psidev-ms-dev — Mass spectroscopy standard development

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

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

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



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ Finland: 080011569

+ UK: 08081095644

+ USA: NEW NUMBER: 1-866-832-8490

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) Meetings and workshops

- PSI Spring Workshop March 12-14 (+ProteomeXchange 15-16)

- Note nearby US HUPO March 4-7 and ABRF March 17-20

-



----

2) mzML 1.1.0

- imzML

- mz5 and mzDB

- digital signatures

-



----

3) TraML development

- TraML version 0.9.5 is available at
http://www.psidev.info/index.php?q=node/405

- TraML was resubmitted to PSI document process

- Currently in community review period

- Discuss response to 5th reviewer

- Discuss Alexey’s use case and needed terms



----

4) MIAPE-MS revision

- Special call on Thursday for MIAPE - *



----

5) Improving the controlled vocabulary

- Proposed “command line parameters” CV term and implications

- CV term requests from Sean



----

6) SRM analysis guidelines and format

- Review MIAPE-Quant for SRM

- Review mzQuantML for SRM





Next meeting:

- Tue Oct 11 8am PDT?

Re: [Psidev-ms-dev] TraML format

[Alexey C. <che...@gm...>]

Dear Eric,

Thank you for your response.
 
Our goal to encode a transition list with very high level of details. 
Design of our experiments consists of:
1) SRM-assay construction for high confident peptides (identified in a lot of ms/ms experiments) of selected proteins. From 10 to 20 fragments are selected from theoretical fragmentation map
2) SRM-assay validation in biosample (two samples to be precise). we achieve two goals:(a) confirmation of presence of selected protein in the sample and (b) ranking of the transitions basing on the intensity/symmetry of peaks and other parameters
3) SRM-measurements of several proteins in biosample with multiplexing (dynamic mode) as additional control

So no quantitation is performed at this stage.

Best regards,
Alexey
 
On 26.09.2011, at 21:52, Eric Deutsch wrote:

> Hi Alexey, I'm not certain I've fully understood your request, but here is
> what I can say:
> 
> 1) There is at present no distinction between direct injection and an SRM
> trace. We can add terms to differentiate this if you think it is
> important.
> 
> 2) TraML is designed as a mechanism for sharing transition lists. It is
> not designed for encoding quantitative results. When you encode in
> <ValidationStatus> are the intensities relative to other fragment ions of
> the same peptide ion, measured in some way. Ideally the relative
> intensities should be the same when measured by direct injection or by a
> full LC run. There is no functionality for encoding that a certain
> transitions is suitable in tissue but not plasma, for example. These are
> all potential use cases, but none of this information is encoded in any of
> the formats we're trying to unify, so for the moment this is beyond our
> scope.
> 
> 3) To the same point, TraML is not intended to convey quantitative
> measurements. We recommend mzQuantML for this.
> 
> Can you clarify: are you trying to encode quantitative results from an SRM
> experiment? OR are you interested in encoding a transition list to be
> share with very high level of detail on its pedigree?
> 
> Thanks,
> Eric
> 
> 
>> From: Alexey Chernobrovkin [mailto:che...@gm...]
>> 
>> Dear All,
>> 
>> I'm trying to fit new TraML format to our set of SRM/MRM data and I
>> have several questions:
>> 1. My transitions were "optimized on specified instrument", but we
>> didn't use direct injection of the peptide. I can't find any MS
>> ontology term which describes using MRM-measurements on biosample for
>> transitions optimization.
>> 2. I want to provide quantitative data with my transition, including:
>> 	- peak area (integrated)
>> 	- peak height (maximal intensity)
>> 	- peak width
>> 	- signal to noise value for the peak
>> Should I provide these data in <ValidationStatus> tag using <cvParam>
>> elements? In this case i have some problems with ms ontology:
>> 	- there is no term "signal to noise" in MS ontology.
>> 3. How (and where) can I specify and annotate the biosample in which
>> measurements were carried out?
>> 
>> Alexey Chernobrovkin
>> -----------------------------------------------------------------------
>> -------
>> All of the data generated in your IT infrastructure is seriously
>> valuable.
>> Why? It contains a definitive record of application performance,
>> security
>> threats, fraudulent activity, and more. Splunk takes this data and
>> makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2dcopy2
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> 
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] TraML format

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

Hi Alexey, I'm not certain I've fully understood your request, but here is
what I can say:

1) There is at present no distinction between direct injection and an SRM
trace. We can add terms to differentiate this if you think it is
important.

2) TraML is designed as a mechanism for sharing transition lists. It is
not designed for encoding quantitative results. When you encode in
<ValidationStatus> are the intensities relative to other fragment ions of
the same peptide ion, measured in some way. Ideally the relative
intensities should be the same when measured by direct injection or by a
full LC run. There is no functionality for encoding that a certain
transitions is suitable in tissue but not plasma, for example. These are
all potential use cases, but none of this information is encoded in any of
the formats we're trying to unify, so for the moment this is beyond our
scope.

3) To the same point, TraML is not intended to convey quantitative
measurements. We recommend mzQuantML for this.

