psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] Unit terms in binaryDataArrays

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

The semantic mapping should allow for a unit term to be specified that 
indicates the unit for a given binaryDataArray. This is particularly 
important for chromatograms, as it's totally arbitrary which time unit 
is chosen for the primary time axis!

-Matt

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

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

I think it's a great idea to add (before finalization) an attribute 
"spotID" which links a MALDI spectrum to a spot. I strongly prefer that 
the semantics of that attribute not be freestyle string but more like 
nativeID. Alternatively, we could have spotID and spotNativeID? In 
either case, we would put those attributes in the index as well.

-Matt


Matthew Chambers wrote:
> I thought about MALDI spot references and I kept coming back to the 
> nativeID concept because of the potential for variability between 
> vendors/labs. Some vendors might use ordinal coordinates to refer to a 
> spot, others might use absolute measurements. As far as I know, these 
> possibilities could concisely be encapsulated in the nativeID concept. 
> It allows us to not force vendors to use one referencing scheme, just 
> like we don't force them to use one referencing scheme for sequential 
> (ESI) data.
>
> For Thermo, I might propose inclusion of all 3 coordinate types in the 
> nativeID of a MALDI scan:
> <sample position, e.g. "H17">,<fine position, e.g. 62x-22>,<absolute 
> position, e.g. 78701x29422>
>
> We could split the fine and absolute positions into X and Y coordinates 
> (separated by commas, e.g. 62,-22,78701,29422)
>
> Did we determine a way to describe which nativeID format is being used? 
> Are we putting them in the CV?
>
> -Matt
>
>
> Eric Deutsch wrote:
>   
>> Hi everyone, the PSI Mass Spectrometry Standards Working Group call is 
>> Tuesday May 27 at 9am PDT:
>>
>>  
>>
>> http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=5&year=2008&hour=17&min=0&sec=0&p1=136 
>> <http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=5&year=2008&hour=17&min=0&sec=0&p1=136>
>>
>>  
>>
>> + Germany: 08001012079
>>
>> + Switzerland: 0800000860
>>
>> + UK: 08081095644
>>
>> + USA: 1-866-314-3683
>>
>> + Generic international: +44 2083222500 (UK number)
>>
>> access code: 297427
>>
>>  
>>
>> The agenda will be to review and discuss what remains to be done to 
>> finish up mzML. This is the last teleconference before ASMS. There 
>> will be no call next week.
>>
>>  
>>
>> Thanks,
>>
>> Eric
>>
>>  
>>
>>
>>     
>
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Re: [Psidev-ms-dev] precursor m/z encoding

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

Hi Darren, there is already an <isolationWindow> element for this. So I
think it should look like this:

  <precursor spectrumRef="S2">
         <isolationWindow>
               <cvParam cvRef="MS" accession="MS:1000040" name="m/z"  
value="796.8"/>
        </isolationWindow>
        <selectedIonList count="1">
             <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000040" name="m/z"  
value="797.3"/>
                 <cvParam cvRef="MS" accession="MS:1000042"
name="intensity" value="120053"/>
             </selectedIon>
        </selectedIonList>
        ...
  </precursor>

But the monoisotopic issue is interesting. Maybe under m/z, we should
have:

m/z
 \_ monoisotopic m/z
 \_ average m/z

Thoughts?

Eric


> -----Original Message-----
> From: psi...@li...
[mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of Darren Kessner
> Sent: Tuesday, May 27, 2008 1:38 PM
> To: Mass spectrometry standard development
> Subject: [Psidev-ms-dev] precursor m/z encoding
> 
> Hi all,
> 
> Just came across an issue in my lab involving precursor encoding.  For
> ms2 scans, we want to know both the isolation m/z and the precursor
> monoisotopic m/z, which may be different.  The isolation m/z is what
> is recorded in the filter string.  The monoisotopic m/z may be
> recorded by the instrument, or it may be calculated by analyzing the
> parent survey scan.
> 
> Here's a suggestion for how to encode this:
> 
>   <precursor spectrumRef="S2">
>         <selectedIonList count="1">
>              <selectedIon>
>                  <cvParam cvRef="MS" accession="MS:1000040" name="m/z"
> value="796.8"/>
>                  <cvParam cvRef="MS" accession="MS:1000xxx"
> name="monoisotopic m/z" value="797.3"/>
>              </selectedIon>
>         </selectedIonList>
>         ...
>   </precursor>
> 
> 
> Does this seem reasonable?  If so, we'll need a term for "monoisotopic
> m/z" -- we have "monoisotopic mass" only.
> 
> 
> Darren
> 
> 
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[Psidev-ms-dev] precursor m/z encoding

[Darren K. <Dar...@cs...>]

Hi all,

Just came across an issue in my lab involving precursor encoding.  For  
ms2 scans, we want to know both the isolation m/z and the precursor  
monoisotopic m/z, which may be different.  The isolation m/z is what  
is recorded in the filter string.  The monoisotopic m/z may be  
recorded by the instrument, or it may be calculated by analyzing the  
parent survey scan.

