Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo

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Hi Brian, I agree, this is an improvement. I tweaked the language a little
so all the definitions are in the same tense and  added a “from”. How does
everyone like these improved definitions?

id: MS:1000894

name: retention time

def: "A time interval from the start of chromatography when a peptide exits
a chromatographic column." [PSI:MS]

id: MS:1000895

name: local retention time

def: "A time interval from the start of chromatography when a peptide exits
an unspecified local chromatographic column and instrumental setup."
[PSI:MS]

id: MS:1000896

name: normalized retention time

def: "A time interval from the start of chromatography when a peptide exits
a standardized reference chromatographic column and instrumental setup."
[PSI:MS]

id: MS:1000897

name: predicted retention time

def: "A time interval from the start of chromatography when a peptide exits
a chromatographic column as predicted by a referenced software
application." [PSI:MS]

*From:* Brian Pratt [mailto:bri...@in...]
*Sent:* Wednesday, September 04, 2013 11:50 AM
*To:* Eric Deutsch
*Cc:* Mass spectrometry standard development;
psi...@li...; psi...@li...
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
psi-ms.obo

It's the "relative to the beginning of a mass spectrometric run"  part that
strikes me as misleading - it doesn't seem proper when the chromatography
may have taken place in a completely different time period than the mass
spec analysis (again, thinking MALDI but trying to be perfectly general and
futureproof).  It just seems inline-LCMS-centric where it should be more
general.

Overall I would think it should use language about the column's history
rather than the mass analyzer's.  So for example

    id: MS:1000897

    name: predicted retention time

should simply read:

    def: "A time interval when a peptide will exit a chromatographic column
as predicted by a referenced software application." [PSI:MS]

and
  id: MS:1000894
  name: retention time
should be
  def: "A time interval at which a peptide exited a chromatographic column."
[PSI:MS]

etc.

Perhaps I am revisiting an already settled issue, but this just isn't
intuitive to me as currently written.  And I might just be the target
audience, as a developer dipping into this on an occasional basis.

Helpfully,

Brian Pratt

On Wed, Sep 4, 2013 at 10:12 AM, Eric Deutsch <
Eri...@sy...> wrote:

Hi Brian, can you elaborate on what is misleading? I don’t see how
concurrent elution and scan are implied in these terms? Maybe the term
“mass spectrometric run” is the vague part? Perhaps “chromatography” should
replace “a mass spectrometric run” for terms 894-896?

For pepXML, you almost surely want “scan start time” since that’s what is
pulled from the raw/mzML files, right? The true retention time of the
peptide ion seen in that scan is far more complex and usually not known
very well. The scan start time is a precise and often sufficiently useful
proxy for the true retention time. Right?

Allowed units are specified in the term metadata, see below..

Eric

id: MS:1000016

name: scan start time

def: "The time that an analyzer started a scan, relative to the start of
the MS run." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000503 ! scan attribute

is_a: MS:1001105 ! peptide result details

is_a: MS:1001405 ! spectrum identification result details

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute

id: MS:1000894

name: retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run." [PSI:MS]

is_a: MS:1000887 ! peptide attribute

id: MS:1000895

name: local retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit an unspecified local
chromatographic column and instrumental setup." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute

id: MS:1000896

name: normalized retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit a standardized reference
chromatographic column and instrumental setup." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute

id: MS:1000897

name: predicted retention time

def: "A time interval relative to the beginning of a mass spectrometric run
when a peptide will exit a chromatographic column as predicted by a
referenced software application." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute

*From:* Brian Pratt [mailto:bri...@in...]
*Sent:* Wednesday, September 04, 2013 9:56 AM
*To:* Mass spectrometry standard development
*Cc:* psi...@li...;
psi...@li...; Eric Deutsch
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
psi-ms.obo

>> What do you think?

I completely agree that these are distinct concepts, and of course I'm not
surprised that everyone else thinks so too.  But the description is
misleading, I think, since it really seems to assume concurrent elution and
scan.  A quibble perhaps but probably worth cleaning up.

The use in question is actually in pepXML related code, so retention time
is the concept we want for sure.  But now I guess I have to think about
managing units?  Or is it defined as being in seconds?  (And if so, perhaps
the description should be enhanced to reflect that?)

Thanks,

Brian

On Wed, Sep 4, 2013 at 9:45 AM, <Eri...@sy...> wrote:

Hi Brian, I'm not certain if that answers your question, but I might add
that ProteoWizard's use of the obsolete retention time(s) should be
changed to either scan start time or retention time. We intend scan start
time to be used in cases where there is a time tag associated with a
definite mass spec acquisition (as is the case in mzML and mzIdentML). The
non-obsolete retention time term should be used as an attribute associated
with a peptide molecule in a chromatographic column independent of an
instrument acquisition event (as is the case in TraML). The MALDI case is
a little more tricky. In practice, a scan start time will likely be
recorded with the instrument and should be written into mzML et al. The
chromatographic retention time might be known and could be recorded
separately (as this will be a different time than the instrument scan
time), but often is not well known when the mzML is written. But as you
allude to, these are now different concepts with different terms, whereas
before it was more muddled.

What do you think?

Regards,
Eric

> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Tuesday, September 03, 2013 11:24 PM
> To: psi...@li...
> Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.50.0 of
> psi-ms.obo
>
> Hi Brian,
>
> yes we obsoletetd the retention time(s) term.
>
> Because we had two terms: retention time and retention time(s), we
> decided to obsolete one and add a term named scan start time for the
> SpectrumIdentificationResult annotation, see our discussion in Issue 74
> on google code:
>
> https://code.google.com/p/psi-pi/issues/detail?id=74&can=1
>
> Best Regards,
> Gerhard
>
>
> Am 04.09.2013 00:38, schrieb Brian Pratt:

> > I'm a little slow noticing this (just now updating ProteoWizard's
> OBO), but
> > I wonder about the now obsoleted
> > id: MS:1001114
> > name: retention time(s)
> > def: "Retention time of the spectrum from the source file." [PSI:PI]
> >
> > Surely chromatography and mass spec can happen in entirely different
> time
> > frames, as with MALDI - or am I misunderstanding something?
> >
> > And how is it different from
> > id: MS:1000894
> > name: retention time
> > def: "A measure of the interval relative to the beginning of a mass
> > spectrometric run when a peptide will exit the chromatographic
> column."
> > [PSI:MS]
> >
> > And doesn't that definition have the same assumption about the column
> being
> > hooked up directly to the mass spec?
> >
> > Cheers,
> > Brian Pratt
> >
> >
> > On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
> > Ger...@ru...> wrote:
> >
> >> Dear proteomics community,
> >>
> >> attached there's the new version 3.50.0 of the psi-ms.obo file.
> >>
> >> It contains the changes concerning the retention time terms (issue
> 74),
> >> changes for the waters instrument term definitions and 3 new terms
> for the
> >> Byonic search engine.
> >>
> >>
> >> Changed CV terms in version 3.50.0 of psi-ms.obo:

> >> ==============================**===================

> >> ************ added the two is_a relations 'is_a: MS:1001105 !
> peptide
> >> result details' and
> >> ************ 'is_a: MS:1001405 ! spectrum identification result
> details'
> >> [Term]
> >> id: MS:1000016
> >> name: scan start time
> >> def: "The time that an analyzer started a scan, relative to the
> start of
> >> the MS run." [PSI:MS]
> >> xref: value-type:xsd\:float "The allowed value-type for this CV
> term."
> >> is_a: MS:1000503 ! scan attribute
> >> is_a: MS:1001105 ! peptide result details
> >> is_a: MS:1001405 ! spectrum identification result details
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >>
> >> ************ Made obsolete
> >> [Term]
> >> id: MS:1001114
> >> name: retention time(s)
> >> def: "OBSOLETE Retention time of the spectrum from the source file."
> >> [PSI:PI]
> >> comment: This term was made obsolete because scan start time
> (MS:1000016)
> >> should be used instead.
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001105 ! peptide result details
> >> is_a: MS:1001405 ! spectrum identification result details
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >> is_obsolete: true
> >>
> >> ************ Changed the definition (removed 'peptide ...').
> >> [Term]
> >> id: MS:1000894
> >> name: retention time
> >> def: "A measure of the interval relative to the beginning of a mass
> >> spectrometric run." [PSI:MS]
> >> is_a: MS:1000887 ! peptide attribute
> >>
> >> ************ Changed the is_a relationship from 'detector type' -->
> 'array
> >> detector' for the next two terms
> >> [Term]
> >> id: MS:1000114
> >> name: microchannel plate detector
> >> def: "A thin plate that contains a closely spaced array of channels
> that
> >> each act as a continuous dynode particle multiplier. A charged
> particle,
> >> fast neutral particle, or photon striking the plate causes a cascade
> of
> >> secondary electrons that ultimately exits the opposite side of the
> plate."
> >> [PSI:MS]
> >> synonym: "multichannel plate" EXACT []
> >> is_a: MS:1000345 ! array detector
> >>
> >> [Term]
> >> id: MS:1000621
> >> name: photodiode array detector
> >> def: "An array detector used to record spectra in the ultraviolet
> and
> >> visible region of light." [PSI:MS]
> >> synonym: "PDA" EXACT []
> >> is_a: MS:1000345 ! array detector
> >>
> >> ************ Added the 'is_a: MS:1000621 ! photodiode array
> detector'
> >> relationship
> >> [Term]
> >> id: MS:1000818
> >> name: Acquity UPLC PDA
> >> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
> >> is_a: MS:1000126 ! Waters instrument model
> >> is_a: MS:1000621 ! photodiode array detector
> >>
> >> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> >> relationship
> >> [Term]
> >> id: MS:1000819
> >> name: Acquity UPLC FLR
> >> def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
> >> is_a: MS:1000126 ! Waters instrument model
> >> is_a: MS:1002308 ! fluorescence detector
> >>
> >> ************ Adapted the definitions for the following Waters
> instruments
> >> to be more specific and unambiguous:
> >> MS:1000159    GCT
> >> MS:1000170    M@LDI L
> >> MS:1000171    M@LDI LR
> >> MS:1000188    Q-Tof micro
> >> MS:1000189    Q-Tof ultima
> >> MS:1000191    quattro micro
> >> MS:1000192    Quattro UItima
> >> MS:1000632    Q-Tof Premier
> >> MS:1001761    ACQUITY UPLC
> >> MS:1001762    ACQUITY UPLC H-Class
> >> MS:1001763    ACQUITY UPLC H-Class Bio
> >> MS:1001764    ACQUITY UPLC I-Class
> >> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> >> MS:1001766    nanoACQUITY UPLC
> >> MS:1001767    nanoACQUITY UPLC System with Technology
> >> MS:1001768    nanoACQUITY UPLC with HDX Technology
> >> MS:1001769    TRIZAIC UPLC nanoTile
> >> MS:1001770    GCT Premier
> >> MS:1001771    MALDI Synapt G2 HDMS
> >> MS:1001772    MALDI Synapt G2 MS
> >> MS:1001773    MALDI Synapt G2-S HDMS
> >> MS:1001774    MALDI Synapt G2-S MS
> >> MS:1001775    MALDI Synapt HDMS
> >> MS:1001776    MALDI Synapt MS
> >> MS:1001777    Synapt G2 HDMS
> >> MS:1001778    Synapt G2 MS
> >> MS:1001779    Synapt G2-S HDMS
> >> MS:1001780    Synapt G2-S MS
> >> MS:1001781    Synapt HDMS
> >> MS:1001782    Synapt MS
> >> MS:1001783    Xevo G2 Q-Tof
> >> MS:1001784    Xevo G2 Tof
> >> MS:1001785    Xevo Q-Tof
> >> MS:1001786    3100
> >> MS:1001787    Acquity SQD
> >> MS:1001788    Acquity TQD
> >> MS:1001789    Quattro micro GC
> >> MS:1001790    Xevo TQ MS
> >> MS:1001791    Xevo TQD
> >> MS:1001792    Xevo TQ-S
> >> MS:1001795    Empower
> >> MS:1001796    Unify
> >>
> >>
> >> New CV terms in version 3.50.0 of psi-ms.obo:

> >> ==============================**===============

> >> [Term]
> >> id: MS:1002308
> >> name: fluorescence detector
> >> def: "A detector using a fluorescent signal after excitation with
> light."
> >> [PSI:MS]
> >> is_a: MS:1000026 ! detector type
> >>
> >> [Term]
> >> id: MS:1002309
> >> name: Byonic: Peptide AbsLogProb
> >> def: "The absolute value of the log-base10 of the Byonic posterior
> error
> >> probability (PEP) of the PSM. " [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001143 ! search engine specific score for PSMs
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> [Term]
> >> id: MS:1002310
> >> name: Byonic: Protein AbsLogProb
> >> def: "The absolute value of the log-base10 of the Byonic posterior
> error
> >> probability (PEP) of the protein. " [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001116 ! single protein result details
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> [Term]
> >> id: MS:1002311
> >> name: Byonic: Peptide AbsLogProb2D
> >> def: "The absolute value of the log-base10 Byonic two-dimensional
> >> posterior error probability (PEP) of the PSM. The two-dimensional
> PEP takes
> >> into account protein ranking information as well as PSM
> information."
> >> [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001143 ! search engine specific score for PSMs
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> Best Regards,
> >> Gerhard
> >>
> >> --
> >> ---
> >> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> >> Bioinformatik / Biostatistik
> >> Medizinisches-Proteom-Center (MPC)
> >> Ruhr-Universität Bochum
> >> Zentrum für klinische Forschung I (ZKF I)
> >> E.049a
> >> Universitätsstraße 150
> >> D-44801 Bochum
> >>  Phone: +49(0)234/32-21006
> >> Fax:    +49(0)234/32-14554
> >> Email:  Ger...@ru...

> >> Web:    http://www.medizinisches-**proteom-
> center.de<http://www.medizinisches-proteom-center.de>
> >>
> >>
> >>
> >> --------------------------------------------------------------------

> ----------
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> >> _______________________________________________
> >> Psidev-ms-dev mailing list
> >> Psi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >>
> >>
> >
> >
> >

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> >
>
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatik / Biostatistik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.049a
> Universitätsstraße 150
> D-44801 Bochum
>
> Phone:        +49(0)234/32-21006
> Fax:  +49(0)234/32-14554
> Email:        Ger...@ru...
> Web:  http://www.medizinisches-proteom-center.de
>
> -----------------------------------------------------------------------
> -------

> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft
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> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
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