to the obo file rather than the xml
file then?  This will make it possible for a parser to grab the obo
file on the fly and make sense of the cvParams, if it hasn't already
seen this CV.


Darren



>> What's the problem with unimod - it's available as an obo file?
>>
>> http://www.unimod.org/obo/unimod.obo
>>
>> David

Re: [Psidev-pi-dev] Non-OBO files in the cvList element

[Robert B. <rob...@pr...>]

Ah, we didn't see the obo file. Looks good, then.

On Tue, Jul 7, 2009 at 2:30 AM, David Creasy <dc...@ma...>wrote:

> Hi Robert,
>
> You'll see from the previous message that the NCBI taxonomy should no
> longer be in the CV list.
>
> What's the problem with unimod - it's available as an obo file?
>
> http://www.unimod.org/obo/unimod.obo
>
> David
>
> Robert Burke wrote:
>
>> Hello everyone (again),
>>
>> We have a concern about non-ontology files listed in the cvList.
>> Databases, such as the UNIMOD, prove a challenge for OBO parsers. When
>> creating enumerations of a controlled vocabulary, a parser will run into the
>> non-obo file and either not know what to do, or have to make an awkward
>> switch. What was the motivation in putting things like UNIMOD and
>> NCBI-TAXONOMY in the cvList instead of a database list, such as the
>> SearchDatabase tags in the DataCollection/Inputs tag? A benefit would also
>> be the fileformat information included.
>>
>> Regards,
>>
>> -RB
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Psidev-pi-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>>
>
> --
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
>
> dc...@ma...
> http://www.matrixscience.com
>
> Matrix Science Ltd. is registered in England and Wales
> Company number 3533898
>

[Psidev-pi-dev] Issue 44 in psi-pi: Issues with all instance docs

[<cod...@go...>]

Comment #20 on issue 44 by dcreasy: Issues with all instance docs
http://code.google.com/p/psi-pi/issues/detail?id=44

The Mascot_MSMS_example.mzid file now has an example of manual validation:

           <ProteinDetectionHypothesis id="PDH_HSP71_RAT"
DBSequence_ref="DBSeq_HSP71_RAT"  passThreshold="false">
             <PeptideHypothesis  PeptideEvidence_Ref="PE_2_1_HSP71_RAT" />
             <cvParam accession="MS:1001171" name="mascot:score"  
cvRef="PSI-MS"
value="40.95" />
             <cvParam accession="MS:1001093" name="sequence coverage"  
cvRef="PSI-MS"
value="2" />
             <cvParam accession="MS:1001097" name="distinct peptide  
sequences"
cvRef="PSI-MS" value="1" />
             <cvParam accession="MS:1001125" name="manual validation"  
cvRef="PSI-MS"
value="Manually rejected this protein for no particular reason. (Example of  
manual
validation for mzIdentML)" />
           </ProteinDetectionHypothesis>


--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings

[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #92 on issue 42 by eisenachM: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

I checked some (from MS:100100X to approx. MS:1001051) CV terms and found  
some errors:

very many CV terms have no "[PSI:PI]" after the definition.
Is it necessary?

MS:1001420, SpectraST:delta:
wrongly spelled: "[:PSI-PI]" instead of "[PSI:PI]"

MS:1001007, sequest:Output lines:
value type missing (xsd:nonNegativeInteger ?)

MS:1001014, database local file path:
value type xsd:string is missing

MS:1001016, database version:
value type xsd:string is missing
There is a "version" attribute in the <Searchdatabase> element.
One of both is not necessary.

MS:1001017, database release date:
value type xsd:string is missing
There is a "releaseDate" attribute in the <Searchdatabase> element.
One of both is not necessary.

MS:1001019, database filtering:
In the definition, what does "public or private" mean?

MS:1001020, DB filter taxonomy:
def should be changed: "A taxonomy filter was applied to the search  
database." [PSI:PI]

MS:1001024, translation frame:
value type is missing
In the Mascot NA example, a <DatabaseTranslation> element is used,
using a "frames" attribute. Is the CV term obsolete?

MS:1001028, sequest:SequenceHeaderFilter:
value type missing (xsd:string ?)

MS:1001032, sequest:SequencePartialFilter:
value type missing (xsd:string ?)