Here's a suggestion for how to encode this:

  <precursor spectrumRef="S2">
        <selectedIonList count="1">
             <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000040" name="m/z"  
value="796.8"/>
                 <cvParam cvRef="MS" accession="MS:1000xxx"  
name="monoisotopic m/z" value="797.3"/>
             </selectedIon>
        </selectedIonList>
        ...
  </precursor>


Does this seem reasonable?  If so, we'll need a term for "monoisotopic  
m/z" -- we have "monoisotopic mass" only.


Darren


IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by
applicable law.  If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED.

If you have received this message in error, please notify us immediately
by calling (310) 423-6428 and destroy the related message.  Thank You for your cooperation.

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

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

Hi everyone, there are the minutes for the telecon of 2008-05-27.

 

Present: Matt, Darren, Eric, Lennart, Pierre-Alain, Jim

 

- schema

+ Discussed Matt's <precursor> issue 2008-05-26

+ Leave the schema as is? Have the semval require <precursor> in certain
cases?

+ Matt will try to make an example of putting the SRM precursor
information in <targetList> and refer to it

+ Document why checksum should be required.

+ Reply to Wilfred

+ Document that by default the validator doesn't allow anything beyond
what is listed in the mapping file

+ Stay at release 0.99.12 for now. Convert to 1.0.0 later this week when
ready.

 

- MIAPE example document?

+ Done except for switching criteria and parameters for creating
peaklists

+ Pierre-Alain and Jim will get together and finish this

+ State of MIAPE-MS

 

- CV status

+ Darren has sent a proposal for of datatype and relationship
"has_units"

+ OBO-Edit will write out all terms including imported terms unless told
not to

+ Figure out how to get OBO-Edit to write out "import" statements

+ Darren will email John Richter-Day about that

                               

- CV template updates to vendors

+ We have had pretty good response from vendors and Luisa is integrating

+ Okay to have some software organized by vendor

 

- documentation

+ Documentation is up to date

+ Lennart will regenerate embedded figures and send to Eric who will
update

 

- website

+ Eric will update web site for 0.99.12

+ Eric will update link from tiny1 to tiny-pwiz

+ Post the mapping file directly

 

- validator

+ Validator will be a little delayed. There are many back-end changes
due to the MI group

+ Does the validator check that if there is an acquisition list, then
there would be a combination type (like sum of spectra) provided?

 

- example files

+ Matt will take a stab at MALDI example

+ Remove tiny4 and point to "small" which includes LTQ-FT demo usage

+ Fredrik sent to Eric nice examples of dta -> mzML and plgs -> mzML.
Eric will post.

+ Matt will generate an example MGF -> mzML using pwiz and post

+ Jim will send Eric some example RAW files and converted files
(including PDA, SRM)

 

- ASMS

+ Eric will have a draft of a poster today and send out for folks to
look at

+ Jim will follow up with Mark about ASMS "Computer applications
interest group"

+ Try to plan for one night going out to dinner as a group Mon, Tue,
Wed. Jim can't due Tue.

+ Or a lunch

 

- Amsterdam

+ Pierre-Alain will do the presentation of the mzML talk during main
conference

+ PSI session during the congress at Sunday 17th 9:30a-12

+ Tentative presenter at PSI session is Jim Shofstahl with backups of
Randy and Pierre-Alain

 

- Open schema issue: where to put "centroided" and "deisotoped"

+ We will allow spectrum representation (like centroid/profile) in the
fileContent section

 

- Next call

+ Same time in two weeks

 

 

 

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

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

I thought about MALDI spot references and I kept coming back to the 
nativeID concept because of the potential for variability between 
vendors/labs. Some vendors might use ordinal coordinates to refer to a 
spot, others might use absolute measurements. As far as I know, these 
possibilities could concisely be encapsulated in the nativeID concept. 
It allows us to not force vendors to use one referencing scheme, just 
like we don't force them to use one referencing scheme for sequential 
(ESI) data.

For Thermo, I might propose inclusion of all 3 coordinate types in the 
nativeID of a MALDI scan:
<sample position, e.g. "H17">,<fine position, e.g. 62x-22>,<absolute 
position, e.g. 78701x29422>

We could split the fine and absolute positions into X and Y coordinates 
(separated by commas, e.g. 62,-22,78701,29422)

Did we determine a way to describe which nativeID format is being used? 
Are we putting them in the CV?