Can you clarify: are you trying to encode quantitative results from an SRM
experiment? OR are you interested in encoding a transition list to be
share with very high level of detail on its pedigree?

Thanks,
Eric


> From: Alexey Chernobrovkin [mailto:che...@gm...]
>
> Dear All,
>
> I'm trying to fit new TraML format to our set of SRM/MRM data and I
> have several questions:
> 1. My transitions were "optimized on specified instrument", but we
> didn't use direct injection of the peptide. I can't find any MS
> ontology term which describes using MRM-measurements on biosample for
> transitions optimization.
> 2. I want to provide quantitative data with my transition, including:
> 	- peak area (integrated)
> 	- peak height (maximal intensity)
> 	- peak width
> 	- signal to noise value for the peak
> Should I provide these data in <ValidationStatus> tag using <cvParam>
> elements? In this case i have some problems with ms ontology:
> 	- there is no term "signal to noise" in MS ontology.
> 3. How (and where) can I specify and annotate the biosample in which
> measurements were carried out?
>
> Alexey Chernobrovkin
> -----------------------------------------------------------------------
> -------
> All of the data generated in your IT infrastructure is seriously
> valuable.
> Why? It contains a definitive record of application performance,
> security
> threats, fraudulent activity, and more. Splunk takes this data and
> makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2dcopy2
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] MIAPE call this week

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

Hi all,

Quick reminder - we have a call this week on Thurs at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?iso=20110929T16&p1=136 to discuss MIAPE modules Quant, MSI etc

Agenda:


-          MIAPE Quant

-          MIAPE MSI

-          CV / validation issues - what is needed for ProteomExchange?

-          AOB - let me know

I realise this is quite a lot to get through, so can everyone look at documents before the call so you're up to speed. Salvador sent round the latest MIAPE Quant draft recently. I think the most recent MIAPE MSI is here: http://www.psidev.info/miape/MIAPE_MSI_1.1.pdf, prior to the removal of the quant parts. A small working group is going to look at this, but if you want to give any opinions, we can have a quick discussion about it in the call.

I'm not sure if there is anything about MIAPE MS to discuss in this forum, let me know if so,
Best wishes
Andy

[Psidev-ms-dev] TraML format

[Alexey C. <che...@gm...>]

Dear All,

I'm trying to fit new TraML format to our set of SRM/MRM data and I have several questions:
1. My transitions were "optimized on specified instrument", but we didn't use direct injection of the peptide. I can't find any MS ontology term which describes using MRM-measurements on biosample for transitions optimization.
2. I want to provide quantitative data with my transition, including:
	- peak area (integrated)
	- peak height (maximal intensity)
	- peak width
	- signal to noise value for the peak
Should I provide these data in <ValidationStatus> tag using <cvParam> elements? In this case i have some problems with ms ontology:
	- there is no term "signal to noise" in MS ontology.
3. How (and where) can I specify and annotate the biosample in which measurements were carried out?

Alexey Chernobrovkin

Re: [Psidev-ms-dev] [Psidev-pi-dev] CV additions and corrections

[Seymour, S. L <Sea...@ab...>]

Hi Matt,

Wow, I clicked on both of them and thought I saw both pointing to
mzOntology, but that's not what I see this time. I see "Proteomics
Standards Initiative Mass Spectrometry Vocabularies". Thanks for setting
me straight! So all the more reason to remove this option from OLS per
my point (3) below? I realize this may still be needed for mzData, and
I'm unclear how upkeep of ontology works with old formats like mzData
and mzXML. Maintenance and conversion to other formats must be really
messy. Seems like all the more reason to get everyone onto mzML. Can
something be done in better naming to at least avoid the confusion I
made picking the wrong ontology?

Ok, looking at the right ontology this time I hope, issues I see: 

(A) Need to add: "Triple Quad 5500"

(B) Term MS:1000652 should be renamed "4800 MALDI TOF/TOF" (slash, not
dash, and trailing noun is not included on any other instrument so I
don't see why here)

(C) The vendor name is not included in any other instrument, so I think
you can remove "AB SCIEX" from the three instruments that have it in
their name term.  

(D) Need to remove one of "4000 Q TRAP" or "4000 QTRAP". It's the same
instrument. It used to be written with a space; now it's without. Same
semantic concept. I'd suggest that we should keep the older term
MS:1000139 but probably rename it without a space. Term MS:1000870 is
redundant and should be removed with a pointer to the correct 139 term,
however those deprecation mechanics work.

(E) MS:1000672 - The question mark should be removed from the term name.

Thanks!

Sean


-----Original Message-----
From: Matthew Chambers [mailto:mat...@gm...] 
Sent: Friday, September 23, 2011 3:22 PM
To: psi...@li...; Mass spectrometry standard
development
Subject: Re: [Psidev-pi-dev] CV additions and corrections

Sorry, you looked at the old mzData CV. The new one is [MS], not [PSI].
I checked and the current CV has AB SCIEX. Vendors aren't separate terms
now, they're just part of the instrument model hierarchy.