MS:1001035, date / time search performed:
value type missing (xsd:dateTime)
The <SpectrumIdentification> element has an "activityDate" attribute.
One of both is not necessary.

MS:1001037, sequest:ShowFragmentIons:
value type missing (xsd:boolean)

MS:1001038, sequest:Consensus:
value type missing (xsd:positiveInteger)

MS:1001051, multiple enzyme combination rules:
value type missing (xsd:string ?)
The term is not referenced in the mapping file (nor is cleavage agent  
details, its
parent).
Additionally the <Enzyme> element has an "independent" attribute.
Can this CV term be deleted?



--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings

Re: [Psidev-pi-dev] Conference call

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

Hi all,

There will be an mzIdentML conference call tomorrow (9th July) at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=9&month=7&year=2009&hour=16&min=0&sec=0&p1=136

Agenda:


 1.  Review minutes from last week: http://www.psidev.info/index.php?q=node/430
 2.  Review issues list: http://code.google.com/p/psi-pi/issues/list
 3.  Plan for resubmission to the process
 4.  AOB

Please send me any other agenda items. I’ve updated the Omssa, X!Tandem and SpectraST examples, which all validate. Can people check their examples validate prior to the call.

We also have this action item from last week: “Task for everyone: check all the the terms in the CV. Be sure that all of them have the correct values (units or no units). Check value, type and unit, and definitions. There will probably be some errors.”

Since we’re now very close to submission, it would be great if everyone could have a look at the CV: http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo. If there are minor fixes, can you post them on the issues list: http://code.google.com/p/psi-pi/issues/detail?id=42 with your proposed fix, and flag anything that we need to discuss on the call.

Thanks!
Andy

Dial in details:

+ Germany: 08001012079
+ Switzerland: 0800000860
+ UK: 08081095644
+ USA: 1-866-314-3683
+ Generic international: +44 2083222500 (UK number)

access code: 297427



From: Jones, Andy [mailto:And...@li...]
Sent: 29 June 2009 17:04
To: 'psi...@li...'
Subject: Re: [Psidev-pi-dev] Conference call

Hi all,

There will be an mzIdentML conference call tomorrow (30th June) at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=6&year=2009&hour=16&min=0&sec=0&p1=136

Agenda:


5.       Review minutes from last week: http://www.psidev.info/index.php?q=node/427

6.       Review issues list: http://code.google.com/p/psi-pi/issues/list

7.       Plan for resubmission to the process

8.       AOB

Please send me any other agenda items.

Cheers,
Andy






Dial in details:

+ Germany: 08001012079
+ Switzerland: 0800000860
+ UK: 08081095644
+ USA: 1-866-314-3683
+ Generic international: +44 2083222500 (UK number)

access code: 297427

Re: [Psidev-pi-dev] Non-OBO files in the cvList element

[David C. <dc...@ma...>]

Hi Robert,

You'll see from the previous message that the NCBI taxonomy should no 
longer be in the CV list.

What's the problem with unimod - it's available as an obo file?

http://www.unimod.org/obo/unimod.obo

David

Robert Burke wrote:
> Hello everyone (again),
> 
> We have a concern about non-ontology files listed in the cvList. 
> Databases, such as the UNIMOD, prove a challenge for OBO parsers. When 
> creating enumerations of a controlled vocabulary, a parser will run into 
> the non-obo file and either not know what to do, or have to make an 
> awkward switch. What was the motivation in putting things like UNIMOD 
> and NCBI-TAXONOMY in the cvList instead of a database list, such as the 
> SearchDatabase tags in the DataCollection/Inputs tag? A benefit would 
> also be the fileformat information included.
> 
> Regards,
> 
> -RB
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898

Re: [Psidev-pi-dev] NCBI-TAXONOMY included in cvList but not used

[David C. <dc...@ma...>]

Hi Robert,

Thanks for pointing this out.
We should now remove the NCBI-TAXONOMY cv tag from all the examples.

See:
http://code.google.com/p/psi-pi/issues/detail?id=42&can=1&q=NCBI#c81

for an example of how it was used until quite recently.