-Matt


Eric Deutsch wrote:
>
> Hi everyone, the PSI Mass Spectrometry Standards Working Group call is 
> Tuesday May 27 at 9am PDT:
>
>  
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=5&year=2008&hour=17&min=0&sec=0&p1=136 
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=5&year=2008&hour=17&min=0&sec=0&p1=136>
>
>  
>
> + Germany: 08001012079
>
> + Switzerland: 0800000860
>
> + UK: 08081095644
>
> + USA: 1-866-314-3683
>
> + Generic international: +44 2083222500 (UK number)
>
> access code: 297427
>
>  
>
> The agenda will be to review and discuss what remains to be done to 
> finish up mzML. This is the last teleconference before ASMS. There 
> will be no call next week.
>
>  
>
> Thanks,
>
> Eric
>
>  
>
>

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

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

Hi everyone, the PSI Mass Spectrometry Standards Working Group call is
Tuesday May 27 at 9am PDT:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=5&year
=2008&hour=17&min=0&sec=0&p1=136

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)

access code: 297427

 

The agenda will be to review and discuss what remains to be done to
finish up mzML. This is the last teleconference before ASMS. There will
be no call next week.

 

Thanks,

Eric

 

Re: [Psidev-ms-dev] Precursor spectrum ref required?

[Fredrik L. <Fre...@im...>]

I think this spectrum reference should remain optional. We cannot 
provide it (at least not correctly) for PKL and MGF to mzML conversion.
On the other hand, I agree that the SRM transitions could be more 
efficiently described. Maybe you could exemplify how you would do it 
using CV terms?

Fredrik

Matthew Chambers skrev:
> It is unclear whether the precursor must have a spectrum reference 
> (either internal or external) for semantic validation. If it is 
> required, we cannot use the current precursor structure to indicate the 
> Q1 selected mz for SRM spectra. I would rather make the precursor 
> spectrum reference obligatory (for semantic validation) and then use 
> single (vastly more space-efficient) CV terms to indicate the Q1 and Q3 
> values for SRM spectra.
>
> Thoughts?
> -Matt
>
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>   

[Psidev-ms-dev] mzML comments

[Wilfred H T. <Ta...@ap...>]

I recently looked over the mzML format draft and have a few comments.


Regarding the schema (http://www.sbeams.org/tmp/mzML0.99.12.html):

* For the "cvParam Mapping Rules," I suggest that the number of "musts" be 
decreased significantly (or changed to "mays"). For example, for the 
element <sourceFile>, there's a rule saying: "MUST supply a *child* term 
of MS:1000561 (data file checksum type) one or more times." This sort of 
information does not seem to be critical for downstream processing of mzML 
files and thus doesn't deserve "must" status. There are quite a few 
similar examples.

* For the elements <fileDescription>, <sourceFileList>, <sourceFile>, 
etc., would it make sense to change the name to be more general (such as 
dataSource) to reflect the fact that not all instrument data is stored in 
files? For example, for the Applied Biosystems|MDS Sciex instruments, some 
instruments (such as the QSTAR or QTRAP systems) store data in .wiff 
files, while other instruments (such as the 4700 and 4800 systems) store 
data in an Oracle database.


Regarding the controlled vocabulary (
http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
):

* Under "spectrum"-->"spectrum representation", the only 2 choices are 
"centroid mass spectrum" and "profile mass spectrum". That doesn't 
adequately capture the full range of spectrum representations. For example 
in addition to centroiding, the data could be de-isotoped, smoothed, 
converted to +1 charge, etc. Also, having just the 2 choices of centroid 
vs. profile is inconsistent with the software processing options listed 
under "data transformation"-->"data processing action", where a much wider 
range of options are listed ("baseline reduction", "charge deconvolution", 
"deisotoping", etc.). It seems desirable to expand the choices under 
"spectrum"-->"spectrum representation" to at least be consistent. 
Alternatively, maybe a slightly different categorization might make sense 
- something like raw data vs. processed data (full data vs. reduced data).

* Under "spectrum"-->"spectrum type", some triple quad-type scans are 
missing - precursor ion (scan Q1, fixed Q3), neutral loss (scan Q1 and Q3 
together with a constant difference between Q1 and Q3).


Please accept my apologies in advance if any of these topics have already 
been discussed/resolved previously, as I am new to this discussion.

Thanks,
Wilfred

[Psidev-ms-dev] Precursor spectrum ref required?

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

It is unclear whether the precursor must have a spectrum reference 
(either internal or external) for semantic validation. If it is 
required, we cannot use the current precursor structure to indicate the 
Q1 selected mz for SRM spectra. I would rather make the precursor 
spectrum reference obligatory (for semantic validation) and then use 
single (vastly more space-efficient) CV terms to indicate the Q1 and Q3 
values for SRM spectra.

Thoughts?
-Matt

[Psidev-ms-dev] new ProteoWizard packages (1.2)

[Darren K. <Dar...@cs...>]

Hi everyone,

I've updated the example files to the latest schema.

