psidev-ms-dev

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

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

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PST:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=09
<http://www.timeanddate.com/worldclock/fixedtime.html?day=09&month=12&year=2
008&hour=16&min=0&sec=0&p1=136>
&month=12&year=2008&hour=16&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

 

Incomplete list of things to discuss. I will try to have a more complete
list of topics before the start of the meeting:

 

- Post recommended change to the spectrum wrt spectrum and acquisition

- Issue of <cvParam cvRef="MS" accession="MS:1000786" name="non-standard
data array" value="karma points"/>

- Desire to revisit id="" index="" nativeID="" (see Dec 8 Re:
[Psidev-ms-dev] spectrum identifiers on list)

  I am reluctant to reopen this can of snakes

- componentList to become optional and InstrumentConfiguration required?

- How do we/can we deal with optional elements that are required by MIAPE?-
Validator (TOPP validator and EBI validator)

- TraML

- more...

- Next call

 

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

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

[updated agenda]

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PST:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=09
<http://www.timeanddate.com/worldclock/fixedtime.html?day=09&month=12&year=2
008&hour=16&min=0&sec=0&p1=136>
&month=12&year=2008&hour=16&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

 

Agenda:

 

- Wilfred suggests:

  (A) Have "MS1 spectrum" and "MSn spectrum" [This is the current situation]


  (B) Have "MS1 spectrum" (or appropriate synonym), "MS2 spectrum" (or
appropriate synonym), and "MSn spectrum" [restrict n >= 3] 

  (C) Have "MSn spectrum" only and rely on mslevel to specify 1, 2, etc. 

  My vote is for option (B) given the high occurrence of MS1 spectra and MS2
spectra, with option (C) coming in second. 

 

- Desire to revisit id="" index="" nativeID="" (see Dec 8 Re:
[Psidev-ms-dev] spectrum identifiers on list)

  I am reluctant to reopen this can of snakes

- I propose that we keep all three attributes as previously decided

  index is xsd:nonNegativeInteger

  id is xs:ID

  nativeID is xs:string with an xsd uniqueness constraint on it

  One may not have two different representations of the same scan in a
single file (document this!)

 

- Approve/modify Eric's proposal of usage of index, id, nativeID within and
from outside mzML

 

- Approve/modify "mass resolution" and "mass resolving power" terms proposed
by Wilfred

 

- Approve/modify Eric's proposal on "other" and "unknown" terms

 

- Post of the recommended change to the spectrum wrt spectrum and
acquisition 12/5 1:17a

 

- componentList to become optional and InstrumentConfiguration required?

 

- How do we/can we deal with optional elements that are required by MIAPE?-
Validator (TOPP validator and EBI validator)

 

- Is this what we want and is it a problem for validators as Marc suggests?

  "isolation m/z lower limit" is PART_OF the description of an "isolation
window"

     "isolation window is PART_OF the description of a "precursor"

        "precursor is PART_OF the description of a "spectrum"

  Can the mapping file not specify that <isolationWindow> must have two
cvParams

  which are PART_OF "isolation window"?

  What to do?

 

- Other issues lost in the shuffle or in the tracker?

  http://sourceforge.net/tracker/?atid=1126041
<http://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

 

- Who will implement the schema changes we discussed?

- Who will update the CV?

- Who will update the mapping file?

- Who will update the documentation?

 

- TraML

 

- Next call? 23rd?

 

 

 

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

[Angel P. <an...@ma...>]

On Tue, Dec 9, 2008 at 3:10 AM, Eric Deutsch <ede...@sy...>wrote:

>  [updated agenda]
>
> Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
> will be Tuesday 8am PST:
>
>
>
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=09&month=12&year=2008&hour=16&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
>
>
>
> Agenda:
>
>
>
> - Wilfred suggests:
>
>   (A) Have "MS1 spectrum" and "MSn spectrum" [This is the current
> situation]
>
>   (B) Have "MS1 spectrum" (or appropriate synonym), "MS2 spectrum" (or
> appropriate synonym), and "MSn spectrum" [restrict n >= 3]
>
>   (C) Have "MSn spectrum" only and rely on mslevel to specify 1, 2, etc.
>
>   My vote is for option (B) given the high occurrence of MS1 spectra and
> MS2 spectra, with option (C) coming in second.
>
>
>
> - Desire to revisit id="" index="" nativeID="" (see Dec 8 Re:
> [Psidev-ms-dev] spectrum identifiers on list)
>
>   I am reluctant to reopen this can of snakes
>
> - I propose that we keep all three attributes as previously decided
>
>   index is xsd:nonNegativeInteger
>

I never understood the need for the index attr. XML is ordered. If you read
in a mzML file, then the 5th spectrum will always be index = 4 and the xpath
will always be /mzML/run/spectrumList/spectrum[4]
Serializing this then requires that you place this same element in the same
position, or else you are not follwoing the XML spec.

-angel

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

[Mike C. <tu...@gm...>]

On Tue, Dec 9, 2008 at 9:24 AM, Angel Pizarro <an...@ma...> wrote:
> I never understood the need for the index attr. XML is ordered. If you read
> in a mzML file, then the 5th spectrum will always be index = 4 and the xpath
> will always be /mzML/run/spectrumList/spectrum[4]
> Serializing this then requires that you place this same element in the same
> position, or else you are not follwoing the XML spec.

My thought was that it is present for the same reason that the
spectrum index is present--that is, it's redundant information somehow
meant to ease use of the file.

If it's not so described already, it would be nice if the
documentation indicated which elements, attributes, etc., are
redundant, just to save readers a lot of time wondering "why is this
here?".

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

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

"Eric Deutsch" <ede...@sy...> wrote on 12/09/2008 12:10:20 
AM:

> [updated agenda]
> Hi everyone, the next PSI Mass Spectrometry Standards Working Group 
> call will be Tuesday 8am PST:
> 
> http://www.timeanddate.com/worldclock/fixedtime.html?
> day=09&month=12&year=2008&hour=16&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
> 
> Agenda:
> 
> - Wilfred suggests:
>   (A) Have "MS1 spectrum" and "MSn spectrum" [This is the current 
situation] 
>   (B) Have "MS1 spectrum" (or appropriate synonym), "MS2 spectrum" 
> (or appropriate synonym), and "MSn spectrum" [restrict n >= 3] 
>   (C) Have "MSn spectrum" only and rely on mslevel to specify 1, 2, etc. 

>   My vote is for option (B) given the high occurrence of MS1 spectra
> and MS2 spectra, with option (C) coming in second. 

I can't seem to get into the conference today, but after sleeping on this, 
my new thinking is that option (A) might be the best option (essentially 
leave things the way they are currently), but rename "MSn spectrum" as 
"N-th generation product ion spectrum" (with "product ion" making it clear 
that this term only really makes sense for N >= 2).

Wilfred

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

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

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PST:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=09
<http://www.timeanddate.com/worldclock/fixedtime.html?day=09&month=12&year=2
008&hour=16&min=0&sec=0&p1=136>
&month=12&year=2008&hour=16&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

 

Agenda:

 

- Any remaining open schema items?

- New MGF terms

- MGF-related terms

- Contact terms required? Basic? MIAPE?

- Must we specify CID/ETD?

- Post from metabolomics person Richard Scheltema

- Issue tracker: https://sourceforge.net/tracker/?atid=1126041
<https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

 

- Next call? 23rd?

