psidev-ms-dev

[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

[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] 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

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