I also posted new binary packages of the latest ProteoWizard builds.   
In particular, msconvert now supports MGF reading, precision selection  
(32 or 64 for m/z and/or intensity arrays), zlib compression of the  
binary data arrays, and centroided data for Thermo RAW files (via  
XCalibur).  A lot of work has been done by Matt Chambers to make our  
Thermo RAW Reader complete.

Links to the packages are on the ProteoWizard home page:
http://proteowizard.sourceforge.net

If you have time, please play around with the tools and let us know if  
there are any problems.  I'm planning on updating docs and fixing any  
bugs next week in preparation for ASMS.


Darren


P.S.  I'll be out of email touch until Tuesday, but I'll be at the  
conference call.

Re: [Psidev-ms-dev] MzML 0.99.12 schema update

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

Hi Matt, thank you for updating the schema. I have updated the
documentation and the development web page.

Thanks,
Eric



> -----Original Message-----
> From: psi...@li...
[mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of Matthew Chambers
> Sent: Thursday, May 22, 2008 8:36 AM
> To: Mass spectrometry standard development
> Subject: [Psidev-ms-dev] MzML 0.99.12 schema update
> 
> - added unitCvRef to cvParam and userParam
> - added sourceFileRef, externalNativeID, and externalSpectrumID to
> PrecursorType
> 
> -Matt
> 
>
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[Psidev-ms-dev] MzML 0.99.12 schema update

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

- added unitCvRef to cvParam and userParam
- added sourceFileRef, externalNativeID, and externalSpectrumID to 
PrecursorType

-Matt

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

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

Hi everyone, there are the minutes for the telecon of 2008-05-20.

 

Present: Matt, Darren, Eric, Jim, Pierre-Alain

 

Thank you to Phil for setting up the call.

 

- schema

+ Discussed Fredrik's suggested changes of 2008-05-20

+ Add unitCvRef attribute to cvParam

+ apply same exact attributes to precursor as there is now for acquisition

+ Matt will make the changes and release 0.99.12

 

- MIAPE example document?

+ Darren and Pierre-Alain will get together and finish this

 

- CV status

+ Darren has sent a proposal for of datatype and has_units

+ Eric will with Luisa 5/15 9:52am

+ Then Darren will go ahead and implemented

 

- CV template updates to vendors

+ Eric has sent out and will follow up

+ Thermo and Waters have returned results

 

- documentation

+ Eric will generate a HTML and .doc spec document for 0.99.12 and post

 

- website

+ Eric will update web site for 0.99.12

 

- validator

+ Eric will contact Lennart and Fredrik and see how to proceed

+ Does the validator check that if there is a acquisition list, then there would be a combination type (like sum of spectra) provided

 

- example files

+ Darren added examples of small with and without compression. Will be released in a few days.

+ Matt will take a stab at MALDI example

+ Remove tiny4 and point to "small" which includes LTQ-FT demo usage

+ Fredrik sent out a nice example of dta -> mzML

+ Matt will generate an example MGF -> mzML using pwiz and post

+ Jim will send Eric some example RAW files and converted files (including PDA, SRM)

 

- ASMS

+ Eric will have a draft of a poster for the next call and send out for folks to look at

+ Eric will follow up with Randy about ASMS "Computer applications interest group"

+ or try mark.sanders@therm

+ Everyone present at the call will be at ASMS

+ Try to plan for one night going out to dinner as a group Mon, Tue, Wed. Jim can't due Tue.

+ Or a lunch

 

- Amsterdam

+ Poster in Eric's name was submitted. No word on acceptance, but Eric cannot attend.

+ PSI session during the congress at Sunday 17th 9:30a-12

+ Tentative presenter at PSI session is Jim Shofstahl with backups of Randy and Pierre-Alain

 

- Open schema issue: where to put "centroided" and "deisotoped"

+ We will allow spectrum representation (like centroid/profile) in the fileContent section

 

- Next call

+ Same time next week

 

 

 

 

 

________________________________

From: Eric Deutsch 
Sent: Tuesday, May 13, 2008 10:12 AM
To: 'Mass spectrometry standard development'
Cc: Eric Deutsch
Subject: PSI-MSS WG call minutes

 

Hi everyone, there are the minutes for the telecon of 2008-05-13.

 

Present: Matt, Darren, Eric, Jim, Pierre-Alain

 

Thank you to Juan Antonio for setting up the call.

 

- Schema updated to 0.99.11

+ Eric will update web site for that

+ Darren has updated the codebase and will check if the latest output validates

 

- MIAPE example document?

+ A few small items left.