 

 

 

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

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

Here are the minutes from today's call:

Any remaining open schema items?
- new subschema for component list
- remove number attribute from scan

New MGF terms and MGF-related terms
- fine to include overlapping terms with PSI-PI
- keep names the same, relations and definitions need to improve

Contact terms required? Basic? MIAPE?
- basic: if contact element included, at least name and organization
- MIAPE: must include contact element, at least name and organization

Must we specify CID/ETD?
- allow multiple dissociation methods
- require at least the base term (to specify unknown method)
- in case of EI where precursor-independent activation is provided by 
the ion source, the ion source itself will imply that activation

Precursor ion spectrum/Neutral loss spectrum support
- [Marc|Wilfred|Frederick] will produce an example for these types (I 
forgot who exactly offered to do this)

Unknown term discussion
- get rid of MS1? what does MSn mean?
- discuss spectrum type possibilities on list
- Spectrum representation: allow base term

Zoom/full spectrum
- zoom term goes to spectrum and becomes binary (there or not there, no 
more full scan)
- scan window and resolution describe the scanning method quantitatively

Post from metabolomics person Richard Scheltema
- mzML doesn't support more than one run
- possible support for 2d chromatograms in 1.2; Richard offered to put 
together a proposal

Next call? 23rd?
- Yes: Eric, Matt, and Jim offer to be there


Issue tracker: 
https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse

-Matt


Eric Deutsch wrote:
>
> Hi everyone, the next PSI Mass Spectrometry Standards Working Group 
> call will be Tuesday 8am PST:
>
>  
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=09&month=12&year=2008&hour=16&min=0&sec=0&p1=136 
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=09&month=12&year=2008&hour=16&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
>
>  
>
> Agenda:
>
>  
>
> - Any remaining open schema items?
>
> - New MGF terms
>
> - MGF-related terms
>
> - Contact terms required? Basic? MIAPE?
>
> - Must we specify CID/ETD?
>
> - Post from metabolomics person Richard Scheltema
>
> - Issue tracker: 
> https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse 
> <https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
>
>  
>
> - Next call? 23rd?
>
>  
>
>  
>
>

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

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

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PST:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=30
<http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=12&year=2
008&hour=16&min=0&sec=0&p1=136>
&month=12&year=2008&hour=16&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

 

Agenda:

 

- Discuss/approve Fredrik's changes to the mzML schema

- xmlns designation

- pwiz examples

- Issue tracker: https://sourceforge.net/tracker/?atid=1126041
<https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

- TraML

 

- Next call? Jan 6th?

 

 

 

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

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

How long until a customer representative shows up? :)

-Matt


Eric Deutsch wrote:
>
> Hi everyone, the next PSI Mass Spectrometry Standards Working Group 
> call will be Tuesday 8am PST:
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=12&year=2008&hour=16&min=0&sec=0&p1=136 
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=12&year=2008&hour=16&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
>
> Agenda:
>
> - Discuss/approve Fredrik’s changes to the mzML schema
>
> - xmlns designation
>
> - pwiz examples
>
> - Issue tracker: 
> https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse 
> <https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
>
> - TraML
>
> - Next call? Jan 6th?
>
>

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

[Shofstahl, J. <jim...@th...>]

Matt,

I don't know but the music is calming down one of our dogs.

Jim Shofstahl

-----Original Message-----
From: Matthew Chambers [mailto:mat...@va...]
Sent: Tuesday, December 30, 2008 8:07 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder

How long until a customer representative shows up? :)

-Matt


Eric Deutsch wrote:
>
> Hi everyone, the next PSI Mass Spectrometry Standards Working Group
> call will be Tuesday 8am PST:
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=12&year=2008&hour=16&min=0&sec=0&p1=136
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=12&year=2008&hour=16&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
>
> Agenda:
>
> - Discuss/approve Fredrik's changes to the mzML schema
>
> - xmlns designation
>
> - pwiz examples
>
> - Issue tracker:
> https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse
> <https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
>
> - TraML
>
> - Next call? Jan 6th?
>
>

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

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

Hi everyone, I guess we don't have a conference host today, so we'll try
again next week. Let's keep up the discussion via the list.