-Matt


On 9/23/2011 4:46 PM, Seymour, Sean L wrote:
> Hi all,
>
> I believe new CV requests are supposed to go to these two mail lists 
> now? My apologies for the spam if not.
>
> In examining several areas of CV using OLS to browse, I see several 
> gaps and correction related to AB SCIEX tools. I'm not sure if this is

> just a disconnect between what information is shown on OLS browsing
the PSI Ontology vs. a master list somewhere else. Issues I see:
>
> (1)Missing from Instrument Additional Description -> Model ->
>
> a."TripleTOF 5600"
> b."QTRAP 5500"
> c."3200 Q TRAP"
> d."4800 MALDI TOF/TOF"
> e."TOF/TOF 5800"
> f."QSTAR Elite"
> g."QSTAR Pulsar"
> h."QSTAR XL"
> i."Triple Quad 5500"
> j."API 5000"
>
> (2)I'm a little unclear how we're dealing with vendor name changes. I 
> see Thermo is listed as "ThermoFinnigan", Waters is not Micromass, and

> us currently listed as "ABI/ SCIEX" which has never really been the 
> name of the company. I can understand how it might be a bit messy to 
> try to track all the name changes all the vendors have gone through, 
> but it seems there should be some convention on what we do here. I
would suggest that using the current name makes the most sense, but to
track back to the same identifier so long as the progression of company
changes is linear (non-branching).
> If this is the case, we should be called "AB SCIEX" now. "ABI" is 
> actually a different company now that doesn't make mass specs.
>
> (3)I'm not sure if this is the right place to point this out, but if 
> you look at the list in the "Search Ontology:" field on OLS, you see 
> both "Mass Spectroscopy CV (PSI-MS) [PSI]" and "PSI Mass Spectrometry 
> Ontology [MS]", both of which point to mzOntology. As I'm sure 
> virtually everyone on these lists knows, 'mass spectroscopy' is
minimally a discouraged term and comes off like nails down a chalkboard
to some. I suggest that option should be removed from the list.
>
> Please let me know if I need to provide any additional information to 
> get these new instruments added to the CV.
>
> Thanks and a good weekend to all!
>
> Sean

------------------------------------------------------------------------
------
All of the data generated in your IT infrastructure is seriously
valuable.
Why? It contains a definitive record of application performance,
security threats, fraudulent activity, and more. Splunk takes this data
and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev


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Re: [Psidev-ms-dev] [Psidev-pi-dev] CV additions and corrections

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

Sorry, you looked at the old mzData CV. The new one is [MS], not [PSI]. I checked and the current CV 
has AB SCIEX. Vendors aren't separate terms now, they're just part of the instrument model hierarchy.

-Matt


On 9/23/2011 4:46 PM, Seymour, Sean L wrote:
> Hi all,
>
> I believe new CV requests are supposed to go to these two mail lists now? My apologies for the spam
> if not.
>
> In examining several areas of CV using OLS to browse, I see several gaps and correction related to
> AB SCIEX tools. I’m not sure if this is just a disconnect between what information is shown on OLS
> browsing the PSI Ontology vs. a master list somewhere else. Issues I see:
>
> (1)Missing from Instrument Additional Description -> Model ->
>
> a.“TripleTOF 5600”
> b.“QTRAP 5500”
> c.“3200 Q TRAP”
> d.“4800 MALDI TOF/TOF”
> e.“TOF/TOF 5800”
> f.“QSTAR Elite”
> g.“QSTAR Pulsar”
> h.“QSTAR XL”
> i.“Triple Quad 5500”
> j.“API 5000”
>
> (2)I’m a little unclear how we’re dealing with vendor name changes. I see Thermo is listed as
> “ThermoFinnigan”, Waters is not Micromass, and us currently listed as “ABI/ SCIEX” which has never
> really been the name of the company. I can understand how it might be a bit messy to try to track
> all the name changes all the vendors have gone through, but it seems there should be some convention
> on what we do here. I would suggest that using the current name makes the most sense, but to track
> back to the same identifier so long as the progression of company changes is linear (non-branching).
> If this is the case, we should be called “AB SCIEX” now. “ABI” is actually a different company now
> that doesn’t make mass specs.
>
> (3)I’m not sure if this is the right place to point this out, but if you look at the list in the
> “Search Ontology:” field on OLS, you see both “Mass Spectroscopy CV (PSI-MS) [PSI]” and “PSI Mass
> Spectrometry Ontology [MS]”, both of which point to mzOntology. As I’m sure virtually everyone on
> these lists knows, ‘mass spectroscopy’ is minimally a discouraged term and comes off like nails down
> a chalkboard to some. I suggest that option should be removed from the list.
>
> Please let me know if I need to provide any additional information to get these new instruments
> added to the CV.
>
> Thanks and a good weekend to all!
>
> Sean

[Psidev-ms-dev] Pending changes in PSI-MS controlled vocabulary (CV terms for mzIdentML)

[David O. <do...@eb...>]

Dear community,

I'm going to try to summarize the pending changes in the controlled 
vocabulary, related to mzIdentML. The final list was sent by Martin 
(Sept 9th) and some suggestions and changes proposals where made:
- Martin sent a list with several terms to be added to the cv: 6 term 
about protein/peptide p/q/e-values, 1 term about FDRScore, 4 terms about 
modification specificity peptide/protein Ct/Nt, 1 term about 
modification motif and 1 term about modification probability
- in Martin proposal we found the obsolescence of the previous terms 
about modification specificity Nt/Ct, and in addition, the obsolescence 
of the term about p-value (now split into peptide and protein terms)
- in Martin proposal, changes in 8 terms where also proposed, mainly 
related, but not limited, to adding some children under  p/q/e-values
- Matt and David (me), showed some concern about obsoleting the previous 
modification specificity terms. No further discussion was maintained 
about this.
- Pierre-Alain proposed some changes in the definitions. First, 
"Peptide/Protein identification confidence metric q,p,e value and 
FDRScore" instead of "Quality measurement" or "Quality estimation" 
(having then something like "q-value for peptides"-> def: 
"Identification confidence metric q-value for peptides." instead of 
"Quality measurement q-value for peptides.", if I've understood 
correctly). This change would also mean changing the definition of the 
parents (e.g. in MS:1001092 we would have "peptide identification 
confidence metric"  instead of "peptide quality estimation measure"). 
Secondly, Pierre-Alain proposed replacing "modification" by "amino acid 
residue modification" (I've changed "amino-acid" by "amino acid" for 
consistency shake in the whole controlled vocabulary). In third place, 
Pierre-Alain also proposed changing "unknown modifications" to "unknown 
amino acid residue modification" in MS:1001460.

Here, what I'm going to do about this, if you agree:
- It seems to me that enough consensus have been reached about the 6 
terms in Martin's proposal about protein/peptide p/q/e-values, 1 term 
about FDRScore, the 1 term about modification motif and the 1 term about 
modification probability. If there's no more comments about this, in a 
couple of days, I'll add these terms to the c.v.
- It also seems that the 8 changes in Martin's proposal are agreed: If 
there's no more comments about this in a couple of days, I'll add these 
terms to the c.v.
- All the changes proposed by Pierre-Alain seem reasonable to me and 
nobody objected: I'll change things in proper places in the coming new 
version (please, check the example of change that I've written before). 
If anybody has something to say about this, please, be quick! (I'm 
planing doing this in a couple of working days).
- About the proposed changes related to modifications specificity, I'll 
wait until we have more comments and consensus. We are talking here 
about 2 obsolescences and 4 new terms.

Best,
david




-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD

[Psidev-ms-dev] mzML parser

[Thaman C. <th...@ut...>]

Is there any mzML python parser available? Couldn't find any.

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

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

Hi Oliver, thank you for your offer and involvement. In the nearest term,
we hope to define a few terms to help properly annotate information about
GC-GC coupling and maybe you can lend some insight there by reviewing the
proposed terms and definitions. Also any experience that can be applied to
converting GCMS data into mzML would be welcome.

Thank you!
Eric


> -----Original Message-----
> From: Oliver Kohlbacher [mailto:oli...@un...]
> Sent: Wednesday, September 14, 2011 3:40 AM
> To: Mass spectrometry standard development
> Cc: Eric Deutsch
> Subject: Re: [Psidev-ms-dev] PSI MSS WG call notes
>
>
> On 13.09.2011, at 17:47, Eric Deutsch wrote:
> > 2) mzML 1.1.0
> > - mzML for metabolomics
> > + Oliver Kolbacher also may be good to get involved in this.
> Can do. Just couldn't make the phone conference (and will be traveling
> a lot over the next two months, so I am not sure how often I will be
> able
> to make it). So it's best if you let me know what sort of input you
> need
> from me and I'll see to it.
>
> Cheers,
>  Oliver
>

[Psidev-ms-dev] TraML format

[Alexey C. <che...@gm...>]

Dear All,

I'm trying to fit new TraML format to our set of SRM/MRM data and I have several questions:
1. My transitions were "optimized on specified instrument", but we didn't use direct injection of the peptide. I can't find any MS ontology term which describes using MRM-measurements on biosample for transitions optimization.
2. I want to provide quantitative data with my transition, including:
	- peak area (integrated)
	- peak height (maximal intensity)
	- peak width
	- signal to noise value for the peak
Should I provide these data in <ValidationStatus> tag using <cvParam> elements? In this case i have some problems with ms ontology:
	- term peak area (MS:1001844) related to the MS1 data only. can I use it for indication of peak area on the chromatogram?
	- there is no term "signal to noise" in MS ontology.
3. How (and where) can I specify and annotate the biosample in which measurements were carried out?

Alexey Chernobrovkin

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

[Oliver K. <oli...@un...>]

On 13.09.2011, at 17:47, Eric Deutsch wrote:
> 2) mzML 1.1.0
> - mzML for metabolomics
> + Oliver Kolbacher also may be good to get involved in this.
Can do. Just couldn't make the phone conference (and will be traveling
a lot over the next two months, so I am not sure how often I will be able
to make it). So it's best if you let me know what sort of input you need
from me and I'll see to it.

Cheers,
 Oliver

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

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

Notes from today’s teleconference.



Present: Steffen, Florian, Eric,



Agenda:

1) Meetings and workshops

- Review of PSI sessions at World HUPO in Geneva

- PSI Spring Workshop San Diego March 12-14, 2012 (+ProteomeXchange 15-16)

+ Start advertizing with vendors

- Note nearby US HUPO San Francisco March 4-7, 2012 and ABRF Orlando March
17-20, 2012

-



----

2) mzML 1.1.0

- mzML for metabolomics

+ Oliver Kolbacher also may be good to get involved in this.

+ We need some CV terms for GC-GC coupling:

  + “modulation time” ?

  + There was a discussion a few months ago. Try to revive this.

+ Bioconductor has now officially accepted mzR package, an mzML reader. This
is a wrapper around pwiz

+ Available now, and will be officially distributed with next release of
Bioconductor

+ The next release of xcms will have an improved mzML reader

- imzML

- mz5 and mzDB

- digital signatures

-



----

3) TraML development

- TraML version 0.9.5 is available at
http://www.psidev.info/index.php?q=node/405

- TraML was resubmitted to PSI document process

- Currently in community review period

+ Clarify with Christian when this is officially over

- Discuss response to 5th reviewer

+ Table this for now until we can get some additional participation

+ Steffen has an R package for writing inclusion lists

+ Steffen will find a hyperlink to it and we will post on the TraML dev page



----

4) MIAPE-MS revision

-



----

5) Improving the controlled vocabulary

- Proposed “command line parameters” CV term and implications

+ This sounds quite sensible to us. Follow up with an email to list

+ Would this include the executable/path or just everything after that.
Probably after.



----

6) SRM analysis guidelines and format

- Review MIAPE-Quant for SRM

- Review mzQuantML for SRM

+ We need to create a sample mzQuantML document for an SRM experiment. Who
will try?



Next meeting:

- Tue Sep 27 8am PDT?

+ Yes

+ Try to get greater participation at next call.

+ Put in hyperlink to dial-in numbers from other countries. Steffen will be
in Finland.

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

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

Hi everyone, let’s have a PSI MSS WG teleconference call tomorrow, Tuesday,
at the usual time.



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: NEW NUMBER: 1-866-832-8490

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) Meetings and workshops

- Review of PSI sessions at World HUPO in Geneva

- PSI Spring Workshop March 12-14 (+ProteomeXchange 15-16)

- Note nearby US HUPO March 4-7 and ABRF March 17-20

-



----

2) mzML 1.1.0

- imzML

- mz5 and mzDB

- digital signatures

-



----

3) TraML development

- TraML version 0.9.5 is available at
http://www.psidev.info/index.php?q=node/405

- TraML was resubmitted to PSI document process

- Currently in community review period

- Discuss response to 5th reviewer



----

4) MIAPE-MS revision

-



----

5) Improving the controlled vocabulary

- Proposed “command line parameters” CV term and implications



----

6) SRM analysis guidelines and format

- Review MIAPE-Quant for SRM

- Review mzQuantML for SRM





Next meeting:

- Tue Sep 27 8am PDT?

Re: [Psidev-ms-dev] Does mzML, WIFF, MGF, DTA, and pepXML contains "mono-isotopic mass weight Information"?

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

Dear Thaman Chand!

 

Thanks for your interest and your contribution!

 

I believe, if you dig deeper into the field you will find that information in the descriptions of 

the formats or example files.

With current spectrometers masses are usually monoisotopic, with old masses the 

parent/precursor mass was sometimes reported as "average isotopic".

 

Only short (and as far as I know, maybe corrected or supplemented by others): 

- in MGF there is an optional MASS tag stating the type, PEPMASS is the precursor mass

- DTA files themselves contain the precursor mas sin the first line, but do NOT contain 

  the mass type; that is e.g. in seuqest.params in the same folder (mass_type_parent tag)

- raw and wiff are instrument files, usually containing the profile

- mzML can be profile OR peak list, in peak list the mass type is probably given as CV term,

  but that should be answered by mzML experts

 

  Best regards!

   Martin

 

 

 

Von: Thaman Chand [mailto:th...@ut...] 
Gesendet: Samstag, 3. September 2011 22:18
An: psi...@li...
Betreff: [Psidev-ms-dev] Does mzML, WIFF, MGF, DTA, and pepXML contains "mono-isotopic mass weight Information"?

 

Hi Experts,

 

I am somehow lost in the beginning phase of my first project in the 
Proteomics department. My main task: "Designing DATABASE" of 
various "FILE" formats existed in the Proteomics research (RAW, wiff, MGF, 
pepXML, dta). Till now main file 
formats are RAW, WIFF, MGF & DTA which are not in XML and XML based: pepXM. 
Obviously there is overlap in information in multiple different data 
file formats/experimental. Though analysis can be made from single file (experimental measurements) or by comparison between “sets of files”. But, what is missing? Understanding the re-occurring pattern in and between experiments.

Of course “Database” is needed in querying experiments/(files) with varied parameters. That’s why file based searching is not efficient to our answer our question. What kind of "search term" in an experiments? "Mono-isotopic mass". 

"Have we seen this mono isotopic mass before in other experiments is 
the main issue in our research"? I have started to work with RAW-> 
mzML (convert). I went through the documentation of mzML available in the HUPO 
trying to design relational schema from mzML schema manually. Though mzML is quite well documented I have confess not being clear. 

Questions

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

 

1) Where information like*"mono isotopic mass"* are 
recorded in the mzML file? Is it precursor charge attribute in the 
spectrum Element? Or am I missing something? 

2) Can I be sure that all RAW and mzML after conversion regardless of 
different vendors consists of "mono-isotpic mass" info? 

3) Further, I am wondering does all mentioned files (wiff, pepXML,dta,mgf) 
too contains "mono-isotopic mass" information? 

Please guide me! 

Regards, 


RawProt 

[Psidev-ms-dev] Does mzML, WIFF, MGF, DTA, and pepXML contains "mono-isotopic mass weight Information"?

[Thaman C. <th...@ut...>]

Hi Experts,

 

I am somehow lost in the beginning phase of my first project in the 
Proteomics department. My main task: "Designing DATABASE" of 
various "FILE" formats existed in the Proteomics research (RAW, wiff, MGF, 
pepXML, dta). Till now main file 
formats are RAW, WIFF, MGF & DTA which are not in XML and XML based: pepXM. 
Obviously there is overlap in information in multiple different data 
file formats/experimental. Though analysis can be made from single file (experimental measurements) or by comparison between “sets of files”. But, what is missing? Understanding the re-occurring pattern in and between experiments.

Of course “Database” is needed in querying experiments/(files) with varied parameters. That’s why file based searching is not efficient to our answer our question. What kind of "search term" in an experiments? "Mono-isotopic mass". 

"Have we seen this mono isotopic mass before in other experiments is 
the main issue in our research"? I have started to work with RAW-> 
mzML (convert). I went through the documentation of mzML available in the HUPO 
trying to design relational schema from mzML schema manually. Though mzML is quite well documented I have confess not being clear. 

Questions

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

1) Where information like*"mono isotopic mass"* are 
recorded in the mzML file? Is it precursor charge attribute in the 
spectrum Element? Or am I missing something? 
2) Can I be sure that all RAW and mzML after conversion regardless of 
different vendors consists of "mono-isotpic mass" info? 

3) Further, I am wondering does all mentioned files (wiff, pepXML,dta,mgf) 
too contains "mono-isotopic mass" information? 

Please guide me! 

Regards, 


RawProt 

[Psidev-ms-dev] TraML 0.9.5 has been resubmitted to doc proc: community review period is open

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

Hi everyone, thank you to those who helped get us to TraML 0.9.5. In case
you have not seen the message on the announce list, TraML 0.9.5 is now
back in the document process in the public comment period. Please forward
this message to anyone who may be interested in commenting or even just
knowing about this.

Thanks,
Eric


-----Original Message-----
From: Christian Stephan [mailto:chr...@ru...]
Sent: Monday, August 29, 2011 1:23 AM
To: psi...@li...
Subject: [Psidev-announce] TraML: Transitions Markup Language is now
available for Public Comment (resubmission)

Dear all,
TraML: Transitions Markup Language is now available for Public Comment on
the PSI Web site (http://www.psidev.info/index.php?q=node/405)
The public comment period enables the wider community to provide feedback
on
a proposed standard before it is formally accepted, and thus is an
important
step in the standardisation process.

This is a resubmission after major changes. To follow this please look at
the point

- Response to the reviewer comments from initial PSI document process
submission

This message is to encourage you to contribute to the standards
development
activity by commenting on the material that is available online. We invite
both positive and negative comments. If negative comments are being made,
these could be on the relevance, clarity, correctness, appropriateness,
etc,
of the proposal as a whole or of specific parts of the proposal.

If you do not feel well placed to comment on this document, but know
someone
who may be, please consider forwarding this request. There is no
requirement
that people commenting should have had any prior contact with the PSI.

If you have comments that you would like to make but would prefer not to
make public, please email these to me directly.

Best regards,


Christian


--
Dr. Christian Stephan
Head of Bioinformatics
Medizinisches Proteom-Center
Zentrum Klinische Forschung (ZKF E.141) Ruhr-Universität-Bochum 44870
Bochum
Phone: +49 234 32 29 288
Fax:   +49 234 32 14 554
http://www.medizinisches-proteom-center.de



--------------------------------------------------------------------------
----
EMC VNX: the world's simplest storage, starting under $10K
The only unified storage solution that offers unified management
Up to 160% more powerful than alternatives and 25% more efficient.
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_______________________________________________
Psidev-announce mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-announce

[Psidev-ms-dev] call today

[Florian R. <fl...@eb...>]

Hi all,

can everyone please use THIS new access code for todays conference?

code: 241416

Thanks,
Florian

Re: [Psidev-ms-dev] New PSI-MS release 3.9.1: mzQuant changes and some little things

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

Many thanks for tidying this all up, David!

> -----Original Message-----
> From: David Ovelleiro [mailto:do...@eb...]
> Sent: Wednesday, August 24, 2011 5:13 AM
> To: 'psi...@li...'; Mass spectrometry standard
> development
> Subject: [Psidev-ms-dev] New PSI-MS release 3.9.1: mzQuant changes and
> some little things
>
> Dear Community,
>
> I've released a new psi-ms version (3.9.1).
> The changes implemented are:
>
>   mzQuantML
> ============
> - the proposed terms have been added
> - the IDs of all of them have been changed: an unexpected version of
> the
> psi-ms had been released using the first 7 IDs of the proposed "quant"
> terms; I've adjusted the IDs (main ID and is_a / part_of terms)
> - in the original mzQuantML proposal there was a gap (MS:1001825 and
> MS:1001826 not used) and a duplication (term MS:1001836 used twice);
> that's why if you compare the published IDs to the proposed, you'll
> find
> at the first terms a displacement of 7, then 5 and at the end of 6
> - adjusting these numbers has been quite complicated... please, take a
> look and verify that everything is correct;
> - a minor change: following the guidelines, the name of the term
> MS:1001861 is changed from "quant. data processing" to "quantification
> data processing"; hope this is what you wanted
>
> TODOs
> ============
> - I've removed all TODOs in the controlled vocabulary; some of them
> have
> been there for years, some are obsolete or are in purgatory; the TODO
> annotation is not contemplated in the Guidelines
> - A complete list of these terms is found there ->
> https://sourceforge.net/tracker/?func=detail&aid=3396860&group_id=65472
> &atid=848524
> , and at the end of this email
> - If anybody is interested on dealing with these TODOs, please, say
> something
>
> One term that should be corrected, I'm not sure in which way
> ===================================================
> This term:
> id: MS:1001065
> name: TODOscoring model
> def: "DELETE. There is Phenyx:ScoringModel for Phenyx! Scoring model
> (more detailed granularity). TODO: add some child terms!" [PSI:PI]
> is_a: MS:1001249 ! search input details
>
> Has a TODO and a DELETE. We should do something. If nobody says
> anything
> against it, I'll obsolete it in a new release.
>
> Best regards,
> David
>
> --
> David Ovelleiro
> Bioinformatician
> PRIDE Group
> Proteomics Services Team, PANDA Group
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
> CB10 1SD
>
>
>
>
>
> Pending TODOs in the c.v.:
> - MS:1000444 -> improve definition (purgatory)
> - MS:1000445 -> improve definition (purgatory)
> - MS:1001065 -> obsolete term???
> - MS:1001101 -> TODO: add child terms.
> - MS:1001130 -> clarify definition
> - MS:1001136 -> clarify definition
> - MS:1001145 -> unknown TODO
> - MS:1001326 -> "TODO_add_others" (purgatory)
> - MS:1001355 -> TODO: What does this mean?
> - MS:1001356 -> TODO: really needed?
> - MS:1001822 -> clarify definition
> - MS:1001842 -> clarify: correct place in obo?
> - MS:1001844 -> How to code normalization method, only as
> dataprocessing
> or here?
> - MS:1001846 -> How to code normalization method, only as
> dataprocessing
> or here?
> - MS:1001849 -> clarify how to specify the two groups!
>
> -----------------------------------------------------------------------
> -------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] New PSI-MS release 3.9.1: mzQuant changes and some little things

[David O. <do...@eb...>]

Dear Community,

I've released a new psi-ms version (3.9.1).
The changes implemented are:

  mzQuantML
============
- the proposed terms have been added
- the IDs of all of them have been changed: an unexpected version of the 
psi-ms had been released using the first 7 IDs of the proposed "quant" 
terms; I've adjusted the IDs (main ID and is_a / part_of terms)
- in the original mzQuantML proposal there was a gap (MS:1001825 and 
MS:1001826 not used) and a duplication (term MS:1001836 used twice); 
that's why if you compare the published IDs to the proposed, you'll find 
at the first terms a displacement of 7, then 5 and at the end of 6
- adjusting these numbers has been quite complicated... please, take a 
look and verify that everything is correct;
- a minor change: following the guidelines, the name of the term 
MS:1001861 is changed from "quant. data processing" to "quantification 
data processing"; hope this is what you wanted

TODOs
============
- I've removed all TODOs in the controlled vocabulary; some of them have 
been there for years, some are obsolete or are in purgatory; the TODO 
annotation is not contemplated in the Guidelines
- A complete list of these terms is found there -> 
https://sourceforge.net/tracker/?func=detail&aid=3396860&group_id=65472&atid=848524 
, and at the end of this email
- If anybody is interested on dealing with these TODOs, please, say 
something

One term that should be corrected, I'm not sure in which way
===================================================
This term:
id: MS:1001065
name: TODOscoring model
def: "DELETE. There is Phenyx:ScoringModel for Phenyx! Scoring model 
(more detailed granularity). TODO: add some child terms!" [PSI:PI]
is_a: MS:1001249 ! search input details

Has a TODO and a DELETE. We should do something. If nobody says anything 
against it, I'll obsolete it in a new release.