+ A final example document will be finished in the next week for inspection

 

- CV status

+ Fredrik volunteers to help with the CV, too

+ Eric has updated the CV a couple times

+ Darren will send around a few examples of datatype and unittype

 

- CV template updates to vendors

+ Eric has sent out and will follow up

+ Thermo and Waters have returned results

 

- documentation

+ Check whether instrumentConfiguration is well defined in xsd

+ Eric will generate a HTML and .doc spec document for 0.99.11 and post

 

- website

+ Eric will update web site for 0.99.11

 

- validator

+ Eric will contact Lennart and Fredrik and see how to proceed

+ Does the validator check that if there is a acquisition list, then there would be a combination type (like sum of spectra) provided

 

- example files

+ Remove tiny4 and point to "small" which includes LTQ-FT demo usage

+ Fredrik sent out a nice example of dta -> mzML

+ Matt will generate an example MGF -> mzML using pwiz and post

+ Jim will send Eric some example RAW files and converted files (including PDA, SRM)

 

- ASMS

+ Eric will follow up with Randy about ASMS "Computer applications interest group"

+ or try mark.sanders@therm

 

- Amsterdam

+ Poster in Eric's name was submitted. No word on acceptance, but Eric cannot attend.

+ PSI session during the congress at Sunday 17th 9:30a-12

+ Tentative presenter at PSI session is Jim Shofstahl with backups of Randy and Pierre-Alain

 

- Open schema issue: where to put "centroided" and "deisotoped"

+ We will allow spectrum representation (like centroid/profile) in the fileContent section

 

- Next call

+ Same time next week. Eric will figure how to start the call

 

 

 

________________________________

From: Eric Deutsch 
Sent: Tuesday, May 06, 2008 10:04 AM
To: 'Mass spectrometry standard development'
Cc: Eric Deutsch
Subject: RE: RE: PSI-MSS WG call Tuesday

 

Hi everyone, here are the minutes for the telecon of 2008-05-06. Please see action items for you. Anyone not on the call willing to help out is welcome.

 

Present: Darren, Matt, Eric, Jim, Pierre-Alain

 

Thank you to Juan Antonio for setting up the call.

 

Agenda:

 

- What is the purpose of <mzML> id and accession attributes?

+ Make the id= attribute optional in schema

+ Recommend in the documentation that you use LSID or local identifiers

+ Make all sample instance documents use a psidev LSID

+ Leave accession= optional as is, perhaps with better documentation

 

- Make <run> instrumentConfigurationRef optional or remove it:

  - if remove, then this attribute can be required in <scan>

  - if optional, semval must insure that it is provide either in <run> or <scan>

  + OR consensus opinion: rename <run> instrumentConfigurationRef to defaultInstrumentConfigurationRef and keep it required

  + Document the intrumentConfiguration a bit better. Applies to LTQ-FT but not LTQ, for example. For different modes, use ParamGroups

 

+ Discussion of issue of how to use ParamGroups without having to do two passes through the file.

 

- Issue of exactly how other spectra are referenced in <acquisition>

+ We agree to move forward with Matt suggestion:

  spectrumRef (infer reference as current file and spectrumRef is IDREF 

  pointing to an existing spectrum's id)

  sourceFileRef + externalNativeID (original file is native)

  sourceFileRef + externalSpectrumID (original file is mzML)

  For example external mzXML files, the externalNativeID would refer to mzXML scanNumber

  In fact, anything that's not mzML would have externNativeID

  Matt says that XML schema can enforce these various options

 

- MIAPE spreadsheet?

+ Pierre-Alain has spreadsheet. Darren added some comments trying to implement it

+ Rename Darren's tiny2 to tiny5 or some other name since "tiny2" is used by another document

+ Get miape-ms.pwiz.mzML posted

+ Pierre-Alain will continue to work on the spreadsheet

+ Before next call, send out or post miape-ms.pwiz.mzML and spreadsheet of issues to discuss

 

- CV?

+ Randy has pink teddy bear, but haven't heard from him

+ Eric will take it and work on some changes to the CV

+ Eric will create the CV spreadsheets and start sending to vendors

+ Some contacts: Bruker :Herbert Thiele?  Waters: Ronan O'Malley?

 

- documentation?

+ latest is posted without figures

 

- schema?

+ Eric will add Darren & Matt as a developers (dkessner) (chambm)

+ Darren will update 0.99.10 to 0.99.11 with changes above

+ Matt can help with multiple accession configs in <acquisition>

 

- website

+ Eric post 0.99.10 schemas

+ Darren verify that tiny.pwiz encodes all ideas of tiny1 and then post as a single tiny1

 

- example files

+ Jim has an example that he will send out

+ Jim will send out examples of the nativeIDs for Thermo

 

 

 

 

________________________________

From: Eric Deutsch 
Sent: Monday, May 05, 2008 12:12 AM
To: 'Mass spectrometry standard development'; Juan Antonio Vizcaíno González
Cc: Eric Deutsch
Subject: RE: PSI-MSS WG call Tuesday

 

Hi everyone, as previously mentioned, the PSI Mass Spectrometry Standards Working Group call is Tuesday May 6 at 9am PDT:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=5&year=2008&hour=17&min=0&sec=0&p1=136

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)

access code: 297427

 

The agenda will be to review and discuss what remains to be done to finish up mzML, including the latest release and some recent issues discovered while making examples.