David

Robert Burke wrote:
> Hi everyone,
> 
> We noticed that there was an NCBI-TAXONOMY cv tag included in every 
> example file, but not used in any. We were wondering what the intended 
> usage was.
> 
> -RB
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898

[Psidev-pi-dev] Non-OBO files in the cvList element

[Robert B. <rob...@pr...>]

Hello everyone (again),

We have a concern about non-ontology files listed in the cvList. Databases,
such as the UNIMOD, prove a challenge for OBO parsers. When creating
enumerations of a controlled vocabulary, a parser will run into the non-obo
file and either not know what to do, or have to make an awkward switch. What
was the motivation in putting things like UNIMOD and NCBI-TAXONOMY in the
cvList instead of a database list, such as the SearchDatabase tags in the
DataCollection/Inputs tag? A benefit would also be the fileformat
information included.

Regards,

-RB

[Psidev-pi-dev] NCBI-TAXONOMY included in cvList but not used

[Robert B. <rob...@pr...>]

Hi everyone,

We noticed that there was an NCBI-TAXONOMY cv tag included in every example
file, but not used in any. We were wondering what the intended usage was.

-RB

Re: [Psidev-pi-dev] Adding proteowizard to the "tools that could / should export mzIdentML" list

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

done, see
 
http://www.psidev.info/index.php?q=node/408
 
 
 
Von: Robert Burke [mailto:rob...@pr...] 
Gesendet: Wednesday, July 01, 2009 9:15 PM
An: psi...@li...
Betreff: [Psidev-pi-dev] Adding proteowizard to the "tools that could / should export mzIdentML" list
 
Hello everyone,

We noticed that proteowizard wasn't on the list of tools that could / should export mzIdentML documents. We're writing a
C++ library for reading/writing MzIdentML with and interface for importing other formats. If you could add a link to our
page as well, a la ProCon, that would be great. 

http://proteowizard.sourceforge.net/

Thanks so much,

Robert Burke

Re: [Psidev-pi-dev] [Fwd: Re: [Psidev-ms-dev] Can mzIdentML encode a spectral library?]

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

Hi Paul,

Thanks for your message about spectral libraries, it was forwarded to the PSI-PI list, since we're developing a format for peptide/protein identifications from mass spec (mzIdentML. In this version 1 of the format, spectral libraries searching will be supported: see an example containing identifications made from SpectraST: http://psi-pi.googlecode.com/svn/trunk/examples/spectraST.mzid, although we do not encode much about the spectral library itself - we currently refer out to the spectral library. Additional CV terms could be added to the DBSequence entries to encode some of the metadata about the library entry within mzIdentML.

> 3) The business end - the spectrum - is a basepeak normalized, annotated
> peaklist.
> 
> 452.9    847    "? 2/2 14.3"
> 462.8    535    "b7-35/-0.46 2/2 5.5"
> 480.3    620    "b7-18/0.04 2/2 10.4"
> 498.2    2165    "b7/-0.06 2/2 9.8"
> 524.0    1397    "? 2/2 8.8"
> 527.0    381    "Int/AAAAGAGA/0.2 2/2 2.1"
> 531.1    1140    "y7/-0.19 2/2 7.9"
> 537.2    675    "? 2/2 8.9"
> 551.2    910    "b8-18/-0.10 2/2 4.7"
> 569.1    4712    "b8/-0.20 2/2 25.4"
> 581.2    289    "? 2/2 3.1"
> 593.7    249    "? 2/1 2.6"
> 595.1    1182    "? 2/2 7.3"
> 602.2    2209    "y8/-0.13 2/2 21.5"
> 608.6    335    "? 2/2 3.9"
> 622.2    1625    "b9-18/-0.13 2/2 6.4"
> 626.2    767    "Int/AAAAAAAAG/0.1 2/2 1.8"
> [..]

mzIdentML has structures for representing peptide identifications and the fragment ions on which those identifications were based. As such, the format could probably encode the basic peptide identifications that are part of a spectral library although this is not really the intended use of mzIdentML. We also do not have a structure to group identifications as replicates or consensus peptide-spectrum matches, but this could be built fairly easily. I think this is the kind of feature we would consider for a future update of the format, if there is enough of a call for developing a standard for representing spectral libraries. If you'd like to contribute to the process, please keep in touch!