 

Thanks,

Eric

 

 

  _____  

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: Monday, December 29, 2008 4:26 PM
To: 'Mass spectrometry standard development'
Cc: 'Eric Deutsch'
Subject: PSI-MSS WG Tuesday call reminder

 

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PST:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=30
<http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=12&year=2
008&hour=16&min=0&sec=0&p1=136>
&month=12&year=2008&hour=16&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

 

Agenda:

 

- Discuss/approve Fredrik's changes to the mzML schema

- xmlns designation

- pwiz examples

- Issue tracker: https://sourceforge.net/tracker/?atid=1126041
<https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

- TraML

 

- Next call? Jan 6th?

 

 

 

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

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

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PST:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=06
<http://www.timeanddate.com/worldclock/fixedtime.html?day=06&month=01&year=2
009&hour=16&min=0&sec=0&p1=136>
&month=01&year=2009&hour=16&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

 

Agenda:

 

- Approve http://psidev.info/files/ms/mzML/xsd/mzML1.1.0 xmlns

- Discuss/approve Fredrik's changes to the mzML schema

- xmlns designation

- pwiz examples

- Issue tracker: https://sourceforge.net/tracker/?atid=1126041
<https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

- TraML

- Next call? Jan 20th?

 

 

 

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

[Mike C. <tu...@gm...>]

On Mon, Jan 5, 2009 at 1:38 PM, Eric Deutsch
<ede...@sy...> wrote:
> - TraML

Searching doesn't turn up anything for me.  What is TraML?

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

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

Hi Mike, TraML is a new format for SRM/MRM transitions exchange that we are
proposing to bring through the PSI MS WG and process. You should be hearing
more about it soon and are invited to participate.

Regards,
Eric


> -----Original Message-----
> From: Mike Coleman [mailto:tu...@gm...]
> Sent: Monday, January 05, 2009 12:02 PM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder
> 
> On Mon, Jan 5, 2009 at 1:38 PM, Eric Deutsch
> <ede...@sy...> wrote:
> > - TraML
> 
> Searching doesn't turn up anything for me.  What is TraML?
> 
> --------------------------------------------------------------------------
> ----
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

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

[Lennart M. <len...@eb...>]

Dear PSI-MS Enthusiasts,


As I am no longer on holiday, I will in fact be able to start the call 
this time.

Sorry about leaving you guys in the dark last time. I was blissfully 
immersed in electronic oblivion for a week...


Cheers,

lnnrt.

Eric Deutsch wrote:
> Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
> will be Tuesday 8am PST:
> 
>  
> 
> http://www.timeanddate.com/worldclock/fixedtime.html?day=06
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=06&month=01&year=2
> 009&hour=16&min=0&sec=0&p1=136>
> &month=01&year=2009&hour=16&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
> 
>  
> 
> Agenda:
> 
>  
> 
> - Approve http://psidev.info/files/ms/mzML/xsd/mzML1.1.0 xmlns
> 
> - Discuss/approve Fredrik's changes to the mzML schema
> 
> - xmlns designation
> 
> - pwiz examples
> 
> - Issue tracker: https://sourceforge.net/tracker/?atid=1126041
> <https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
> &group_id=65472&func=browse
> 
> - TraML
> 
> - Next call? Jan 20th?
> 
>  
> 
>  
> 
>  
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

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

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

Present: Matt, Marc, Darren, Fredrik, Eric

 

Agenda:

- What still needs to be addressed before submission?

+ Fredrik

+ Extra validation rules

+ Sample files are part of submission. So units CV must be fixed.

- Update of schema to explicit typing (no functional change?)

+ Seems fine

- Fredrik proposes a change to schema for "neutral loss / SRM scans
revisited" (01-23)

+ Fredrik will send out an example of what he thinks the SRM scans should
look like

+ Fredrik sent out an example of better way of neutral loss. Everyone on the
call agreed

+ Except replace isolation width with a lower and upper bound.

+ Approve change that Fredrik proposes.

+ Fredrik will check in xsd

+ Fredrik will update his example with lower and upper bound

+ Marc will update mapping file

+ Fredrik will email out a revised proposal for SRM scan encoding

- Problem with Thermo native ID format (01-14)

+ Definitely must be fixed. We decided to go with "controllerType=MS
controllerNumber=1 scan=1"

- ASMS abstract

+ Make sure recent contributors are on the author list

+ Discuss who is presenting author next week

- New terms: "sum peak picking" and "max peak picking" under "peak picking"
(2) (01-23)

  (or height and area?)

+ choose maximum and integrated peak picking

+ Marc will add these

- Resolve "MSn spectrum" problem (01-23)

+ Deprecate "product ion spectrum" (already synonym of "MSn spectrum"

+ Add "Nth generation product ion spectrum" as synonym to "MSn spectrum"

+ Keep "MSn spectrum" as is

+ Approve the hierarchy from Matt on 01-21 except replace "product ion
spectrum" with "MSn spectrum"

- Retention time unit problem (01-23)

+ Policy should be for entries that can have a single unit, they should have
a single unit: retention time will only allow "minute", wavelength will only
allow "namometers"

+ In a few case software should support multiple HAS_UNITS lines (so for
mass tolerance term, there would be two HAS_UNITS: "m/z" and "ppm".
Intensities should be "counts" or "eV".

+ Eric will send out an email about this policy for further haggling

- Marc suggests adding some additional units (01-23)

+ Fine, but use a single term wherever feasible. Repost.

- Issue tracker: https://sourceforge.net/tracker/?atid=1126041
<https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

- Next call? Feb 3?

+ Yes Feb 3

 

 

 

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

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

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PST:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=20
<http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=01&year=2
009&hour=16&min=0&sec=0&p1=136>
&month=01&year=2009&hour=16&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

 

Agenda:

 

- Approve/refine http://psi.hupo.org/ms/mzml xmlns and schemaLocation

- pwiz examples

- validator(s)

- Web site and spec doc

- Issue tracker: https://sourceforge.net/tracker/?atid=1126041
<https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

- PSI document process

- mzML at US HUPO

- mzML at ASMS

- Next call? Jan 27th?

 

 

 

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

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

Attendees: Matt, Darren, Jim, Fredrik, Eric, Marc

 

Agenda:

 

- Approve/refine http://psi.hupo.org/ms/mzml xmlns and schemaLocation

 

Fine. Fredrik suggests trying to get a redirect at psi.hupo.org.

Marc points out that overriding the remote URL for xsd is possible.

 

- pwiz examples

 

Pwiz examples are complete except NS. Darren will update.

Fredrik will update/complete the neutral loss scan and precursor ion
spectrum examples and post

 

- validator(s)

 

Marc says that he updated validator today to the latest version of mzML
1.1.0

Marc wants to change the mapping file rule names to ones more readable ones.
He will do so.

Still need some mapping rules for neutral loss scan and precursor ion
spectrum?

The terms are just the same as regular scans. Marc will update mapping file

Marc points out that <scan> is now optional. Is this intentional or a
problem?

If there's no retention time, then scan would not be needed.

Seems like it's not a problem.

Make sure there is a hyperlink to the TOPP validator at the web site.

 

- Web site and spec doc

 

Web site is currently down.

Eric will update the web site or spec doc.

 

- Issue tracker: https://sourceforge.net/tracker/?atid=1126041
<https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

 

"spectrum type" issue still open?

Still need to make sure that we have needed validation rules

Can we specify how the centroiding intensities are derived? Max? AUC? Maybe
this should be in the data processing section instead of spectrum section.
Marc will email a proposal

Marc will refresh the tracker, retiring as necessary, and alert us to other
things.

 

- PSI document process

 

The 1.1 release may need to go through the doc proc. SG will decide.

 

- mzML at US HUPO

 

No poster at US HUPO

Darren has a pwiz poster and willl include mzML info

 

- mzML at ASMS

 

Matt sent around abstract. Review and discuss

 

- Spectrum type hierarchy.

 

This issue is still open. Discuss this further via email.

 

- Next call? Jan 27th?