 

Thanks,

Eric

 

Re: [Psidev-ms-dev] pkl, mgf, ... to mzML,mzXML,...

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

MSConvert in ProteoWizard will now do MGF->mzML/mzXML but not PKL. A PKL 
reader implementation should be trivial though.

-Matt


Rune Schjellerup Philosof wrote:
> I can't find a converter for pkl or mgf to mzML or mzXML conversion.
> Does any of you know of such a converter?
>
> -
> Rune
>
>   

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

[Fredrik L. <Fre...@im...>]

Hi All,

some minor mzML schema things that maybe should be addressed:

1) CV params: In most cases when there is a unit it will come from a  
different ontology than the actual CV param. Should there maybe be an  
optional attribute unitCvRef of type XS:IDREF?
For example, currently we have:
             <cvParam cvRef="MS" accession="MS:1000486" name="source  
potential" value="4.20" unitAccession="UO:0000248" unitName="kilovolt"/>
which would be:
             <cvParam cvRef="MS" accession="MS:1000486" name="source  
potential" value="4.20" unitCvRef="UO" unitAccession="UO:0000248"  
unitName="kilovolt"/>
I think this would make things a bit more consistent.

2) precursor element (discussed previously, but I just wanted to bring  
it up again):
Should there be optional externalSpectrumID, externalNativeID and  
sourceFileRef attributes as for acquisition elements?
I see no negative effects, so I am for this change.

Regards

Fredrik



20 maj 2008 kl. 08.51 skrev Eric Deutsch:

> Hi everyone, the PSI Mass Spectrometry Standards Working Group call  
> is Tuesday May 6 at 9am PDT:
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=5&year=2008&hour=17&min=0&sec=0&p1=136
>
> + Germany: 08001012079
> + Switzerland: 0800000860
> + UK: 08081095644
> + USA: 1-866-314-3683
> + Generic international: +44 2083222500 (UK number)
> access code: 297427
>
> The agenda will be to review and discuss what remains to be done to  
> finish up mzML.
>
> Thanks,
> Eric
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] pkl, mgf, ... to mzML,mzXML,...

[Rune S. P. <ru...@ph...>]

I can't find a converter for pkl or mgf to mzML or mzXML conversion.
Does any of you know of such a converter?

-
Rune

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

[Rune S. P. <ru...@ph...>]

Sorry I didn't reply earlier.
I really don't have time for any work on example..
Just a few weeks away from my master thesis deadline, and there are too 
many things that need to be wrapped up.

Eric Deutsch skrev:
>
>   - MS^E example (I think Rune sent one out. Is it great?)
>
> +See if Rune would do it
>
>
>   - Example that Rune suggests about lockspray reference scans 
> (implying multiple samples)
>
> +Rune??
>

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

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

Hi everyone, the PSI Mass Spectrometry Standards Working Group call is
Tuesday May 6 at 9am PDT:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=5&year
=2008&hour=17&min=0&sec=0&p1=136

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)

access code: 297427

 

The agenda will be to review and discuss what remains to be done to
finish up mzML.

 

Thanks,

Eric

 

Re: [Psidev-ms-dev] Documentation updated to mzML 0.99.11

[Darren K. <Dar...@cs...>]

Hi guys,

I also updated the examples to validate with schema 0.99.11.


Darren



On May 13, 2008, at 2:55 PM, Eric Deutsch wrote:

> Hi everyone, I have updated the mzML development web page:
>
> http://psidev.info/index.php?q=node/257
>
> to show the latest revision 0.99.11. The latest schemas are there  
> and HTML and .doc documentation have been updated. Please let us  
> know if you see any problems. There are still some outstanding CV  
> work to be done.
>
> Any changes that still might be made will surely be trivial, so more  
> implementation work on this near-final version is encouraged.
>
> Thank you!
> Eric
>
>
> ----------------------------------
> Eric Deutsch, Ph.D.
> Institute for Systems Biology
> 1441 North 34th Street
> Seattle WA 98103
> Tel: 206-732-1397
> Fax: 206-732-1260
> Email: ede...@sy...
> WWW: http://www.systemsbiology.org/Senior_Research_Scientists/Eric_Deutsch
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by
applicable law.  If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED.

If you have received this message in error, please notify us immediately
by calling (310) 423-6428 and destroy the related message.  Thank You for your cooperation.

[Psidev-ms-dev] Documentation updated to mzML 0.99.11

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

Hi everyone, I have updated the mzML development web page:

 

http://psidev.info/index.php?q=node/257

 

to show the latest revision 0.99.11. The latest schemas are there and
HTML and .doc documentation have been updated. Please let us know if you
see any problems. There are still some outstanding CV work to be done.

 

Any changes that still might be made will surely be trivial, so more
implementation work on this near-final version is encouraged.

 

Thank you!

Eric

 

 

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

Eric Deutsch, Ph.D.
Institute for Systems Biology
1441 North 34th Street
Seattle WA 98103
Tel: 206-732-1397
Fax: 206-732-1260
Email: ede...@sy...
WWW:
http://www.systemsbiology.org/Senior_Research_Scientists/Eric_Deutsch

 

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

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

Hi everyone, there are the minutes for the telecon of 2008-05-13.

 

Present: Matt, Darren, Eric, Jim, Pierre-Alain

 

Thank you to Juan Antonio for setting up the call.

 

- Schema updated to 0.99.11

+ Eric will update web site for that

+ Darren has updated the codebase and will check if the latest output validates

 

- MIAPE example document?

+ A few small items left.

+ A final example document will be finished in the next week for inspection

 

- CV status

+ Fredrik volunteers to help with the CV, too

+ Eric has updated the CV a couple times

+ Darren will send around a few examples of datatype and unittype

 

- CV template updates to vendors

+ Eric has sent out and will follow up

+ Thermo and Waters have returned results

 

- documentation

+ Check whether instrumentConfiguration is well defined in xsd

+ Eric will generate a HTML and .doc spec document for 0.99.11 and post

 

- website

+ Eric will update web site for 0.99.11

 

- validator

+ Eric will contact Lennart and Fredrik and see how to proceed

+ Does the validator check that if there is a acquisition list, then there would be a combination type (like sum of spectra) provided

 

- example files

+ Remove tiny4 and point to "small" which includes LTQ-FT demo usage

+ Fredrik sent out a nice example of dta -> mzML

+ Matt will generate an example MGF -> mzML using pwiz and post

+ Jim will send Eric some example RAW files and converted files (including PDA, SRM)

 

- ASMS

+ Eric will follow up with Randy about ASMS "Computer applications interest group"

+ or try mark.sanders@therm

 

- Amsterdam

+ Poster in Eric's name was submitted. No word on acceptance, but Eric cannot attend.

+ PSI session during the congress at Sunday 17th 9:30a-12

+ Tentative presenter at PSI session is Jim Shofstahl with backups of Randy and Pierre-Alain

 

- Open schema issue: where to put "centroided" and "deisotoped"

+ We will allow spectrum representation (like centroid/profile) in the fileContent section

 

- Next call

+ Same time next week. Eric will figure how to start the call

 

 

 

________________________________

From: Eric Deutsch 
Sent: Tuesday, May 06, 2008 10:04 AM
To: 'Mass spectrometry standard development'
Cc: Eric Deutsch
Subject: RE: RE: PSI-MSS WG call Tuesday

 

Hi everyone, here are the minutes for the telecon of 2008-05-06. Please see action items for you. Anyone not on the call willing to help out is welcome.

 

Present: Darren, Matt, Eric, Jim, Pierre-Alain

 

Thank you to Juan Antonio for setting up the call.

 

Agenda:

 

- What is the purpose of <mzML> id and accession attributes?

+ Make the id= attribute optional in schema

+ Recommend in the documentation that you use LSID or local identifiers

+ Make all sample instance documents use a psidev LSID

+ Leave accession= optional as is, perhaps with better documentation

 

- Make <run> instrumentConfigurationRef optional or remove it:

  - if remove, then this attribute can be required in <scan>

  - if optional, semval must insure that it is provide either in <run> or <scan>

  + OR consensus opinion: rename <run> instrumentConfigurationRef to defaultInstrumentConfigurationRef and keep it required

  + Document the intrumentConfiguration a bit better. Applies to LTQ-FT but not LTQ, for example. For different modes, use ParamGroups

 

+ Discussion of issue of how to use ParamGroups without having to do two passes through the file.

 

- Issue of exactly how other spectra are referenced in <acquisition>

+ We agree to move forward with Matt suggestion:

  spectrumRef (infer reference as current file and spectrumRef is IDREF 

  pointing to an existing spectrum's id)

  sourceFileRef + externalNativeID (original file is native)

  sourceFileRef + externalSpectrumID (original file is mzML)

  For example external mzXML files, the externalNativeID would refer to mzXML scanNumber

  In fact, anything that's not mzML would have externNativeID

  Matt says that XML schema can enforce these various options

 

- MIAPE spreadsheet?

+ Pierre-Alain has spreadsheet. Darren added some comments trying to implement it

+ Rename Darren's tiny2 to tiny5 or some other name since "tiny2" is used by another document

+ Get miape-ms.pwiz.mzML posted

+ Pierre-Alain will continue to work on the spreadsheet

+ Before next call, send out or post miape-ms.pwiz.mzML and spreadsheet of issues to discuss

 

- CV?

+ Randy has pink teddy bear, but haven't heard from him

+ Eric will take it and work on some changes to the CV

+ Eric will create the CV spreadsheets and start sending to vendors

+ Some contacts: Bruker :Herbert Thiele?  Waters: Ronan O'Malley?

 

- documentation?

+ latest is posted without figures

 

- schema?

+ Eric will add Darren & Matt as a developers (dkessner) (chambm)

+ Darren will update 0.99.10 to 0.99.11 with changes above

+ Matt can help with multiple accession configs in <acquisition>

 

- website

+ Eric post 0.99.10 schemas

+ Darren verify that tiny.pwiz encodes all ideas of tiny1 and then post as a single tiny1

 

- example files

+ Jim has an example that he will send out

+ Jim will send out examples of the nativeIDs for Thermo

 

 

 

 

________________________________

From: Eric Deutsch 
Sent: Monday, May 05, 2008 12:12 AM
To: 'Mass spectrometry standard development'; Juan Antonio Vizcaíno González
Cc: Eric Deutsch
Subject: RE: PSI-MSS WG call Tuesday

 

Hi everyone, as previously mentioned, the PSI Mass Spectrometry Standards Working Group call is Tuesday May 6 at 9am PDT:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=5&year=2008&hour=17&min=0&sec=0&p1=136

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)

access code: 297427

 

The agenda will be to review and discuss what remains to be done to finish up mzML, including the latest release and some recent issues discovered while making examples.

 

Thanks,

Eric

 

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

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

Hi everyone, the PSI Mass Spectrometry Standards Working Group call is Tuesday May 6 at 9am PDT:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=13&month=5&year=2008&hour=17&min=0&sec=0&p1=136

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)

access code: 297427

 

The agenda will be to review and discuss what remains to be done to finish up mzML, including the latest release and some recent issues discovered while making examples.

 

- Schema updated to 0.99.11

- MIAPE spreadsheet?

- CV status

- CV template updates to vendors

- documentation

- website

- example files

- Open schema issue: where to put "centroided" and "deisotoped"

 

Thanks,

Eric

 

Re: [Psidev-ms-dev] Centroid vs. Profile for mass spectra

[Darren K. <Dar...@cs...>]

Hi all,

Just wanted to throw another possibility out there -- add a  
dataProcessingRef to <run>, and include run-level processing in a  
single <dataProcessing> element.


Darren


On May 12, 2008, at 10:58 AM, Matthew Chambers wrote:

> Hi all,
>
> I'm trying to map mzXML's various ways of indicating profile vs.
> centroid mode spectra to mzML. The mapping would work best if the
> optional dataProcessing attributes ("centroided" and "deisotoped",  
> which
> refer to the entire file) in mzXML map to the fileContent element in
> mzML. But MS_centroid_mass_spectrum and MS_profile_mass_spectrum are  
> not
> currently "data file content" types so they would not validate if they
> were in fileContent.
>
> It looks like the semantic validator requires that either centroid or
> profile mass spectrum appear in each spectrum_description (if I'm
> reading the ms-mapping file correctly), so that's good. The only  
> thing a
> converter from an ambiguous-data-mode file (like DTA/MGF/possibly  
> mzXML)
> to mzML can do is assume that the data is one way or the other. I
> suppose it could do some heuristics to guess intelligently, too.
>
> -Matt
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by
applicable law.  If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED.

If you have received this message in error, please notify us immediately
by calling (310) 423-6428 and destroy the related message.  Thank You for your cooperation.

[Psidev-ms-dev] Centroid vs. Profile for mass spectra

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

Hi all,

I'm trying to map mzXML's various ways of indicating profile vs. 
centroid mode spectra to mzML. The mapping would work best if the 
optional dataProcessing attributes ("centroided" and "deisotoped", which 
refer to the entire file) in mzXML map to the fileContent element in 
mzML. But MS_centroid_mass_spectrum and MS_profile_mass_spectrum are not 
currently "data file content" types so they would not validate if they 
were in fileContent.

It looks like the semantic validator requires that either centroid or 
profile mass spectrum appear in each spectrum_description (if I'm 
reading the ms-mapping file correctly), so that's good. The only thing a 
converter from an ambiguous-data-mode file (like DTA/MGF/possibly mzXML) 
to mzML can do is assume that the data is one way or the other. I 
suppose it could do some heuristics to guess intelligently, too.

-Matt