Best wishes
Andy




> -----Original Message-----
> From: Matthew Chambers [mailto:mat...@va...]
> Sent: 01 July 2009 16:15
> To: psi...@li...
> Subject: [Psidev-pi-dev] [Fwd: Re: [Psidev-ms-dev] Can mzIdentML encode a
> spectral library?]
> 
> Forwarding this thread to a more appropriate list. :) I realize it's
> much too late to put spectral library support into mzIdentML for this
> revision, but has your WG considered supporting this in a future
> revision or a separate format?
> 
> -Matt
> 
> 
> -------- Original Message --------
> Subject: 	Re: [Psidev-ms-dev] Can mzIdentML encode a spectral library?
> Date: 	Wed, 01 Jul 2009 11:04:42 -0400
> From: 	Paul Rudnick <rud...@ni...>
> Reply-To: 	pau...@ni..., Mass spectrometry standard development
> <psi...@li...>
> To: 	Mass spectrometry standard development
> <psi...@li...>
> References:
> 	<2DC...@sy...>
> <0274A8AD633F4B0D82C189942EC38A32@fozzie>
> <2B6...@sy...>
> <1246389681.5287.369.camel@paddy> <4A4...@va...>
> 
> 
> 
> Matt and other Fearless PSI volunteers -
> 
> If you think you may be able to squeeze spectral libraries into an
> evolving format, I'd like to help out.
> 
> Here are a couple of items that might be useful:
> 
> 1)  Spectral libraries are typically one of two types: 'replicate' or
> 'consensus.'  The latter indicating that multiple spectra identifying
> the same peptide ion have been used to generate the final spectrum.
> This also means that the stats in the annotation may have additional
> variance values.
> 
> 2) The first section of metadata is evidence supporting that spectrum.
> This includes things like search engine scores, sample sources and
> quality metrics -- e.g., fraction of unexplained abundance, similarity
> of replicates, etc.  Many of these are internal to us and not used by
> all library generators, however, some might well be required.
> 
> Here's that section from the first spectrum in the human library (ion trap),
> 
> Name: AAAAAAAAAAAAAAAGAGAGAK/1
> MW: 1596.846
> Comment: Spec=Consensus Pep=Tryptic
> Fullname=R.AAAAAAAAAAAAAAAGAGAGAK.Q/1 Mods=0 Parent=1596.846
> Inst=it
> Mz_diff=-0.066 Mz_exact=1596.8457 Mz_av=1597.771
> Protein="IPI00220844.1|SWISS-PROT:P55011-3|ENSEMBL:ENSP00000340878
> Tax_Id=9606 Splice Isoform 2 of Solute carrier family 12 member 2"
> Pseq=36 Organism="human"
> Se=3^X2:ex=2.25065e-009/2.249e-
> 009,td=6.9122e+010/6.888e+010,sd=0/0,hs=59.9/4,bs=1.3e-012,b2=4.5e-
> 009,bd=1.38e+011^O2:ex=0.00144675/0.001383,td=402850/3.852e+005,pr=4.23
> 5e-009/4.035e-009,bs=6.35e-
> 005,b2=0.00283,bd=788000^P2:sc=27.5/0.8,dc=18/0.4,ps=2.015/0.125,bs=0
> Sample=1/human_ncrr_hprob_cam,2,2 Nreps=2/2 Missing=0.2229/0.0094
> Parent_med=1596.78/0.16 Max2med_orig=29.6/5.3 Dotfull=0.728/0.000
> Dot_cons=0.870/0.005 Unassign_all=0.171 Unassigned=0.000 Dotbest=0.88
> Flags=0,0,0 Naa=22 DUScorr=0.85/3.3/15 Dottheory=0.83 Pfin=1.5e+013
> Probcorr=1 Tfratio=1.6e+008 Pfract=0
> Num peaks: 109
> 
> 3) The business end - the spectrum - is a basepeak normalized, annotated
> peaklist.
> 
> 452.9    847    "? 2/2 14.3"
> 462.8    535    "b7-35/-0.46 2/2 5.5"
> 480.3    620    "b7-18/0.04 2/2 10.4"
> 498.2    2165    "b7/-0.06 2/2 9.8"
> 524.0    1397    "? 2/2 8.8"
> 527.0    381    "Int/AAAAGAGA/0.2 2/2 2.1"
> 531.1    1140    "y7/-0.19 2/2 7.9"
> 537.2    675    "? 2/2 8.9"
> 551.2    910    "b8-18/-0.10 2/2 4.7"
> 569.1    4712    "b8/-0.20 2/2 25.4"
> 581.2    289    "? 2/2 3.1"
> 593.7    249    "? 2/1 2.6"
> 595.1    1182    "? 2/2 7.3"
> 602.2    2209    "y8/-0.13 2/2 21.5"
> 608.6    335    "? 2/2 3.9"
> 622.2    1625    "b9-18/-0.13 2/2 6.4"
> 626.2    767    "Int/AAAAAAAAG/0.1 2/2 1.8"
> [..]
> 
> This is MSP format (also used for small molecules), and it is simple
> ASCII.  Additional "formats" are usually borne for the purposes of
> searching (e.g, indexing).  MSP is easy to work with but it is not a
> standard -- a common, cross-domain representation would be better :)
> 
> Paul
> 
> Matthew Chambers wrote:
> > I brought this issue up in the call because I think that the "evidence"
> > tag in traML is too weak to go in a standard - I was proposing that a
> > better way to do it might be to refer to an mzIdentML file for a more
> > complete context of the evidence.
> >
> > I know very little about metabolomics, but the spectra libraries we're
> > talking about are indeed proteomics-oriented. But I don't think you need
> > to shut up - indeed, I think this may be another case where we can and
> > should standardize within and even across domains because the
> > annotations of a peptide's spectrum could be even more rich and detailed
> > than that of a smaller molecule. In the spectral library domain just for
> > peptides, there are at least 5 common formats already
> > (http://peptide.nist.gov): MSP/ASCII, a multi-file NIST binary format,
> > SpectraST, BiblioSpec, and X!Hunter. I'm sure you have a few more in the
> > metabolomics domain. A lack of standards makes life so much more
> > interesting, don't you think? ;)
> >
> > -Matt
> >
> >
> > Steffen Neumann wrote:
> >
> >> On Tue, 2009-06-30 at 08:32 -0700, Eric Deutsch wrote:
> >>
> >>
> >>> +Can mzIdentML encode a spectral library?
> >>>
> >>>
> >> I am unsure whether this was discussed during the conference call,
> >> or is left as an open point to the list.
> >>
> >> Anyway, I am inclined to say "no" about this,
> >> for two reasons:
> >>
> >> 1) I don't know enough about analys^H^H^H^H^mzIdentML,
> >>    because my very brief looks made it look like proteomics-only.
> >>    (Or are you actually referring to a proteomics-spectral library?!
> >>     in that case I'll shut up and you can skip the rest of this mail.)
> >>
> >> 2) A spectral library will (at least in the future)
> >>    contain sets of spectra (different eV, MS1-MS^n, ...)
> >>    and associated annotations, which might be as complicated
> >>    as a molecule and its fragmentation brake-down products.
> >>    This requires a rich set of links between individual peaks
> >>    and their (molecular) annotation.
> >>
> >> So for small molecules (read: metabolomics stuff) we have started
> >> to create mzAnnotate under the umbrella of the Metabolomics Standards
> >> Initiative (MSI). http://msi-workgroups.sourceforge.net/exchange-format/
> >>
> >> We have drafted some use cases, shown on
> >> http://sourceforge.net/apps/mediawiki/metware/index.php?title=MzAnnotate
> >> and prepared a converter for both the spectral library www.massbank.jp
> >> and our own MassFrontier clone MetFrag, and will present these
> >> on the MSI mailing list soon.
> >>
> >> Yours,
> >> Steffen
> >>
> >>
> >>
> >
> > ------------------------------------------------------------------------------
> > _______________________________________________
> > Psidev-ms-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >
> 
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> 
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

[Psidev-pi-dev] Adding proteowizard to the "tools that could / should export mzIdentML" list

[Robert B. <rob...@pr...>]

Hello everyone,

We noticed that proteowizard wasn't on the list of tools that could / should
export mzIdentML documents. We're writing a C++ library for reading/writing
MzIdentML with and interface for importing other formats. If you could add a
link to our page as well, a la ProCon, that would be great.

http://proteowizard.sourceforge.net/

Thanks so much,

Robert Burke

[Psidev-pi-dev] [Fwd: Re: [Psidev-ms-dev] Can mzIdentML encode a spectral library?]

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

Forwarding this thread to a more appropriate list. :) I realize it's 
much too late to put spectral library support into mzIdentML for this 
revision, but has your WG considered supporting this in a future 
revision or a separate format?

-Matt


-------- Original Message --------
Subject: 	Re: [Psidev-ms-dev] Can mzIdentML encode a spectral library?
Date: 	Wed, 01 Jul 2009 11:04:42 -0400
From: 	Paul Rudnick <rud...@ni...>
Reply-To: 	pau...@ni..., Mass spectrometry standard development 
<psi...@li...>
To: 	Mass spectrometry standard development 
<psi...@li...>
References: 	<2DC...@sy...> 
<0274A8AD633F4B0D82C189942EC38A32@fozzie> 
<2B6...@sy...> 
<1246389681.5287.369.camel@paddy> <4A4...@va...>



Matt and other Fearless PSI volunteers -

If you think you may be able to squeeze spectral libraries into an 
evolving format, I'd like to help out.

Here are a couple of items that might be useful:

1)  Spectral libraries are typically one of two types: 'replicate' or 
'consensus.'  The latter indicating that multiple spectra identifying 
the same peptide ion have been used to generate the final spectrum.  
This also means that the stats in the annotation may have additional 
variance values.

2) The first section of metadata is evidence supporting that spectrum.  
This includes things like search engine scores, sample sources and 
quality metrics -- e.g., fraction of unexplained abundance, similarity 
of replicates, etc.  Many of these are internal to us and not used by 
all library generators, however, some might well be required.

Here's that section from the first spectrum in the human library (ion trap),

Name: AAAAAAAAAAAAAAAGAGAGAK/1
MW: 1596.846
Comment: Spec=Consensus Pep=Tryptic 
Fullname=R.AAAAAAAAAAAAAAAGAGAGAK.Q/1 Mods=0 Parent=1596.846 Inst=it 
Mz_diff=-0.066 Mz_exact=1596.8457 Mz_av=1597.771 
Protein="IPI00220844.1|SWISS-PROT:P55011-3|ENSEMBL:ENSP00000340878 
Tax_Id=9606 Splice Isoform 2 of Solute carrier family 12 member 2" 
Pseq=36 Organism="human" 
Se=3^X2:ex=2.25065e-009/2.249e-009,td=6.9122e+010/6.888e+010,sd=0/0,hs=59.9/4,bs=1.3e-012,b2=4.5e-009,bd=1.38e+011^O2:ex=0.00144675/0.001383,td=402850/3.852e+005,pr=4.235e-009/4.035e-009,bs=6.35e-005,b2=0.00283,bd=788000^P2:sc=27.5/0.8,dc=18/0.4,ps=2.015/0.125,bs=0 
Sample=1/human_ncrr_hprob_cam,2,2 Nreps=2/2 Missing=0.2229/0.0094 
Parent_med=1596.78/0.16 Max2med_orig=29.6/5.3 Dotfull=0.728/0.000 
Dot_cons=0.870/0.005 Unassign_all=0.171 Unassigned=0.000 Dotbest=0.88 
Flags=0,0,0 Naa=22 DUScorr=0.85/3.3/15 Dottheory=0.83 Pfin=1.5e+013 
Probcorr=1 Tfratio=1.6e+008 Pfract=0
Num peaks: 109

3) The business end - the spectrum - is a basepeak normalized, annotated 
peaklist.

452.9    847    "? 2/2 14.3"
462.8    535    "b7-35/-0.46 2/2 5.5"
480.3    620    "b7-18/0.04 2/2 10.4"
498.2    2165    "b7/-0.06 2/2 9.8"
524.0    1397    "? 2/2 8.8"
527.0    381    "Int/AAAAGAGA/0.2 2/2 2.1"
531.1    1140    "y7/-0.19 2/2 7.9"
537.2    675    "? 2/2 8.9"
551.2    910    "b8-18/-0.10 2/2 4.7"
569.1    4712    "b8/-0.20 2/2 25.4"
581.2    289    "? 2/2 3.1"
593.7    249    "? 2/1 2.6"
595.1    1182    "? 2/2 7.3"
602.2    2209    "y8/-0.13 2/2 21.5"
608.6    335    "? 2/2 3.9"
622.2    1625    "b9-18/-0.13 2/2 6.4"
626.2    767    "Int/AAAAAAAAG/0.1 2/2 1.8"
[..]

This is MSP format (also used for small molecules), and it is simple 
ASCII.  Additional "formats" are usually borne for the purposes of 
searching (e.g, indexing).  MSP is easy to work with but it is not a 
standard -- a common, cross-domain representation would be better :)

Paul

Matthew Chambers wrote:
> I brought this issue up in the call because I think that the "evidence" 
> tag in traML is too weak to go in a standard - I was proposing that a 
> better way to do it might be to refer to an mzIdentML file for a more 
> complete context of the evidence.
>
> I know very little about metabolomics, but the spectra libraries we're 
> talking about are indeed proteomics-oriented. But I don't think you need 
> to shut up - indeed, I think this may be another case where we can and 
> should standardize within and even across domains because the 
> annotations of a peptide's spectrum could be even more rich and detailed 
> than that of a smaller molecule. In the spectral library domain just for 
> peptides, there are at least 5 common formats already 
> (http://peptide.nist.gov): MSP/ASCII, a multi-file NIST binary format, 
> SpectraST, BiblioSpec, and X!Hunter. I'm sure you have a few more in the 
> metabolomics domain. A lack of standards makes life so much more 
> interesting, don't you think? ;)
>
> -Matt
>
>
> Steffen Neumann wrote:
>   
>> On Tue, 2009-06-30 at 08:32 -0700, Eric Deutsch wrote:
>>   
>>     
>>> +Can mzIdentML encode a spectral library?
>>>     
>>>       
>> I am unsure whether this was discussed during the conference call, 
>> or is left as an open point to the list.
>>
>> Anyway, I am inclined to say "no" about this,
>> for two reasons: 
>>
>> 1) I don't know enough about analys^H^H^H^H^mzIdentML,
>>    because my very brief looks made it look like proteomics-only.
>>    (Or are you actually referring to a proteomics-spectral library?!
>>     in that case I'll shut up and you can skip the rest of this mail.)
>>
>> 2) A spectral library will (at least in the future)
>>    contain sets of spectra (different eV, MS1-MS^n, ...) 
>>    and associated annotations, which might be as complicated 
>>    as a molecule and its fragmentation brake-down products.
>>    This requires a rich set of links between individual peaks 
>>    and their (molecular) annotation.
>>
>> So for small molecules (read: metabolomics stuff) we have started
>> to create mzAnnotate under the umbrella of the Metabolomics Standards
>> Initiative (MSI). http://msi-workgroups.sourceforge.net/exchange-format/
>>
>> We have drafted some use cases, shown on
>> http://sourceforge.net/apps/mediawiki/metware/index.php?title=MzAnnotate
>> and prepared a converter for both the spectral library www.massbank.jp 
>> and our own MassFrontier clone MetFrag, and will present these
>> on the MSI mailing list soon.
>>
>> Yours,
>> Steffen
>>
>>   
>>     
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>   


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

[Psidev-pi-dev] Minutes from Phone Conference (June 30)

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

Hi all,

Minutes from yesterday's phone conference can be found here:

http://www.psidev.info/index.php?q=node/430

Cheers,

Juan Antonio





Juan Antonio Vizcaíno, Ph.D.
EMBL European Bioinformatics Institute
Proteomics Services Team, PANDA Group
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD
Tel: +44 (0) 1223 492 686
Fax: +44 (0) 1223 494 468
Skype: javizca

[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #91 on issue 42 by andrewrobertjones: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

I have updated the mapping for threshold to include:

"search engine specific input parameter" and changed XOR to OR

--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings

[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #90 on issue 42 by andrewrobertjones: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

This has been added to the CV for prot:FDR threshold

relationship: has_units UO:0000186 ! dimensionless unit
relationship: has_units UO:0000187 ! percent

The same needs to be added for pep:FDR threshold

--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings

[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #89 on issue 42 by dcreasy: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

Latest Mascot examples give these errors. I think that the mapping needs to  
be changed!

Obsolete CV term: 'MS:1001020 - DB filter taxonomy' at element
'/mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseFilters/Filter/FilterType'
CV term used in invalid element: 'MS:1001316 - mascot:SigThreshold' at  
element
'/mzIdentML/AnalysisProtocolCollection/ProteinDetectionProtocol/Threshold'
CV term used in invalid element: 'MS:1001316 - mascot:SigThreshold' at  
element
'/mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Threshold'
Violated mapping rule 'ProteinDetectionProtocolThreshold_rule' at element
'/mzIdentML/AnalysisProtocolCollection/ProteinDetectionProtocol/Threshold'  
exactly
one of the allowed terms must be used!
Violated mapping rule 'SpectrumIdentificationProtocolThreshold_rule' at  
element
'/mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Threshold'
exactly one of the allowed terms must be used!


--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings

[Psidev-pi-dev] Issue 44 in psi-pi: Issues with all instance docs

[<cod...@go...>]

Comment #19 on issue 44 by patri...@matrixscience.com: Issues with all  
instance docs
http://code.google.com/p/psi-pi/issues/detail?id=44

Could we have an example with a modification with a neutral loss defined?

--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings

[Psidev-pi-dev] Conference call - new access code

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

Hi all,
The call will go ahead today although there is a different access code from usual: 241416

Otherwise the dial-in details are the same,
Cheers
Andy


From: Juan Antonio Vizcaíno [mailto:ju...@eb...]
Sent: 30 June 2009 09:19
To: Jones, Andy
Subject: Re: [Psidev-pi-dev] Conference call

Hi Andy,

It seems that the MS people will have their usual phone conference today at 4 pm. Eric sent the e-mail late last night.

So we will have to make the phone conference using another participant access code: 241416.

I think nothing else needs to be changed, although this is the first time we are doing this and there's noone around to ask (holidays or conferences).

Cheers,

Juan


On 29 Jun 2009, at 17:04, Jones, Andy wrote:


Hi all,

There will be an mzIdentML conference call tomorrow (30th June) at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=6&year=2009&hour=16&min=0&sec=0&p1=136

Agenda:

1.       Review minutes from last week: http://www.psidev.info/index.php?q=node/427
2.       Review issues list: http://code.google.com/p/psi-pi/issues/list
3.       Plan for resubmission to the process
4.       AOB

Please send me any other agenda items.

Cheers,
Andy






Dial in details:

+ Germany: 08001012079
+ Switzerland: 0800000860
+ UK: 08081095644
+ USA: 1-866-314-3683
+ Generic international: +44 2083222500 (UK number)



------------------------------------------------------------------------------
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...<mailto:Psi...@li...>
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

Juan Antonio Vizcaíno, Ph.D.
EMBL European Bioinformatics Institute
Proteomics Services Team, PANDA Group
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD
Tel: +44 (0) 1223 492 686
Fax: +44 (0) 1223 494 468
Skype: javizca

Re: [Psidev-pi-dev] Conference call

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

Hi all,

There will be an mzIdentML conference call tomorrow (30th June) at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=6&year=2009&hour=16&min=0&sec=0&p1=136

Agenda:


1.       Review minutes from last week: http://www.psidev.info/index.php?q=node/427

2.       Review issues list: http://code.google.com/p/psi-pi/issues/list

3.       Plan for resubmission to the process

4.       AOB

Please send me any other agenda items.

Cheers,
Andy






Dial in details:

+ Germany: 08001012079
+ Switzerland: 0800000860
+ UK: 08081095644
+ USA: 1-866-314-3683
+ Generic international: +44 2083222500 (UK number)

access code: 297427

[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #88 on issue 42 by a.bertsch0815: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

Implemented changes in CV and mapping file
Addressing comments 81-84,86,87
Semantic Validator is also up-to-date

--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings

[Psidev-pi-dev] Issue 44 in psi-pi: Issues with all instance docs

[<cod...@go...>]

Updates:
	Labels: Milestone-Release1.0

Comment #18 on issue 44 by eisenachM: Issues with all instance docs
http://code.google.com/p/psi-pi/issues/detail?id=44

Just to check for correct use:

The MPC example uses a decoy DB derived from a IPI_human DB.
As DatabaseName the cvParam "IPI_human" (without "_decoy" as part of the  
name)
and as further CVParams the decoy type and generation details are described.

--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings