psidev-ms-dev

[Psidev-ms-dev] Need help with mzData converter ...

[Pancerella, C. M <ca...@sa...>]

Hi.

I'm looking for a converter that converts from mzData into either a text =
or CSV representation.  I'd prefer open source source code, as I want to =
use this in a project that we're doing. =20

thanks.
Carmen

Carmen Pancerella, PhD
Advanced Software Research & Development
Sandia National Laboratories
P.O. Box 969, Mailstop 9152
Livermore, CA 94551-0969
=20
Fax: (508) 300-8815
Phone: (617) 630-0316
=20
ca...@sa...

[Psidev-ms-dev] Need help with mzData converter ...

[Alexandre M. <ol...@ge...>]

Hi

go 4 a try at http://insilicospectro.vital-it.ch/cgis.html

If it fit your needs, you also install it locally and have it directly
scripted.
It's perl, opensource, and should work more or less on any decent OS.

please let us know if you have any trouble

regards
Alex

[sorry for the duplicate if any]

Pancerella, Carmen M wrote:
>
> Hi.
>
> I'm looking for a converter that converts from mzData into either a
> text or CSV representation.  I'd prefer open source source code, as I
> want to use this in a project that we're doing. 
>
> thanks.
> Carmen
>
>

-- 
Alexandre Masselot, phD
Senior bioinformatician
www.genebio.com
voice: +41 22 702 99 00

[Psidev-ms-dev] Retention time in PSI-MS ontology

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

Hi,



I am processing some mzXML files into mzData for insertion into the 
PRIDE database, and I can't seem to find an ontology term for 'retention 
time' in the PSI-MS ontology.

If there is one, and I just can't find it for some silly reason, please 
let me know.

If there isn't any, could this be added? It seems like a sensible thing 
as it is a common enough piece of data.


Thanks in advance,


lnnrt.

Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

[Kent L. <knl...@in...>]

Hi Lennart,

There is not currently a term labeled retention time in the MS CV.  The
current terms for the purpose are:

[Term]
id: PSI:1000038
name: Time In Minutes
def: "Acquisition time in minutes." [PSI:GPS]
is_a: PSI:1000460 ! Unit
relationship: part_of PSI:1000459 ! Spectrum Instrument Description

[Term]
id: PSI:1000039
name: Time In Seconds
def: "Acquisition time in seconds." [PSI:GPS]
is_a: PSI:1000460 ! Unit
relationship: part_of PSI:1000459 ! Spectrum Instrument Description

Regards,

Kent

> -----Original Message-----
> From: psi...@li... [mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of Lennart Martens
> Sent: Thursday, November 09, 2006 9:27 AM
> To: psi...@li...
> Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
> 
> Hi,
> 
> 
> 
> I am processing some mzXML files into mzData for insertion into the
> PRIDE database, and I can't seem to find an ontology term for 'retention
> time' in the PSI-MS ontology.
> 
> If there is one, and I just can't find it for some silly reason, please
> let me know.
> 
> If there isn't any, could this be added? It seems like a sensible thing
> as it is a common enough piece of data.
> 
> 
> Thanks in advance,
> 
> 
> lnnrt.
> 
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

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

Hi Kent,


Thanks for pointing that out, but I had seen these myself and assumed 
that they were used to document the actual acquisition time during which 
the final spectrum was acquired (the final spectrum represented in the 
mzData binary arrays is thus a summation over all the individual 
detector recordings during that time slot).

As such, I would expect this value to be either constant (I guess most 
mass specs do not allow dynamic setting of this value, but I could be 
wrong) and certainly small (say from 0.5 to 8 seconds). Having '900' in 
the seconds field, say, would therefore probably lead to confusion?


Cheers,

lnnrt.

Kent Laursen wrote:
> Hi Lennart,
> 
> There is not currently a term labeled retention time in the MS CV.  The
> current terms for the purpose are:
> 
> [Term]
> id: PSI:1000038
> name: Time In Minutes
> def: "Acquisition time in minutes." [PSI:GPS]
> is_a: PSI:1000460 ! Unit
> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
> 
> [Term]
> id: PSI:1000039
> name: Time In Seconds
> def: "Acquisition time in seconds." [PSI:GPS]
> is_a: PSI:1000460 ! Unit
> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
> 
> Regards,
> 
> Kent
> 
>> -----Original Message-----
>> From: psi...@li... [mailto:psidev-ms-dev-
>> bo...@li...] On Behalf Of Lennart Martens
>> Sent: Thursday, November 09, 2006 9:27 AM
>> To: psi...@li...
>> Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
>>
>> Hi,
>>
>>
>>
>> I am processing some mzXML files into mzData for insertion into the
>> PRIDE database, and I can't seem to find an ontology term for 'retention
>> time' in the PSI-MS ontology.
>>
>> If there is one, and I just can't find it for some silly reason, please
>> let me know.
>>
>> If there isn't any, could this be added? It seems like a sensible thing
>> as it is a common enough piece of data.
>>
>>
>> Thanks in advance,
>>
>>
>> lnnrt.
>>
>> -------------------------------------------------------------------------
>> Using Tomcat but need to do more? Need to support web services, security?
>> Get stuff done quickly with pre-integrated technology to make your job
>> easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> 
> 

-- 
Dr. Lennart Martens

Senior Software Developer
Proteomics Services
Sequence Database Group
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
United Kingdom

Tel.:  +44 (0)1223 492 610 (Direct Line)
Fax:  +44 (0)1223 494 484
Skype: lennart_martens

Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

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

Hi,

A related issue is for the case of peak lists which have been generated 
from the combination of several scans. The 'TimeInMinutes' for these is 
obviously also a range of time. I've solved this by just putting the 
start acquisition time of the first spectrum in the range, but one could 
of course as well put the average time.  The same question appears as 
Lennart writes for individual scans if one want to be exact: is it the 
start time, or average, or end time of the scan which should be in the 
field? Is there any consensus opinion on which should be written, and is 
it documented somewhere?
I don't think this is very important for peak lists since there are 
references to all the scans in the raw file that were combined in the 
form of a list of acquisition-acqNumbers, but if mzData is to represent 
raw data it could become important for LC-MS alignment etc.

Regards

Fredrik Levander


Lennart Martens wrote:
> Hi Kent,
>
>
> Thanks for pointing that out, but I had seen these myself and assumed 
> that they were used to document the actual acquisition time during which 
> the final spectrum was acquired (the final spectrum represented in the 
> mzData binary arrays is thus a summation over all the individual 
> detector recordings during that time slot).
>
> As such, I would expect this value to be either constant (I guess most 
> mass specs do not allow dynamic setting of this value, but I could be 
> wrong) and certainly small (say from 0.5 to 8 seconds). Having '900' in 
> the seconds field, say, would therefore probably lead to confusion?
>
>
> Cheers,
>
> lnnrt.
>
> Kent Laursen wrote:
>   
>> Hi Lennart,
>>
>> There is not currently a term labeled retention time in the MS CV.  The
>> current terms for the purpose are:
>>
>> [Term]
>> id: PSI:1000038
>> name: Time In Minutes
>> def: "Acquisition time in minutes." [PSI:GPS]
>> is_a: PSI:1000460 ! Unit
>> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
>>
>> [Term]
>> id: PSI:1000039
>> name: Time In Seconds
>> def: "Acquisition time in seconds." [PSI:GPS]
>> is_a: PSI:1000460 ! Unit
>> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
>>
>> Regards,
>>
>> Kent
>>
>>     
>>> -----Original Message-----
>>> From: psi...@li... [mailto:psidev-ms-dev-
>>> bo...@li...] On Behalf Of Lennart Martens
>>> Sent: Thursday, November 09, 2006 9:27 AM
>>> To: psi...@li...
>>> Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
>>>
>>> Hi,
>>>
>>>
>>>
>>> I am processing some mzXML files into mzData for insertion into the
>>> PRIDE database, and I can't seem to find an ontology term for 'retention
>>> time' in the PSI-MS ontology.
>>>
>>> If there is one, and I just can't find it for some silly reason, please
>>> let me know.
>>>
>>> If there isn't any, could this be added? It seems like a sensible thing
>>> as it is a common enough piece of data.
>>>
>>>
>>> Thanks in advance,
>>>
>>>
>>> lnnrt.
>>>
>>> -------------------------------------------------------------------------
>>> Using Tomcat but need to do more? Need to support web services, security?
>>> Get stuff done quickly with pre-integrated technology to make your job
>>> easier
>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>       
>>     
>
>   

Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

[Kent L. <knl...@in...>]

Hi Lennart,

Retention time is a chromatography term.  If you are referring to the time
between mass spectrum acquisitions, this can be computed by subtracting
consecutive absolute acquisition times.  However, these time intervals are
not necessarily identical/constant, so it is more precise to do the math on
acquisition times.

As far as I know, there is not a term for what you are describing.  Since it
would be useful to add this term to MS CV (time in between mass spec scans,
so to speak) you can email this request to Trish.  Perhaps something like
duty cycle would fit nicely with instrument description.

FYI, the upcoming merger will address separation as pragmatically necessary.

Regards,

Kent

> -----Original Message-----
> From: Lennart Martens [mailto:len...@eb...]
> Sent: Thursday, November 09, 2006 10:37 AM
> To: Kent Laursen; psi...@li...
> Subject: Re: [Psidev-ms-dev] Retention time in PSI-MS ontology
> 
> Hi Kent,
> 
> 
> Thanks for pointing that out, but I had seen these myself and assumed
> that they were used to document the actual acquisition time during which
> the final spectrum was acquired (the final spectrum represented in the
> mzData binary arrays is thus a summation over all the individual
> detector recordings during that time slot).
> 
> As such, I would expect this value to be either constant (I guess most
> mass specs do not allow dynamic setting of this value, but I could be
> wrong) and certainly small (say from 0.5 to 8 seconds). Having '900' in
> the seconds field, say, would therefore probably lead to confusion?
> 
> 
> Cheers,
> 
> lnnrt.
> 
> Kent Laursen wrote:
> > Hi Lennart,
> >
> > There is not currently a term labeled retention time in the MS CV.  The
> > current terms for the purpose are:
> >
> > [Term]
> > id: PSI:1000038
> > name: Time In Minutes
> > def: "Acquisition time in minutes." [PSI:GPS]
> > is_a: PSI:1000460 ! Unit
> > relationship: part_of PSI:1000459 ! Spectrum Instrument Description
> >
> > [Term]
> > id: PSI:1000039
> > name: Time In Seconds
> > def: "Acquisition time in seconds." [PSI:GPS]
> > is_a: PSI:1000460 ! Unit
> > relationship: part_of PSI:1000459 ! Spectrum Instrument Description
> >
> > Regards,
> >
> > Kent
> >
> >> -----Original Message-----
> >> From: psi...@li... [mailto:psidev-ms-
> dev-
> >> bo...@li...] On Behalf Of Lennart Martens
> >> Sent: Thursday, November 09, 2006 9:27 AM
> >> To: psi...@li...
> >> Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
> >>
> >> Hi,
> >>
> >>
> >>
> >> I am processing some mzXML files into mzData for insertion into the
> >> PRIDE database, and I can't seem to find an ontology term for
> 'retention
> >> time' in the PSI-MS ontology.
> >>
> >> If there is one, and I just can't find it for some silly reason, please
> >> let me know.
> >>
> >> If there isn't any, could this be added? It seems like a sensible thing
> >> as it is a common enough piece of data.
> >>
> >>
> >> Thanks in advance,
> >>
> >>
> >> lnnrt.
> >>
> >> -----------------------------------------------------------------------
> --
> >> Using Tomcat but need to do more? Need to support web services,
> security?
> >> Get stuff done quickly with pre-integrated technology to make your job
> >> easier
> >> Download IBM WebSphere Application Server v.1.0.1 based on Apache
> Geronimo
> >> http://sel.as-
> us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> >> _______________________________________________
> >> Psidev-ms-dev mailing list
> >> Psi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >
> >
> 
> --
> Dr. Lennart Martens
> 
> Senior Software Developer
> Proteomics Services
> Sequence Database Group
> EMBL-European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> United Kingdom
> 
> Tel.:  +44 (0)1223 492 610 (Direct Line)
> Fax:  +44 (0)1223 494 484
> Skype: lennart_martens

Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

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

Hi Lennart,
The intention was certainly that these are for the retention time, but I 
can't see any documentation that confirms this.  Certainly Mascot 
Distiller, Mascot, Bruker CompassXport, the Sciex wiff converter, 
Bioworks and the Insilicos viewer all assume that this is the case.

Best regards,
David



Lennart Martens wrote:
> Hi Kent,
> 
> 
> Thanks for pointing that out, but I had seen these myself and assumed 
> that they were used to document the actual acquisition time during which 
> the final spectrum was acquired (the final spectrum represented in the 
> mzData binary arrays is thus a summation over all the individual 
> detector recordings during that time slot).
> 
> As such, I would expect this value to be either constant (I guess most 
> mass specs do not allow dynamic setting of this value, but I could be 
> wrong) and certainly small (say from 0.5 to 8 seconds). Having '900' in 
> the seconds field, say, would therefore probably lead to confusion?
> 
> 
> Cheers,
> 
> lnnrt.
> 
> Kent Laursen wrote:
>> Hi Lennart,
>>
>> There is not currently a term labeled retention time in the MS CV.  The
>> current terms for the purpose are:
>>
>> [Term]
>> id: PSI:1000038
>> name: Time In Minutes
>> def: "Acquisition time in minutes." [PSI:GPS]
>> is_a: PSI:1000460 ! Unit
>> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
>>
>> [Term]
>> id: PSI:1000039
>> name: Time In Seconds
>> def: "Acquisition time in seconds." [PSI:GPS]
>> is_a: PSI:1000460 ! Unit
>> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
>>
>> Regards,
>>
>> Kent
>>
>>> -----Original Message-----
>>> From: psi...@li... [mailto:psidev-ms-dev-
>>> bo...@li...] On Behalf Of Lennart Martens
>>> Sent: Thursday, November 09, 2006 9:27 AM
>>> To: psi...@li...
>>> Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
>>>
>>> Hi,
>>>
>>>
>>>
>>> I am processing some mzXML files into mzData for insertion into the
>>> PRIDE database, and I can't seem to find an ontology term for 'retention
>>> time' in the PSI-MS ontology.
>>>
>>> If there is one, and I just can't find it for some silly reason, please
>>> let me know.
>>>
>>> If there isn't any, could this be added? It seems like a sensible thing
>>> as it is a common enough piece of data.
>>>
>>>
>>> Thanks in advance,
>>>
>>>
>>> lnnrt.
>>>
>>> -------------------------------------------------------------------------
>>> Using Tomcat but need to do more? Need to support web services, security?
>>> Get stuff done quickly with pre-integrated technology to make your job
>>> easier
>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
> 

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

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

*** please note change of address ***

Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

[frank g. <Fra...@ne...>]

Hi


I don't mean to review the MS-CV but......
Just as a side issue to this thread you should be looking to use the
PATO units ontology now instead of creating your own.
http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/
Any missing term or request should be sent to
obo...@li....

As a result, the defintion of "Time in minutes" (The term itself should
probably just be "minutes") should be something like the "measure of
time represented in minutes", not Acquisition time. Please ensure you
remove context of use from the semantic meaning of the term.

Cheers
Frank =20

-----Original Message-----
From: psi...@li...
[mailto:psi...@li...] On Behalf Of David
Creasy
Sent: Thursday, November 09, 2006 4:23 PM
To: len...@eb...
Cc: psi...@li...
Subject: Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

Hi Lennart,
The intention was certainly that these are for the retention time, but I
can't see any documentation that confirms this.  Certainly Mascot
Distiller, Mascot, Bruker CompassXport, the Sciex wiff converter,
Bioworks and the Insilicos viewer all assume that this is the case.

Best regards,
David



Lennart Martens wrote:
> Hi Kent,
>=20
>=20
> Thanks for pointing that out, but I had seen these myself and assumed=20
> that they were used to document the actual acquisition time during=20
> which the final spectrum was acquired (the final spectrum represented=20
> in the mzData binary arrays is thus a summation over all the=20
> individual detector recordings during that time slot).
>=20
> As such, I would expect this value to be either constant (I guess most

> mass specs do not allow dynamic setting of this value, but I could be
> wrong) and certainly small (say from 0.5 to 8 seconds). Having '900'=20
> in the seconds field, say, would therefore probably lead to confusion?
>=20
>=20
> Cheers,
>=20
> lnnrt.
>=20
> Kent Laursen wrote:
>> Hi Lennart,
>>
>> There is not currently a term labeled retention time in the MS CV. =20
>> The current terms for the purpose are:
>>
>> [Term]
>> id: PSI:1000038
>> name: Time In Minutes
>> def: "Acquisition time in minutes." [PSI:GPS]
>> is_a: PSI:1000460 ! Unit
>> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
>>
>> [Term]
>> id: PSI:1000039
>> name: Time In Seconds
>> def: "Acquisition time in seconds." [PSI:GPS]
>> is_a: PSI:1000460 ! Unit
>> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
>>
>> Regards,
>>
>> Kent
>>
>>> -----Original Message-----
>>> From: psi...@li...=20
>>> [mailto:psidev-ms-dev- bo...@li...] On Behalf Of=20
>>> Lennart Martens
>>> Sent: Thursday, November 09, 2006 9:27 AM
>>> To: psi...@li...
>>> Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
>>>
>>> Hi,
>>>
>>>
>>>
>>> I am processing some mzXML files into mzData for insertion into the=20
>>> PRIDE database, and I can't seem to find an ontology term for=20
>>> 'retention time' in the PSI-MS ontology.
>>>
>>> If there is one, and I just can't find it for some silly reason,=20
>>> please let me know.
>>>
>>> If there isn't any, could this be added? It seems like a sensible=20
>>> thing as it is a common enough piece of data.
>>>
>>>
>>> Thanks in advance,
>>>
>>>
>>> lnnrt.
>>>
>>> --------------------------------------------------------------------
>>> ----- Using Tomcat but need to do more? Need to support web=20
>>> services, security?
>>> Get stuff done quickly with pre-integrated technology to make your=20
>>> job easier Download IBM WebSphere Application Server v.1.0.1 based=20
>>> on Apache Geronimo
>>> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
12
>>> 1642 _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>=20

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

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

*** please note change of address ***

------------------------------------------------------------------------
-
Using Tomcat but need to do more? Need to support web services,
security?
Get stuff done quickly with pre-integrated technology to make your job
easier Download IBM WebSphere Application Server v.1.0.1 based on Apache
Geronimo
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
121642
_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

[Kent L. <knl...@in...>]

Sir,

I thank you for your quasi-intentional review of the MS-CV, and agree with
your points:

-Don't redefine a term that can be re-used from a shared CV
-Avoid obfuscating a terms meaning through inappropriate contextualization

As you know, part of this is just the inevitable and necessary cleanup that
occurs as the different standards working groups interoperate with greater
earnest.

Please keep the observations and corrections coming; more perspectives lead
to better factoring of domain concepts in the various CV's and ontologies.

As a side note, we are hoping/expecting that MS CV will be registered and
posted on the OBO site prior to next weeks meeting.

Regards,

Kent


> -----Original Message-----
> From: psi...@li... [mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of frank gibson
> Sent: Friday, November 10, 2006 4:42 AM
> To: David Creasy; len...@eb...
> Cc: psi...@li...
> Subject: Re: [Psidev-ms-dev] Retention time in PSI-MS ontology
> 
> Hi
> 
> 
> I don't mean to review the MS-CV but......
> Just as a side issue to this thread you should be looking to use the
> PATO units ontology now instead of creating your own.
> http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/
> Any missing term or request should be sent to
> obo...@li....
> 
> As a result, the defintion of "Time in minutes" (The term itself should
> probably just be "minutes") should be something like the "measure of
> time represented in minutes", not Acquisition time. Please ensure you
> remove context of use from the semantic meaning of the term.
> 
> Cheers
> Frank
> 
> -----Original Message-----
> From: psi...@li...
> [mailto:psi...@li...] On Behalf Of David
> Creasy
> Sent: Thursday, November 09, 2006 4:23 PM
> To: len...@eb...
> Cc: psi...@li...
> Subject: Re: [Psidev-ms-dev] Retention time in PSI-MS ontology
> 
> Hi Lennart,
> The intention was certainly that these are for the retention time, but I
> can't see any documentation that confirms this.  Certainly Mascot
> Distiller, Mascot, Bruker CompassXport, the Sciex wiff converter,
> Bioworks and the Insilicos viewer all assume that this is the case.
> 
> Best regards,
> David
> 
> 
> 
> Lennart Martens wrote:
> > Hi Kent,
> >
> >
> > Thanks for pointing that out, but I had seen these myself and assumed
> > that they were used to document the actual acquisition time during
> > which the final spectrum was acquired (the final spectrum represented
> > in the mzData binary arrays is thus a summation over all the
> > individual detector recordings during that time slot).
> >
> > As such, I would expect this value to be either constant (I guess most
> 
> > mass specs do not allow dynamic setting of this value, but I could be
> > wrong) and certainly small (say from 0.5 to 8 seconds). Having '900'
> > in the seconds field, say, would therefore probably lead to confusion?
> >
> >
> > Cheers,
> >
> > lnnrt.
> >
> > Kent Laursen wrote:
> >> Hi Lennart,
> >>
> >> There is not currently a term labeled retention time in the MS CV.
> >> The current terms for the purpose are:
> >>
> >> [Term]
> >> id: PSI:1000038
> >> name: Time In Minutes
> >> def: "Acquisition time in minutes." [PSI:GPS]
> >> is_a: PSI:1000460 ! Unit
> >> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
> >>
> >> [Term]
> >> id: PSI:1000039
> >> name: Time In Seconds
> >> def: "Acquisition time in seconds." [PSI:GPS]
> >> is_a: PSI:1000460 ! Unit
> >> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
> >>
> >> Regards,
> >>
> >> Kent
> >>
> >>> -----Original Message-----
> >>> From: psi...@li...
> >>> [mailto:psidev-ms-dev- bo...@li...] On Behalf Of
> >>> Lennart Martens
> >>> Sent: Thursday, November 09, 2006 9:27 AM
> >>> To: psi...@li...
> >>> Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
> >>>
> >>> Hi,
> >>>
> >>>
> >>>
> >>> I am processing some mzXML files into mzData for insertion into the
> >>> PRIDE database, and I can't seem to find an ontology term for
> >>> 'retention time' in the PSI-MS ontology.
> >>>
> >>> If there is one, and I just can't find it for some silly reason,
> >>> please let me know.
> >>>
> >>> If there isn't any, could this be added? It seems like a sensible
> >>> thing as it is a common enough piece of data.
> >>>
> >>>
> >>> Thanks in advance,
> >>>
> >>>
> >>> lnnrt.
> >>>
> >>> --------------------------------------------------------------------
> >>> ----- Using Tomcat but need to do more? Need to support web
> >>> services, security?
> >>> Get stuff done quickly with pre-integrated technology to make your
> >>> job easier Download IBM WebSphere Application Server v.1.0.1 based
> >>> on Apache Geronimo
> >>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=12
> >>> 1642 _______________________________________________
> >>> Psidev-ms-dev mailing list
> >>> Psi...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >>
> >
> 
> --
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
> 
> dc...@ma...
> http://www.matrixscience.com
> 
> *** please note change of address ***
> 
> ------------------------------------------------------------------------
> -
> Using Tomcat but need to do more? Need to support web services,
> security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier Download IBM WebSphere Application Server v.1.0.1 based on Apache
> Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> 
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

[Randy J. <rkj...@in...>]

Hi everyone,

Short version:

This is confusing and we need to deal with it directly in the CV.  Below is
a long discussion - the short version is that 1000038/1000039 are meant to
be relative acquisition times which in chromatography system would be
'retention time' but this is not true for non-chromatography systems, so we
need to clean up the nomenclature.

Long version:

There are two terms in the CV which are meant to represent relative
acquitisiton time from the start of overall acquisition process.  The data
type is expected to be a floating point number - not a date/time stamp.

As such, it is ideally suited (and intentionally designed) to hold a
retention time.  However, since 'retention time' is not globally applicable
to all separation methods, and since not all flow-based methods or
sequential acquisition methods involve separation at all (flow-injection,
etc.), then calling this term 'retention time' was overly specific.

For MALDI system where multiple spectra would be collected from a single
spot, the idea of recoring the time from the first spectrum acquired for a
spot seemed to match this defintion of acquisition time, and since mzData
1.05 files cannot handle multiple samples, then each spot on the plate would
get it's own mzData file whose admin description could include creation
dates and times.

As for the precise meaning of a relative acquisition time (in minutes or
seconds), we are somewhat at the mercy of the base acquisition system.

There are two time-frames which need be considered: analyzer time, and
flow-system time.

A typical analyzer takes some finite time to perform a single acquisition.
Most systems combine multiple low-level acquisitions into a single reported
acquisition (like most ion traps and TOF systems).  Some systems record the
time representing the start of an atomic operation which results in the
production of a single reported spectrum.  Other systems record the
concluding time of the spectrum.

It is not usually critical to determine if the time indicated is at the
start of the spectrum scan, or the end, since it is a very short time in
almost all systems and is consistently done within individual analyzers.

For most systems used in protoemics, there flow-system time is a completely
different thing.  In data-dependent acquisitions, there can be large
variations is the cycle-time of the instrument, so there will usually not be
a 'sampling frequency' in the usual sense - although you can configure
experiments so have s fixed sampling frequency.

This means that the acquisition time marks the time from the start of the
acquisition at which the particular spectrum is recorded.  If several
spectra are combined then you are working in flow-system time, and there are
several ways to describe what has been done.

The very best way to handle this is to use the
'acqSpecification/acquisition' elements to record exactly which acquisitions
are combined - including their acquisition times.

As for the acquitision time of the combined spectrum, it is then possible to
indicate either the start of the sequence, or, if you are processing
chromatographic peaks, you can record a peak parameter like the apex time,
or the centroid of the peak (which is what most chromatographers think of as
'retention time').

This suggests that we should have new CV terms to allow the specification of
'retention time' from the chromatographic point of view, and perhaps clean
up the nomenclature to specify that 1000038/1000039 are relative acquisition
times.  We should also consider adding a true datetime stamp CV term which
could be used to store a timestamp for the sample - especially if we move to
allowing multiple samples in a single file (proposed for dataXML).

Suggestions about additions/changes to the CV?

Randy

-----Original Message-----
From: psi...@li...
[mailto:psi...@li...] On Behalf Of David
Creasy
Sent: Thursday, November 09, 2006 11:23 AM
To: len...@eb...
Cc: psi...@li...
Subject: Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

Hi Lennart,
The intention was certainly that these are for the retention time, but I 
can't see any documentation that confirms this.  Certainly Mascot 
Distiller, Mascot, Bruker CompassXport, the Sciex wiff converter, 
Bioworks and the Insilicos viewer all assume that this is the case.

Best regards,
David



Lennart Martens wrote:
> Hi Kent,
> 
> 
> Thanks for pointing that out, but I had seen these myself and assumed 
> that they were used to document the actual acquisition time during which 
> the final spectrum was acquired (the final spectrum represented in the 
> mzData binary arrays is thus a summation over all the individual 
> detector recordings during that time slot).
> 
> As such, I would expect this value to be either constant (I guess most 
> mass specs do not allow dynamic setting of this value, but I could be 
> wrong) and certainly small (say from 0.5 to 8 seconds). Having '900' in 
> the seconds field, say, would therefore probably lead to confusion?
> 
> 
> Cheers,
> 
> lnnrt.
> 
> Kent Laursen wrote:
>> Hi Lennart,
>>
>> There is not currently a term labeled retention time in the MS CV.  The
>> current terms for the purpose are:
>>
>> [Term]
>> id: PSI:1000038
>> name: Time In Minutes
>> def: "Acquisition time in minutes." [PSI:GPS]
>> is_a: PSI:1000460 ! Unit
>> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
>>
>> [Term]
>> id: PSI:1000039
>> name: Time In Seconds
>> def: "Acquisition time in seconds." [PSI:GPS]
>> is_a: PSI:1000460 ! Unit
>> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
>>
>> Regards,
>>
>> Kent
>>
>>> -----Original Message-----
>>> From: psi...@li... [mailto:psidev-ms-dev-
>>> bo...@li...] On Behalf Of Lennart Martens
>>> Sent: Thursday, November 09, 2006 9:27 AM
>>> To: psi...@li...
>>> Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
>>>
>>> Hi,
>>>
>>>
>>>
>>> I am processing some mzXML files into mzData for insertion into the
>>> PRIDE database, and I can't seem to find an ontology term for 'retention
>>> time' in the PSI-MS ontology.
>>>
>>> If there is one, and I just can't find it for some silly reason, please
>>> let me know.
>>>
>>> If there isn't any, could this be added? It seems like a sensible thing
>>> as it is a common enough piece of data.
>>>
>>>
>>> Thanks in advance,
>>>
>>>
>>> lnnrt.
>>>
>>>
-------------------------------------------------------------------------
>>> Using Tomcat but need to do more? Need to support web services,
security?
>>> Get stuff done quickly with pre-integrated technology to make your job
>>> easier
>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache
Geronimo
>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
> 

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

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

*** please note change of address ***

-------------------------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job
easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

[Pierre-Alain B. <pie...@is...>]

Thanks Randy for these precisions.
This tells me that we really need a god sample of use cases. Eric has a 
number of high-level descriptions that we have prepared during one of 
the sessions in Washington (this was done by Jim, Sean, Ronan, myself 
and a couple of others I am sorry to have not in mind right now).
For each of them, It would be nice to think at generating 1) a more 
formal list of these usecases in the documentation of the standard and 
2) a number of typical instanciations.
Maybe in Seattle these usecases can be listed again and "checked" if 
considered or not during these 2 days.

Pierre-Alain


Randy Julian wrote:

>Hi everyone,
>
>Short version:
>
>This is confusing and we need to deal with it directly in the CV.  Below is
>a long discussion - the short version is that 1000038/1000039 are meant to
>be relative acquisition times which in chromatography system would be
>'retention time' but this is not true for non-chromatography systems, so we
>need to clean up the nomenclature.
>
>Long version:
>
>There are two terms in the CV which are meant to represent relative
>acquitisiton time from the start of overall acquisition process.  The data
>type is expected to be a floating point number - not a date/time stamp.
>
>As such, it is ideally suited (and intentionally designed) to hold a
>retention time.  However, since 'retention time' is not globally applicable
>to all separation methods, and since not all flow-based methods or
>sequential acquisition methods involve separation at all (flow-injection,
>etc.), then calling this term 'retention time' was overly specific.
>
>For MALDI system where multiple spectra would be collected from a single
>spot, the idea of recoring the time from the first spectrum acquired for a
>spot seemed to match this defintion of acquisition time, and since mzData
>1.05 files cannot handle multiple samples, then each spot on the plate would
>get it's own mzData file whose admin description could include creation
>dates and times.
>
>As for the precise meaning of a relative acquisition time (in minutes or
>seconds), we are somewhat at the mercy of the base acquisition system.
>
>There are two time-frames which need be considered: analyzer time, and
>flow-system time.
>
>A typical analyzer takes some finite time to perform a single acquisition.
>Most systems combine multiple low-level acquisitions into a single reported
>acquisition (like most ion traps and TOF systems).  Some systems record the
>time representing the start of an atomic operation which results in the
>production of a single reported spectrum.  Other systems record the
>concluding time of the spectrum.
>
>It is not usually critical to determine if the time indicated is at the
>start of the spectrum scan, or the end, since it is a very short time in
>almost all systems and is consistently done within individual analyzers.
>
>For most systems used in protoemics, there flow-system time is a completely
>different thing.  In data-dependent acquisitions, there can be large
>variations is the cycle-time of the instrument, so there will usually not be
>a 'sampling frequency' in the usual sense - although you can configure
>experiments so have s fixed sampling frequency.
>
>This means that the acquisition time marks the time from the start of the
>acquisition at which the particular spectrum is recorded.  If several
>spectra are combined then you are working in flow-system time, and there are
>several ways to describe what has been done.
>
>The very best way to handle this is to use the
>'acqSpecification/acquisition' elements to record exactly which acquisitions
>are combined - including their acquisition times.
>
>As for the acquitision time of the combined spectrum, it is then possible to
>indicate either the start of the sequence, or, if you are processing
>chromatographic peaks, you can record a peak parameter like the apex time,
>or the centroid of the peak (which is what most chromatographers think of as
>'retention time').
>
>This suggests that we should have new CV terms to allow the specification of
>'retention time' from the chromatographic point of view, and perhaps clean
>up the nomenclature to specify that 1000038/1000039 are relative acquisition
>times.  We should also consider adding a true datetime stamp CV term which
>could be used to store a timestamp for the sample - especially if we move to
>allowing multiple samples in a single file (proposed for dataXML).
>
>Suggestions about additions/changes to the CV?
>
>Randy
>
>-----Original Message-----
>From: psi...@li...
>[mailto:psi...@li...] On Behalf Of David
>Creasy
>Sent: Thursday, November 09, 2006 11:23 AM
>To: len...@eb...
>Cc: psi...@li...
>Subject: Re: [Psidev-ms-dev] Retention time in PSI-MS ontology
>
>Hi Lennart,
>The intention was certainly that these are for the retention time, but I 
>can't see any documentation that confirms this.  Certainly Mascot 
>Distiller, Mascot, Bruker CompassXport, the Sciex wiff converter, 
>Bioworks and the Insilicos viewer all assume that this is the case.
>
>Best regards,
>David
>
>
>
>Lennart Martens wrote:
>  
>
>>Hi Kent,
>>
>>
>>Thanks for pointing that out, but I had seen these myself and assumed 
>>that they were used to document the actual acquisition time during which 
>>the final spectrum was acquired (the final spectrum represented in the 
>>mzData binary arrays is thus a summation over all the individual 
>>detector recordings during that time slot).
>>
>>As such, I would expect this value to be either constant (I guess most 
>>mass specs do not allow dynamic setting of this value, but I could be 
>>wrong) and certainly small (say from 0.5 to 8 seconds). Having '900' in 
>>the seconds field, say, would therefore probably lead to confusion?
>>
>>
>>Cheers,
>>
>>lnnrt.
>>
>>Kent Laursen wrote:
>>    
>>
>>>Hi Lennart,
>>>
>>>There is not currently a term labeled retention time in the MS CV.  The
>>>current terms for the purpose are:
>>>
>>>[Term]
>>>id: PSI:1000038
>>>name: Time In Minutes
>>>def: "Acquisition time in minutes." [PSI:GPS]
>>>is_a: PSI:1000460 ! Unit
>>>relationship: part_of PSI:1000459 ! Spectrum Instrument Description
>>>
>>>[Term]
>>>id: PSI:1000039
>>>name: Time In Seconds
>>>def: "Acquisition time in seconds." [PSI:GPS]
>>>is_a: PSI:1000460 ! Unit
>>>relationship: part_of PSI:1000459 ! Spectrum Instrument Description
>>>
>>>Regards,
>>>
>>>Kent
>>>
>>>      
>>>
>>>>-----Original Message-----
>>>>From: psi...@li... [mailto:psidev-ms-dev-
>>>>bo...@li...] On Behalf Of Lennart Martens
>>>>Sent: Thursday, November 09, 2006 9:27 AM
>>>>To: psi...@li...
>>>>Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
>>>>
>>>>Hi,
>>>>
>>>>
>>>>
>>>>I am processing some mzXML files into mzData for insertion into the
>>>>PRIDE database, and I can't seem to find an ontology term for 'retention
>>>>time' in the PSI-MS ontology.
>>>>
>>>>If there is one, and I just can't find it for some silly reason, please
>>>>let me know.
>>>>
>>>>If there isn't any, could this be added? It seems like a sensible thing
>>>>as it is a common enough piece of data.
>>>>
>>>>
>>>>Thanks in advance,
>>>>
>>>>
>>>>lnnrt.
>>>>
>>>>
>>>>        
>>>>
>-------------------------------------------------------------------------
>  
>
>>>>Using Tomcat but need to do more? Need to support web services,
>>>>        
>>>>
>security?
>  
>
>>>>Get stuff done quickly with pre-integrated technology to make your job
>>>>easier
>>>>Download IBM WebSphere Application Server v.1.0.1 based on Apache
>>>>        
>>>>
>Geronimo
>  
>
>>>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>>>_______________________________________________
>>>>Psidev-ms-dev mailing list
>>>>Psi...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>>        
>>>>
>
>  
>

-- 
--
 Dr. Pierre-Alain Binz
 Swiss Institute of Bioinformatics
 Proteome Informatics Group
 1, Rue Michel Servet
 CH-1211 Geneve 4
 Switzerland
 - - - - - - - - - - - - - - - - -
 Tel: +41-22-379 50 50
 Fax: +41-22-379 58 58
 Pie...@is...
 http://www.expasy.org/people/Pierre-Alain.Binz.html

Re: [Psidev-ms-dev] Need help with mzData converter ...

[Simon A. <sim...@bb...>]

On 23 Oct 2006, at 17:10, Pancerella, Carmen M wrote:

> Hi.
>
> I'm looking for a converter that converts from mzData into either a  
> text or CSV representation.  I'd prefer open source source code, as  
> I want to use this in a project that we're doing.
What information are you looking to extract from the mzData?  Being  
XML mzData files are already text (albeit structured text).  Trying  
to make a more plain text format which kept all of the information in  
the original file would end up being a mess.

We've written an opensource mzData viewer which parses the XML files  
and extracts out the core data.  Maybe some of the classes in there  
would help you get started? Adding a text output to it wouldn't be  
hard.  You can find it at: http://www.bioinformatics.bbsrc.ac.uk/ 
projects/mzviewer/

Simon.