 

Yes Tue 27th

 

 

 

 

 

 

 

 

  _____  

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: Monday, January 19, 2009 11:51 PM
To: 'Mass spectrometry standard development'
Cc: 'Eric Deutsch'
Subject: PSI-MSS WG Tuesday call reminder

 

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PST:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=20
<http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=01&year=2
009&hour=16&min=0&sec=0&p1=136>
&month=01&year=2009&hour=16&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

 

Agenda:

 

- Approve/refine http://psi.hupo.org/ms/mzml xmlns and schemaLocation

- pwiz examples

- validator(s)

- Web site and spec doc

- Issue tracker: https://sourceforge.net/tracker/?atid=1126041
<https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

- PSI document process

- mzML at US HUPO

- mzML at ASMS

- Next call? Jan 27th?

 

 

 

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

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

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PST:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=27
<http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=2
009&hour=16&min=0&sec=0&p1=136>
&month=01&year=2009&hour=16&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

 

Agenda:

- What still needs to be addressed before submission?

- Update of schema to explicit typing (no functional change?)

- Fredrik proposes a change to schema for "neutral loss / SRM scans
revisited" (01-23)

- Problem with Thermo native ID format (01-14)

- ASMS abstract

- New terms: "sum peak picking" and "max peak picking" under "peak picking"
(2) (01-23)

  (or height and area?)

- Resolve "MSn spectrum" problem (01-23)

- Retention time unit problem (01-23)

- Marc suggests adding some additional units (01-23)

- Issue tracker: https://sourceforge.net/tracker/?atid=1126041
<https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

- Next call? Feb 3?

 

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

[Shofstahl, J. <jim...@th...>]

I was wondering if anybody else is enjoying the music this morning?

Jim Shofstahl

From: Eric Deutsch [mailto:ede...@sy...]
Sent: Monday, January 26, 2009 12:38 PM
To: 'Mass spectrometry standard development'
Cc: 'Eric Deutsch'
Subject: [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PST:

http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=2009&hour=16&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

Agenda:
- What still needs to be addressed before submission?
- Update of schema to explicit typing (no functional change?)
- Fredrik proposes a change to schema for "neutral loss / SRM scans revisited" (01-23)
- Problem with Thermo native ID format (01-14)
- ASMS abstract
- New terms: "sum peak picking" and "max peak picking" under "peak picking" (2) (01-23)
  (or height and area?)
- Resolve "MSn spectrum" problem (01-23)
- Retention time unit problem (01-23)
- Marc suggests adding some additional units (01-23)
- Issue tracker: https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse
- Next call? Feb 3?

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

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

I'm right there with ya.

-Matt


Shofstahl, Jim wrote:
>
> I was wondering if anybody else is enjoying the music this morning?
>
>  
>
> Jim Shofstahl
>
>  
>
> *From:* Eric Deutsch [mailto:ede...@sy...]
> *Sent:* Monday, January 26, 2009 12:38 PM
> *To:* 'Mass spectrometry standard development'
> *Cc:* 'Eric Deutsch'
> *Subject:* [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder
>
>  
>
> Hi everyone, the next PSI Mass Spectrometry Standards Working Group 
> call will be Tuesday 8am PST:
>
>  
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=2009&hour=16&min=0&sec=0&p1=136 
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=2009&hour=16&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
>
>  
>
> Agenda:
>
> - What still needs to be addressed before submission?
>
> - Update of schema to explicit typing (no functional change?)
>
> - Fredrik proposes a change to schema for "neutral loss / SRM scans 
> revisited" (01-23)
>
> - Problem with Thermo native ID format (01-14)
>
> - ASMS abstract
>
> - New terms: "sum peak picking" and "max peak picking" under "peak 
> picking" (2) (01-23)
>
>   (or height and area?)
>
> - Resolve "MSn spectrum" problem (01-23)
>
> - Retention time unit problem (01-23)
>
> - Marc suggests adding some additional units (01-23)
>
> - Issue tracker: 
> https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse 
> <https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
>
> - Next call? Feb 3?
>
>  
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
> http://p.sf.net/sfu/sf-spreadtheword
> ------------------------------------------------------------------------
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>   

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

[Marc S. <stu...@gm...>]

Yes, Fredric and me too...

Shofstahl, Jim wrote:
>
> I was wondering if anybody else is enjoying the music this morning?
>
>  
>
> Jim Shofstahl
>
>  
>
> *From:* Eric Deutsch [mailto:ede...@sy...]
> *Sent:* Monday, January 26, 2009 12:38 PM
> *To:* 'Mass spectrometry standard development'
> *Cc:* 'Eric Deutsch'
> *Subject:* [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder
>
>  
>
> Hi everyone, the next PSI Mass Spectrometry Standards Working Group 
> call will be Tuesday 8am PST:
>
>  
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=2009&hour=16&min=0&sec=0&p1=136 
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=2009&hour=16&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
>
>  
>
> Agenda:
>
> - What still needs to be addressed before submission?
>
> - Update of schema to explicit typing (no functional change?)
>
> - Fredrik proposes a change to schema for "neutral loss / SRM scans 
> revisited" (01-23)
>
> - Problem with Thermo native ID format (01-14)
>
> - ASMS abstract
>
> - New terms: "sum peak picking" and "max peak picking" under "peak 
> picking" (2) (01-23)
>
>   (or height and area?)
>
> - Resolve "MSn spectrum" problem (01-23)
>
> - Retention time unit problem (01-23)
>
> - Marc suggests adding some additional units (01-23)
>
> - Issue tracker: 
> https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse 
> <https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
>
> - Next call? Feb 3?
>
>  
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
> http://p.sf.net/sfu/sf-spreadtheword
> ------------------------------------------------------------------------
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>   

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

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

Who runs the conference service? It would be nice if a customer service 
representative could start the call in a pinch...

-Matt


Marc Sturm wrote:
> Yes, Fredric and me too...
>
> Shofstahl, Jim wrote:
>   
>> I was wondering if anybody else is enjoying the music this morning?
>>
>>  
>>
>> Jim Shofstahl
>>
>>  
>>
>> *From:* Eric Deutsch [mailto:ede...@sy...]
>> *Sent:* Monday, January 26, 2009 12:38 PM
>> *To:* 'Mass spectrometry standard development'
>> *Cc:* 'Eric Deutsch'
>> *Subject:* [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder
>>
>>  
>>
>> Hi everyone, the next PSI Mass Spectrometry Standards Working Group 
>> call will be Tuesday 8am PST:
>>
>>  
>>
>> http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=2009&hour=16&min=0&sec=0&p1=136 
>> <http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=2009&hour=16&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
>>
>>  
>>
>> Agenda:
>>
>> - What still needs to be addressed before submission?
>>
>> - Update of schema to explicit typing (no functional change?)
>>
>> - Fredrik proposes a change to schema for "neutral loss / SRM scans 
>> revisited" (01-23)
>>
>> - Problem with Thermo native ID format (01-14)
>>
>> - ASMS abstract
>>
>> - New terms: "sum peak picking" and "max peak picking" under "peak 
>> picking" (2) (01-23)
>>
>>   (or height and area?)
>>
>> - Resolve "MSn spectrum" problem (01-23)
>>
>> - Retention time unit problem (01-23)
>>
>> - Marc suggests adding some additional units (01-23)
>>
>> - Issue tracker: 
>> https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse 
>> <https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
>>
>> - Next call? Feb 3?
>>
>>  
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by:
>> SourcForge Community
>> SourceForge wants to tell your story.
>> http://p.sf.net/sfu/sf-spreadtheword
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>   
>>     
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
> http://p.sf.net/sfu/sf-spreadtheword
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>   

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

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

Hi everyone, sorry for the snag. I can't get ahold of the EBI folks, who are
the only ones able to start the call. Please all hang up and just monitor
your email. I'll email if I can find someone to start the call.

Thanks!
Eric


> -----Original Message-----
> From: Matthew Chambers [mailto:mat...@va...]
> Sent: Tuesday, January 27, 2009 8:15 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder
> 
> Who runs the conference service? It would be nice if a customer service
> representative could start the call in a pinch...
> 
> -Matt
> 
> 
> Marc Sturm wrote:
> > Yes, Fredric and me too...
> >
> > Shofstahl, Jim wrote:
> >
> >> I was wondering if anybody else is enjoying the music this morning?
> >>
> >>
> >>
> >> Jim Shofstahl
> >>
> >>
> >>
> >> *From:* Eric Deutsch [mailto:ede...@sy...]
> >> *Sent:* Monday, January 26, 2009 12:38 PM
> >> *To:* 'Mass spectrometry standard development'
> >> *Cc:* 'Eric Deutsch'
> >> *Subject:* [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder
> >>
> >>
> >>
> >> Hi everyone, the next PSI Mass Spectrometry Standards Working Group
> >> call will be Tuesday 8am PST:
> >>
> >>
> >>
> >>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=
> 2009&hour=16&min=0&sec=0&p1=136
> >>
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year
> =2009&hour=16&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
> >>
> >>
> >>
> >> Agenda:
> >>
> >> - What still needs to be addressed before submission?
> >>
> >> - Update of schema to explicit typing (no functional change?)
> >>
> >> - Fredrik proposes a change to schema for "neutral loss / SRM scans
> >> revisited" (01-23)
> >>
> >> - Problem with Thermo native ID format (01-14)
> >>
> >> - ASMS abstract
> >>
> >> - New terms: "sum peak picking" and "max peak picking" under "peak
> >> picking" (2) (01-23)
> >>
> >>   (or height and area?)
> >>
> >> - Resolve "MSn spectrum" problem (01-23)
> >>
> >> - Retention time unit problem (01-23)
> >>
> >> - Marc suggests adding some additional units (01-23)
> >>
> >> - Issue tracker:
> >>
> https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse
> >>
> <https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
> >>
> >> - Next call? Feb 3?
> >>
> >>
> >>
> >> -----------------------------------------------------------------------
> -
> >>
> >> -----------------------------------------------------------------------
> -------
> >> This SF.net email is sponsored by:
> >> SourcForge Community
> >> SourceForge wants to tell your story.
> >> http://p.sf.net/sfu/sf-spreadtheword
> >> -----------------------------------------------------------------------
> -
> >>
> >> _______________________________________________
> >> Psidev-ms-dev mailing list
> >> Psi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >>
> >>
> >
> > ------------------------------------------------------------------------
> ------
> > This SF.net email is sponsored by:
> > SourcForge Community
> > SourceForge wants to tell your story.
> > http://p.sf.net/sfu/sf-spreadtheword
> > _______________________________________________
> > Psidev-ms-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >
> >
> 
> --------------------------------------------------------------------------
> ----
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
> http://p.sf.net/sfu/sf-spreadtheword
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

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

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

Hi, is there going to be a call now?

Fredrik

Eric Deutsch wrote:
>
> Hi everyone, the next PSI Mass Spectrometry Standards Working Group 
> call will be Tuesday 8am PST:
>
>  
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=2009&hour=16&min=0&sec=0&p1=136 
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=01&year=2009&hour=16&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
>
>  
>
> Agenda:
>
> - What still needs to be addressed before submission?
>
> - Update of schema to explicit typing (no functional change?)
>
> - Fredrik proposes a change to schema for "neutral loss / SRM scans 
> revisited" (01-23)
>
> - Problem with Thermo native ID format (01-14)
>
> - ASMS abstract
>
> - New terms: "sum peak picking" and "max peak picking" under "peak 
> picking" (2) (01-23)
>
>   (or height and area?)
>
> - Resolve "MSn spectrum" problem (01-23)
>
> - Retention time unit problem (01-23)
>
> - Marc suggests adding some additional units (01-23)
>
> - Issue tracker: 
> https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse 
> <https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
>
> - Next call? Feb 3?
>
>  
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
> http://p.sf.net/sfu/sf-spreadtheword
> ------------------------------------------------------------------------
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>