Best regards,
David

-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD





Pending TODOs in the c.v.:
- MS:1000444 -> improve definition (purgatory)
- MS:1000445 -> improve definition (purgatory)
- MS:1001065 -> obsolete term???
- MS:1001101 -> TODO: add child terms.
- MS:1001130 -> clarify definition
- MS:1001136 -> clarify definition
- MS:1001145 -> unknown TODO
- MS:1001326 -> "TODO_add_others" (purgatory)
- MS:1001355 -> TODO: What does this mean?
- MS:1001356 -> TODO: really needed?
- MS:1001822 -> clarify definition
- MS:1001842 -> clarify: correct place in obo?
- MS:1001844 -> How to code normalization method, only as dataprocessing 
or here?
- MS:1001846 -> How to code normalization method, only as dataprocessing 
or here?
- MS:1001849 -> clarify how to specify the two groups!

Re: [Psidev-ms-dev] List of new c.v. terms and some changes proposed by the team working in mzQuantML

[<do...@eb...>]

You are right Eric.
The reason why the term has been made obsolete is in fact inserted as a
comment, though.
The initial proposal definition
"Quantitation software version. TODO: OBSOLETE, because part of mzQuantML
schema!" [PSI:PI]

will be changed to:
----------
def: "OBSOLETE Quantitation software version" [PSI:PI]
comment: This term was made obsolete because part of mzQuantML schema.
----------

Thanks,
David

Re: [Psidev-ms-dev] List of new c.v. terms and some changes proposed by the team working in mzQuantML

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

I believe the SOP states that for an obsoleted term, both the
"is_obsolete: true" should be set and the definition should begin with the
word OBSOLETE (in case some software does not handle "is_obsolete: true"
appropriately, and the definition should also include a sentence on why
the term was obsoleted.

Thanks,
Eric


> -----Original Message-----
> From: David Ovelleiro [mailto:do...@eb...]
> Sent: Thursday, August 18, 2011 6:07 AM
> To: 'psi...@li...'; Mass spectrometry standard
> development
> Subject: Re: [Psidev-ms-dev] List of new c.v. terms and some changes
> proposed by the team working in mzQuantML
>
> Dear all,
>
> After reviewing the new 76 term additions modification, I'm absolutely
> OK with the changes.
> Only a couple of things:
> - the 8 "TODOs" comments inside the new proposal should be removed;
> maybe the TODOs should be done before submitting the new terms, but I
> understand the need of integrating these terms ASAP: the complete
> description of the terms could be added in a next release
> - in addition, the term MS:1001140 should actually be made obsolete
> after removing the OBSOLETE tag in the definition (adding the line
> "is_obsolete: true")
>
> A part from this (quite trivial), everything fine to me. I'm going to
> wait a couple of working days and if nobody has anything to say, I'll
> submit the changes.
>
> Best regards,
> David
>
>
> --
> David Ovelleiro
> Bioinformatician
> PRIDE Group
> Proteomics Services Team, PANDA Group
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
> CB10 1SD
>
>
>
>
>
> -----------------------------------------------------------------------
> -------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] List of new c.v. terms and some changes proposed by the team working in mzQuantML

[David O. <do...@eb...>]

Dear all,

After reviewing the new 76 term additions modification, I'm absolutely 
OK with the changes.
Only a couple of things:
- the 8 "TODOs" comments inside the new proposal should be removed; 
maybe the TODOs should be done before submitting the new terms, but I 
understand the need of integrating these terms ASAP: the complete 
description of the terms could be added in a next release
- in addition, the term MS:1001140 should actually be made obsolete 
after removing the OBSOLETE tag in the definition (adding the line 
"is_obsolete: true")

A part from this (quite trivial), everything fine to me. I'm going to 
wait a couple of working days and if nobody has anything to say, I'll 
submit the changes.

Best regards,
David


-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD

Re: [Psidev-ms-dev] [Psidev-pi-dev] List of new c.v. terms and some changes proposed by the team working in mzQuantML

[David O. <do...@eb...>]

Sorry,

The link to the complete obo (with mzQuantML added) is really in:
http://mzquantml.googlecode.com/svn/trunk/cv/psi-ms_3_7_3_with_quant.obo
All the documents under:
http://code.google.com/p/mzquantml/source/browse/trunk/cv/

David

[Psidev-ms-dev] List of new c.v. terms and some changes proposed by the team working in mzQuantML

[David O. <do...@eb...>]

Dear all,

Related to the development of the mzQuantML standard, the team working 
on it has a proposal to change and add several terms in the PSI-MS cv. 
There's more than 70 terms to be added or changed (the changes are 
mainly about re-location).
Martin Eisenacher has made a very complete documentation about where the 
changes are in the controlled voc. and why the need them. I was waiting 
for some information from Martin but, in order to make things faster, 
I'm sending you this message now.

I'll attach the changes that Martin has compiled in one small obo file.

A complete obo file (to be used with diff purposes) is located at
http://code.google.com/p/mzquantml/source/browse/trunk/cv/quant_obo_3_7_3_new_and_edited_terms.txt

The explanation of why and where can be found in this document in two 
formats:
http://mzquantml.googlecode.com/svn/trunk/cv/quant_obo_diff_description.pdf
http://mzquantml.googlecode.com/svn/trunk/cv/quant_obo_diff_description.pptx

Please, take a look into the changes proposed and make your comments and 
suggestions. After everybody is OK with this, I'll submitt the changes 
in the PSI-MS cv.

Best,

-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD