psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] [Psidev-pi-dev] New version 3.46.0 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Hi Jun,

see the responses of Matt and Pierre-Alain to release candidate 
3.46.0_rc4 from Feb. 21st:


On 2/21/2013 9:45 AM, Gerhard Mayer wrote:
 > ************ Changed name from "selected ion m/z" to "selected 
precursor m/z" (to make it more clear
 > for use in SRM)
 > [Term]
 > id: MS:1000744
 > name: selected precursor m/z
 > def: "Mass-to-charge ratio of the precursor ion selected for 
fragmentation." [PSI:MS]
 > xref: value-type:xsd\:float "The allowed value-type for this CV term."
 > is_a: MS:1000455 ! ion selection attribute
 > relationship: has_units MS:1000040 ! m/z

Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.46.0_rc4 of 
psi-ms.obo
From: Matt Chambers <matt.chambers42@gm...> - 2013-02-21 15:58
What is the rationale behind this change? This is going to require a 
pervasive "Replace All In
Files" in pwiz and its dependent projects.

-Matt


Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.46.0_rc4 of 
psi-ms.obo
From: pierre-alain binz <pierre-alain.binz@is...> - 2013-02-21 16:34
I believe we have both following cases:
1) this ID is valid for all types of selected ions and would also be
valid for SIM well as SRM, product ion scan and selection of ions in EI
mode (such as in GC-MS). In SIM (in MS1 mode only) there is not a
concept of precursor and in EI the selection is in resulting spectra,
more rarely the molecular ion is selected.
2) this ID is specific to SRM and product ion scan and refers to a
selected precursor that will then be further analysed (i.e. fragmented)

I thought that case 2 was the idea here and for that reason I proposed
to change the name. But after looking at the CV, we have no term that
would fit the MS1 only or EI modes. And in addition, if that is causing
unnecessary bunch of changes in codes, that's not ideal.
Therefore I agree it is probably more appropriate to have a generic term
here and adapt the def:

[Term]
id: MS:1000744
name: selected ion m/z
def: "Mass-to-charge ratio of an selected ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000040 ! m/z

Pierre-Alain


In case you really need a specific term, maybe it would make sense to 
define an own term for this?, like e.g.

[Term]*
*id: MS:1002234
name: selected precursor m/z
def: "Mass-to-charge ratio of the precursor ion selected for 
fragmentation." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000744 ! selected ion m/z
relationship: has_units MS:1000040 ! m/z

Best Regards,
Gerhard

Am 22.02.2013 13:09, schrieb Fan, Jun:
> Hi Gerhard
>
>         Is there any particular reason why pierre's comment on 3.46.0_rc3 about MS:1000744 (name changed to "selected precursor m/z") not accepted in the newest release? I raised this issue as in SRM both precursor and product ions can be considered as selected which is not clear when saying selected ion. I would like to further suggest the name changed to "precursor ion m/z" to look consistent with MS:1001225 product ion m/z.
>
> Best regards!
>
> Jun Fan
> Research Fellow, Cranfield Health
> Cranfield University, Cranfield, Bedfordshire MK43 0AL
> W: www.cranfield.ac.uk  E: j....@cr...
>
>
>
> This email and any attachments to it may be confidential and are intended only for the named addressee. If you are not the named addressee, please accept our apology, notify the sender immediately and then delete the email. We request that you do not disclose, use, copy or distribute any information within it.
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>
> -----Original Message-----
> From: psi...@li... [mailto:psi...@li...]
> Sent: 22 February 2013 07:51
> To: psi...@li...
> Subject: Psidev-pi-dev Digest, Vol 63, Issue 6
>
> Send Psidev-pi-dev mailing list submissions to
> 	psi...@li...
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>
>
> Today's Topics:
>
>     1. Final version of mzQuantML successfully through	PSI	document
>        process (pierre-alain binz)
>     2. New version 3.46.0 of psi-ms.obo (Gerhard Mayer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 22 Feb 2013 08:29:57 +0100
> From: pierre-alain binz <pie...@is...>
> Subject: [Psidev-pi-dev] Final version of mzQuantML successfully
> 	through	PSI	document process
> To: psi...@eb..., PSI PI Dev
> 	<psi...@li...>
> Message-ID: <512...@is...>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear all,
>    
>    this is to announce that mzQuantML went successfully through the PSI document process and the document type changed to "Final".
>    
>    The current version 1.0.0 can be found here:
>    http://psidev.info/mzquantml
>    
>
> Best regards,
>
> Pierre-Alain Binz (handling editor for mzQuantML)
>
> --
> Pierre-Alain Binz, PhD
> Project Manager
> Swiss-Prot group
> SIB Swiss Institute of Bioinformatics
> Michel-Servet 1
> CH-1211 Geneva 4
> Switzerland
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: 22 Feb 2013 08:50:39 +0100
> From: "Gerhard Mayer" <Ger...@ru...>
> Subject: [Psidev-pi-dev] New version 3.46.0 of psi-ms.obo
> To: psi...@li...,
> 	"psi...@li..."
> 	<psi...@li...>, 	"Mass spectrometry standard
> 	development"	<psi...@li...>
> Message-ID: <512...@ru...>
> Content-Type: text/plain; charset="iso-8859-15"
>
> Dear proteomics community,
>
> attached there's the version 3.46.0 of the psi-ms.obo file.
>
> Some new terms for describing SRM transitions as well as
> some terms for ProteomeDiscoverer input parameters were added.
>
> Changed CV terms in version 3.46.0 of psi-ms.obo:
> =================================================
> ************ 1) Changed the definition from
> ************    "Collision energy required to fragment an ion
> represented as a percent value." to
> ************    "Instrument setting, expressed in percent, for adjusting
> collisional energies of ions in an effort to provide equivalent
> excitation of all ions."
> ************ 2) Added the has_units relationship
> [Term]
> id: MS:1000138
> name: normalized collision energy
> def: "Instrument setting, expressed in percent, for adjusting
> collisional energies of ions in an effort to provide equivalent
> excitation of all ions." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000510 ! precursor activation attribute
> relationship: has_units UO:0000187 ! percent
>
>
> ************ Changed the definition to "Mass-to-charge ratio of an
> selected ion."
> [Term]
> id: MS:1000744
> name: selected ion m/z
> def: "Mass-to-charge ratio of an selected ion." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000455 ! ion selection attribute
> relationship: has_units MS:1000040 ! m/z
>
>
> ************ 1) Changed the definition from
> ************    "The intensity of the product ion." to
> ************    "The intensity of a single product ion."
> ************    to make clear the difference to the new term "average
> product ion intensity" (MS:1002226)
> ************ 2) Added the float value type
> [Term]
> id: MS:1001226
> name: product ion intensity
> def: "The intensity of a single product ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> synonym: "fragment ion intensity" EXACT []
> is_a: MS:1001221 ! fragmentation information
> relationship: has_units MS:1000131 ! number of detector counts
> relationship: has_units MS:1000132 ! percent of base peak
> relationship: has_units MS:1000814 ! counts per second
> relationship: has_units MS:1000905 ! percent of base peak times 100
>
>
> ************ Renamed ProteomeDiscoverer:Minimum Peak Count -->
> ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
> [Term]
> id: MS:1001609
> name: ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
> def: "Minimum number of peaks in a tandem mass spectrum that is allowed
> to pass the filter and to be subjected to further processing in the
> workflow." [PSI:MS]
> xref: value-type:xsd\:int "The allowed value-type for this CV term."
> is_a: MS:1002101 ! ProteomeDiscoverer input parameter
>
>
> ************ Renamed ProteomeDiscoverer:Total Intensity Threshold -->
> ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
> [Term]
> id: MS:1001615
> name: ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
> def: "Used to filter out tandem mass spectra that have a total intensity
> current(sum of the intensities of all peaks in a spectrum) below the
> specified value." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002101 ! ProteomeDiscoverer input parameter
>
>
>
> New CV terms in version 3.46.0 of psi-ms.obo:
> =============================================
> [Term]
> id: MS:1002218
> name: percent collision energy ramp start
> def: "Collision energy at the start of the collision energy ramp in
> percent, normalized to the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000138 ! percent collision energy
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002219
> name: percent collision energy ramp end
> def: "Collision energy at the end of the collision energy ramp in
> percent, normalized to the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000138 ! percent collision energy
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002220
> name: MRMaid
> def: "A web-based SRM assay design tool whose transitions are generated
> by mining the millions of identified peptide spectra held in the EBI's
> PRIDE database." [PSI:PI]
> is_a: MS:1000871 ! SRM software
>
> [Term]
> id: MS:1002221
> name: MRMaid:peptide score
> def: "Score in MRMaid to indicate the expected performance of the
> peptide in SRM." [PSI:PI]
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1002222
> name: SRM transition attribute
> def: "Attribute associated with a SRM transition." [PSI:MS]
> is_a: MS:1000455 ! ion selection attribute
> relationship: part_of MS:1000908 ! transition
>
> [Term]
> id: MS:1002223
> name: precursor ion detection probability
> def: "Probability of detecting precursor when parent protein is
> present." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002222 ! SRM transition attribute
>
> [Term]
> id: MS:1002224
> name: product ion detection probability
> def: "Probability of detecting product ion when precursor ion is
> present." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002222 ! SRM transition attribute
>
> [Term]
> id: MS:1002225
> name: average product ion intensity
> def: "Average value of product ion intensity in a collection of
> identified spectra." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001226 ! product ion intensity
>
> [Term]
> id: MS:1002226
> name: product ion intensity standard deviation
> def: "Standard deviation of product ion intensity in a collection of
> identified spectra." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001226 ! product ion intensity
>
> [Term]
> id: MS:1002227
> name: number of product ion observations
> def: "The number of times the specific product ion has been observed in
> a series of SRM experiments." [PSI:PI]
> xref: value-type:xsd\:int "The allowed value-type for this CV term."
> is_a: MS:1002222 ! SRM transition attribute
>
> [Term]
> id: MS:1002228
> name: number of precursor ion observations
> def: "The number of times the specific precursor ion has been observed
> in a series of SRM experiments." [PSI:PI]
> xref: value-type:xsd\:int "The allowed value-type for this CV term."
> is_a: MS:1002222 ! SRM transition attribute
>
> [Term]
> id: MS:1002229
> name: ProteomeDiscoverer:Mascot:Significance Middle
> def: "Calculated relaxed significance when performing a decoy search for
> high-confidence peptides." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002101 ! ProteomeDiscoverer input parameter
>
> [Term]
> id: MS:1002230
> name: ProteomeDiscoverer:Mascot:Significance High
> def: "Calculated relaxed significance when performing a decoy search for
> medium-confidence peptides." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002101 ! ProteomeDiscoverer input parameter
>
> [Term]
> id: MS:1002231
> name: ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})
> is_a: MS:1001180 ! GUID regular expression
>
> [Term]
> id: MS:1002232
> name: ProteomeDiscoverer:Default FDR calculator
> def: "The default FDR calculator." [PSI:PI]
> is_a: MS:1002101 ! ProteomeDiscoverer input parameter
> relationship: has_regexp MS:1002231 !
> ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})
>
> [Term]
> id: MS:1002233
> name: ProteomeDiscoverer:SEQUEST:Low resolution spectra contained
> def: "Flag indicating if low-resolution speatra are taken into
> consideration." [PSI:PI]
> xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
> is_a: MS:1002101 ! ProteomeDiscoverer input parameter
>
>
> 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

[Psidev-ms-dev] New version 3.46.0 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the version 3.46.0 of the psi-ms.obo file.

Some new terms for describing SRM transitions as well as
some terms for ProteomeDiscoverer input parameters were added.

Changed CV terms in version 3.46.0 of psi-ms.obo:
=================================================
************ 1) Changed the definition from
************    "Collision energy required to fragment an ion 
represented as a percent value." to
************    "Instrument setting, expressed in percent, for adjusting 
collisional energies of ions in an effort to provide equivalent 
excitation of all ions."
************ 2) Added the has_units relationship
[Term]
id: MS:1000138
name: normalized collision energy
def: "Instrument setting, expressed in percent, for adjusting 
collisional energies of ions in an effort to provide equivalent 
excitation of all ions." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000187 ! percent


************ Changed the definition to "Mass-to-charge ratio of an 
selected ion."
[Term]
id: MS:1000744
name: selected ion m/z
def: "Mass-to-charge ratio of an selected ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000040 ! m/z


************ 1) Changed the definition from
************    "The intensity of the product ion." to
************    "The intensity of a single product ion."
************    to make clear the difference to the new term "average 
product ion intensity" (MS:1002226)
************ 2) Added the float value type
[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100


************ Renamed ProteomeDiscoverer:Minimum Peak Count --> 
ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
[Term]
id: MS:1001609
name: ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
def: "Minimum number of peaks in a tandem mass spectrum that is allowed 
to pass the filter and to be subjected to further processing in the 
workflow." [PSI:MS]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter


************ Renamed ProteomeDiscoverer:Total Intensity Threshold --> 
ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
[Term]
id: MS:1001615
name: ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
def: "Used to filter out tandem mass spectra that have a total intensity 
current(sum of the intensities of all peaks in a spectrum) below the 
specified value." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter



New CV terms in version 3.46.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002218
name: percent collision energy ramp start
def: "Collision energy at the start of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! percent collision energy
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002219
name: percent collision energy ramp end
def: "Collision energy at the end of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! percent collision energy
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002220
name: MRMaid
def: "A web-based SRM assay design tool whose transitions are generated 
by mining the millions of identified peptide spectra held in the EBI's 
PRIDE database." [PSI:PI]
is_a: MS:1000871 ! SRM software

[Term]
id: MS:1002221
name: MRMaid:peptide score
def: "Score in MRMaid to indicate the expected performance of the 
peptide in SRM." [PSI:PI]
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002222
name: SRM transition attribute
def: "Attribute associated with a SRM transition." [PSI:MS]
is_a: MS:1000455 ! ion selection attribute
relationship: part_of MS:1000908 ! transition

[Term]
id: MS:1002223
name: precursor ion detection probability
def: "Probability of detecting precursor when parent protein is 
present." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute

[Term]
id: MS:1002224
name: product ion detection probability
def: "Probability of detecting product ion when precursor ion is 
present." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of 
identified spectra." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of 
identified spectra." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002227
name: number of product ion observations
def: "The number of times the specific product ion has been observed in 
a series of SRM experiments." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute

[Term]
id: MS:1002228
name: number of precursor ion observations
def: "The number of times the specific precursor ion has been observed 
in a series of SRM experiments." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute

[Term]
id: MS:1002229
name: ProteomeDiscoverer:Mascot:Significance Middle
def: "Calculated relaxed significance when performing a decoy search for 
high-confidence peptides." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002230
name: ProteomeDiscoverer:Mascot:Significance High
def: "Calculated relaxed significance when performing a decoy search for 
medium-confidence peptides." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002231
name: ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})
is_a: MS:1001180 ! GUID regular expression

[Term]
id: MS:1002232
name: ProteomeDiscoverer:Default FDR calculator
def: "The default FDR calculator." [PSI:PI]
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
relationship: has_regexp MS:1002231 ! 
([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})

[Term]
id: MS:1002233
name: ProteomeDiscoverer:SEQUEST:Low resolution spectra contained
def: "Flag indicating if low-resolution speatra are taken into 
consideration." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter


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

Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.46.0_rc4 of psi-ms.obo

[pierre-alain b. <pie...@is...>]

I believe we have both following cases:
1) this ID is valid for all types of selected ions and would also be 
valid for SIM well as SRM, product ion scan and selection of ions in EI 
mode (such as in GC-MS). In SIM (in MS1 mode only) there is not a 
concept of precursor and in EI the selection is in resulting spectra, 
more rarely the molecular ion is selected.
2) this ID is specific to SRM and product ion scan and refers to a 
selected precursor that will then be further analysed (i.e. fragmented)

I thought that case 2 was the idea here and for that reason I proposed 
to change the name. But after looking at the CV, we have no term that 
would fit the MS1 only or EI modes. And in addition, if that is causing 
unnecessary bunch of changes in codes, that's not ideal.
Therefore I agree it is probably more appropriate to have a generic term 
here and adapt the def:

[Term]
id: MS:1000744
name: selected ion m/z
def: "Mass-to-charge ratio of an selected ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000040 ! m/z


Pierre-Alain


On 21.02.2013 16:58, Matt Chambers wrote:
> What is the rationale behind this change? This is going to require a pervasive "Replace All In
> Files" in pwiz and its dependent projects.
>
> -Matt
>
>
> On 2/21/2013 9:45 AM, Gerhard Mayer wrote:
>> ************ Changed name from "selected ion m/z" to "selected precursor m/z" (to make it more clear
>> for use in SRM)
>> [Term]
>> id: MS:1000744
>> name: selected precursor m/z
>> def: "Mass-to-charge ratio of the precursor ion selected for fragmentation." [PSI:MS]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000455 ! ion selection attribute
>> relationship: has_units MS:1000040 ! m/z
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
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Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.46.0_rc4 of psi-ms.obo

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

What is the rationale behind this change? This is going to require a pervasive "Replace All In 
Files" in pwiz and its dependent projects.

-Matt


On 2/21/2013 9:45 AM, Gerhard Mayer wrote:
> ************ Changed name from "selected ion m/z" to "selected precursor m/z" (to make it more clear
> for use in SRM)
> [Term]
> id: MS:1000744
> name: selected precursor m/z
> def: "Mass-to-charge ratio of the precursor ion selected for fragmentation." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000455 ! ion selection attribute
> relationship: has_units MS:1000040 ! m/z

[Psidev-ms-dev] Release candidate 3.46.0_rc4 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.46.0_rc4 of the psi-ms.obo file.

Some new terms for describing SRM transitions are added and in addition
some terms for ProteomeDiscoverer input parameters were added.


Changed CV terms in version 3.46.0_rc4 of psi-ms.obo:
=====================================================
************ 1) Changed the definition from
************    "Collision energy required to fragment an ion 
represented as a percent value." to
************    "Instrument setting, expressed in percent, for adjusting 
collisional energies of ions in an effort to provide equivalent 
excitation of all ions."
************ 2) Added the has_units relationship
[Term]
id: MS:1000138
name: normalized collision energy
def: "Instrument setting, expressed in percent, for adjusting 
collisional energies of ions in an effort to provide equivalent 
excitation of all ions." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000187 ! percent


************ Changed name from "selected ion m/z" to "selected precursor 
m/z" (to make it more clear for use in SRM)
[Term]
id: MS:1000744
name: selected precursor m/z
def: "Mass-to-charge ratio of the precursor ion selected for 
fragmentation." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000040 ! m/z


************ 1) Changed the definition from
************    "The intensity of the product ion." to
************    "The intensity of a single product ion."
************    to make clear the difference to the new term "average 
product ion intensity" (MS:1002226)
************ 2) Added the float value type
[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100

************ Renamed ProteomeDiscoverer:Minimum Peak Count --> 
ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
[Term]
id: MS:1001609
name: ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
def: "Minimum number of peaks in a tandem mass spectrum that is allowed 
to pass the filter and to be subjected to further processing in the 
workflow." [PSI:MS]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

************ Renamed ProteomeDiscoverer:Total Intensity Threshold --> 
ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
[Term]
id: MS:1001615
name: ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
def: "Used to filter out tandem mass spectra that have a total intensity 
current(sum of the intensities of all peaks in a spectrum) below the 
specified value." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter




New CV terms in version 3.46.0_rc4 of psi-ms.obo:
=================================================
[Term]
id: MS:1002218
name: percent collision energy ramp start
def: "Collision energy at the start of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! percent collision energy
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002219
name: percent collision energy ramp end
def: "Collision energy at the end of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! percent collision energy
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002220
name: MRMaid
def: "A web-based SRM assay design tool whose transitions are generated 
by mining the millions of identified peptide spectra held in the EBI's 
PRIDE database." [PSI:PI]
is_a: MS:1000871 ! SRM software

[Term]
id: MS:1002221
name: MRMaid:peptide score
def: "Score in MRMaid to indicate the expected performance of the 
peptide in SRM." [PSI:PI]
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002222
name: SRM transition attribute
def: "Attribute associated with a SRM transition." [PSI:MS]
is_a: MS:1000455 ! ion selection attribute
relationship: part_of MS:1000908 ! transition

[Term]
id: MS:1002223
name: precursor ion detection probability
def: "Probability of detecting precursor when parent protein is 
present." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute

[Term]
id: MS:1002224
name: product ion detection probability
def: "Probability of detecting product ion when precursor ion is 
present." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of 
identified spectra." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of 
identified spectra." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002227
name: number of product ion observations
def: "The number of times the specific product ion has been observed in 
a series of SRM experiments." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute

[Term]
id: MS:1002228
name: number of precursor ion observations
def: "The number of times the specific precursor ion has been observed 
in a series of SRM experiments." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute

[Term]
id: MS:1002229
name: ProteomeDiscoverer:Mascot:Significance Middle
def: "Calculated relaxed significance when performing a decoy search for 
high-confidence peptides." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002230
name: ProteomeDiscoverer:Mascot:Significance High
def: "Calculated relaxed significance when performing a decoy search for 
medium-confidence peptides." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002231
name: ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})
is_a: MS:1001180 ! GUID regular expression

[Term]
id: MS:1002232
name: ProteomeDiscoverer:Default FDR calculator
def: "The default FDR calculator." [PSI:PI]
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
relationship: has_regexp MS:1002231 ! 
([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})

[Term]
id: MS:1002233
name: ProteomeDiscoverer:SEQUEST:Low resolution spectra contained
def: "Flag indicating if low-resolution speatra are taken into 
consideration." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter


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

Re: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

[Stein, S. E. Dr. <ste...@ni...>]

Is fine with me - ss

-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...] 
Sent: Thursday, February 21, 2013 2:32 AM
To: psi...@li...
Subject: Re: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

Hi Matt, hi Steve,

What about defining the term as follows?

[Term]
id: MS:1000138
name: normalized collision energy
def: "Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000187 ! percent

Best regards,
Gerhard


Am 18.02.2013 22:51, schrieb Stein, Stephen E. Dr.:
> Hi Matt,
>
> That Thermo value is inherently 'proprietary' - it is an instrument setting without clear physical meaning. By default is it usually set to 35% for ion trap fragmentation and generally has little effect on fragmentation. It is very important (and has a different meaning) for HCD. If you want to avoid instrument specific parameters - I suggest that you leave it out.
>
> We find that two different instruments with the same Normalized CE can have quite different collision energies. Collision voltage is the proper measure of collision energy for HCD (or QTOF or QQQ) fragmentation of an ion (actual Energy depends on charge). I point out that if the charge is unknown, so is the collision energy - the voltage is always known and reported by the instrument.
>
> ss
>
>
> -----Original Message-----
> From: Matt Chambers [mailto:mat...@gm...]
> Sent: Monday, February 18, 2013 4:32 PM
> To: psi...@li...
> Subject: Re: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of 
> psi-ms.obo
>
> Hi Steve,
>
> When possible, I'd prefer staying away from vendor-specific terms (especially trademarked ones) simply because it prevents potential downstream problems with intellectual property, i.e. one vendor trying to display trademarked CV params of another vendor. Genericizing this as a concept seems straightforward. In fact, this is term 138: it seems we'd already done so a long time ago and forgotten about it, thanks for digging it up Gerhard!
>
> When I read Thermo's brochure on NCE it seems pretty clear to me that it's a function of m/z (not mass, sorry) of the ion being dissociated; what am I missing?
>
> PSB 104. Normalized Collision Energy(TM) Technology 
> https://static.thermoscientific.com/images/D13507~.pdf
>
> If the definition is bad about the gas phase, should we just ditch that part or how should it be improved?
>
> Thanks,
> -Matt
>
>
> On 2/18/2013 12:46 PM, Stein, Stephen E. Dr. wrote:
>> I am concerned with:
>> id: MS:1000138
>> name: percent collision energy
>> def: "Energy for an ion experiencing collision with a stationary gas 
>> particle resulting in dissociation of the ion in percent, normalized 
>> to the mass of the ion." [PSI:PI]
>>
>> Assuming this is for a Thermo instrument, the correct term is "Normalized Collision Energy". Thermo algorithms use this value to adjust actual energies to try to equally fragment all ions, regardless of m/z and, for HCD, charge state. Thermo seems to pick a 100% value and sets actual energies as a percent of this. Actual collision energies are the fundamental, transferrable quantities. For HCD these values are output with each spectrum.
>>
>> I suggest calling this parametert 'Normalized Collision Energy - a Thermo proprietary term. A definition might be 'Thermo-specific instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions.
>>
>> Someone from Thermo might do better.
>>
>> Sorry, gas molecules are not 'particles', nor are they 'stationary'. Nor is the energy normalized to the 'mass of the ion'.
>>
>> Steve Stein
>> -----Original Message-----
>> From: Gerhard Mayer [mailto:Ger...@ru...]
>> Sent: Monday, February 18, 2013 4:07 AM
>> To: psi...@li...;
>> psi...@li...; Mass spectrometry standard 
>> development
>> Subject: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo
>>
>> Dear proteomics community,
>>
>> attached there's the release candidate 3.46.0_rc3 of the psi-ms.obo file.
>>
>> As I notticed now, we have already a term (MS:1000138) for the 'percent collision energy'.
>> Also some new terms for describing SRM transitions are added now.
>>
>>
>> Changed CV terms in version 3.46.0_rc3 of psi-ms.obo:
>> =====================================================
>> ************ 1) Changed the definition from
>> ************    "Collision energy required to fragment an ion
>> represented as a percent value." to
>> ************    "Energy for an ion experiencing collision with a
>> stationary gas particle resulting in dissociation of the ion in 
>> percent, normalized to the mass of the ion."
>> ************ 2) Added the has_units relationship [Term]
>> id: MS:1000138
>> name: percent collision energy
>> def: "Energy for an ion experiencing collision with a stationary gas 
>> particle resulting in dissociation of the ion in percent, normalized 
>> to the mass of the ion." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000045 ! collision energy
>> relationship: has_units UO:0000187 ! percent
>>
>>
>> ************ Changed name from "selected ion m/z" to "selected 
>> peptide ion m/z" (to make it more clear for use in SRM) [Term]
>> id: MS:1000744
>> name: selected peptide ion m/z
>> def: "Mass-to-charge ratio of the ion selected for fragmentation."
>> [PSI:MS]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000455 ! ion selection attribute
>> relationship: has_units MS:1000040 ! m/z
>>
>>
>> ************ 1) Changed the definition from
>> ************    "The intensity of the product ion." to
>> ************    "The intensity of a single product ion."
>> ************    to make clear the difference to the new term "average
>> product ion intensity" (MS:1002226)
>> ************ 2) Added the float value type [Term]
>> id: MS:1001226
>> name: product ion intensity
>> def: "The intensity of a single product ion." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> synonym: "fragment ion intensity" EXACT []
>> is_a: MS:1001221 ! fragmentation information
>> relationship: has_units MS:1000131 ! number of detector counts
>> relationship: has_units MS:1000132 ! percent of base peak
>> relationship: has_units MS:1000814 ! counts per second
>> relationship: has_units MS:1000905 ! percent of base peak times 100
>>
>>
>>
>> New CV terms in version 3.46.0_rc3 of psi-ms.obo:
>> =================================================
>> [Term]
>> id: MS:1002218
>> name: percent collision energy ramp start
>> def: "Collision energy at the start of the collision energy ramp in 
>> percent, normalized to the mass of the ion." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000138 ! percent collision energy
>> relationship: has_units UO:0000187 ! percent
>>
>> [Term]
>> id: MS:1002219
>> name: percent collision energy ramp end
>> def: "Collision energy at the end of the collision energy ramp in 
>> percent, normalized to the mass of the ion." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000138 ! percent collision energy
>> relationship: has_units UO:0000187 ! percent
>>
>> [Term]
>> id: MS:1002220
>> name: MRMaid
>> def: "A web-based SRM assay design tool whose transitions are 
>> generated by mining the millions of identified peptide spectra held 
>> in the EBI's PRIDE database." [PSI:PI]
>> is_a: MS:1000871 ! SRM software
>>
>> [Term]
>> id: MS:1002221
>> name: MRMaid:peptide score
>> def: "Score in MRMaid to indicate the expected performance of the 
>> peptide in SRM." [PSI:PI]
>> is_a: MS:1001143 ! search engine specific score for peptides
>> is_a: MS:1001153 ! search engine specific score
>>
>> [Term]
>> id: MS:1002222
>> name: transition attribute
>> def: "Attribute associated with a SRM transition." [PSI:MS]
>> is_a: MS:1000547 ! object attribute
>> relationship: part_of MS:1000908 ! transition
>>
>> [Term]
>> id: MS:1002223
>> name: peptide ion probability
>> def: "Probability of detecting peptide when parent protein is present."
>> [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1002222 ! transition attribute
>>
>> [Term]
>> id: MS:1002224
>> name: product ion probability
>> def: "Probability of detecting product ion when parental peptide ion 
>> is present." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1002222 ! transition attribute
>>
>> [Term]
>> id: MS:1002225
>> name: product ion observed times
>> def: "The times the specific product ion has been observed in a 
>> series of experiments." [PSI:PI]
>> xref: value-type:xsd\:int "The allowed value-type for this CV term."
>> is_a: MS:1002222 ! transition attribute
>>
>> [Term]
>> id: MS:1002226
>> name: average product ion intensity
>> def: "Average value of product ion intensity in a collection of 
>> identified spectra." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1001226 ! product ion intensity
>>
>> [Term]
>> id: MS:1002227
>> name: product ion intensity standard deviation
>> def: "Standard deviation of product ion intensity in a collection of 
>> identified spectra." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1001226 ! product ion intensity
>>
>> Best Regards,
>> Gerhard
>>
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> development, from weekly thought leadership blogs to news, videos, 
> case studies, tutorials, tech docs, whitepapers, evaluation guides, 
> and opinion stories. Check out the most recent posts - join the 
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev


--
---
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


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Re: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Hi Matt, hi Steve,

What about defining the term as follows?

[Term]
id: MS:1000138
name: normalized collision energy
def: "Instrument setting, expressed in percent, for adjusting 
collisional energies of ions in an effort to provide equivalent 
excitation of all ions." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000187 ! percent

Best regards,
Gerhard


Am 18.02.2013 22:51, schrieb Stein, Stephen E. Dr.:
> Hi Matt,
>
> That Thermo value is inherently 'proprietary' - it is an instrument setting without clear physical meaning. By default is it usually set to 35% for ion trap fragmentation and generally has little effect on fragmentation. It is very important (and has a different meaning) for HCD. If you want to avoid instrument specific parameters - I suggest that you leave it out.
>
> We find that two different instruments with the same Normalized CE can have quite different collision energies. Collision voltage is the proper measure of collision energy for HCD (or QTOF or QQQ) fragmentation of an ion (actual Energy depends on charge). I point out that if the charge is unknown, so is the collision energy - the voltage is always known and reported by the instrument.
>
> ss
>
>
> -----Original Message-----
> From: Matt Chambers [mailto:mat...@gm...]
> Sent: Monday, February 18, 2013 4:32 PM
> To: psi...@li...
> Subject: Re: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo
>
> Hi Steve,
>
> When possible, I'd prefer staying away from vendor-specific terms (especially trademarked ones) simply because it prevents potential downstream problems with intellectual property, i.e. one vendor trying to display trademarked CV params of another vendor. Genericizing this as a concept seems straightforward. In fact, this is term 138: it seems we'd already done so a long time ago and forgotten about it, thanks for digging it up Gerhard!
>
> When I read Thermo's brochure on NCE it seems pretty clear to me that it's a function of m/z (not mass, sorry) of the ion being dissociated; what am I missing?
>
> PSB 104. Normalized Collision Energy(TM) Technology https://static.thermoscientific.com/images/D13507~.pdf
>
> If the definition is bad about the gas phase, should we just ditch that part or how should it be improved?
>
> Thanks,
> -Matt
>
>
> On 2/18/2013 12:46 PM, Stein, Stephen E. Dr. wrote:
>> I am concerned with:
>> id: MS:1000138
>> name: percent collision energy
>> def: "Energy for an ion experiencing collision with a stationary gas
>> particle resulting in dissociation of the ion in percent, normalized
>> to the mass of the ion." [PSI:PI]
>>
>> Assuming this is for a Thermo instrument, the correct term is "Normalized Collision Energy". Thermo algorithms use this value to adjust actual energies to try to equally fragment all ions, regardless of m/z and, for HCD, charge state. Thermo seems to pick a 100% value and sets actual energies as a percent of this. Actual collision energies are the fundamental, transferrable quantities. For HCD these values are output with each spectrum.
>>
>> I suggest calling this parametert 'Normalized Collision Energy - a Thermo proprietary term. A definition might be 'Thermo-specific instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions.
>>
>> Someone from Thermo might do better.
>>
>> Sorry, gas molecules are not 'particles', nor are they 'stationary'. Nor is the energy normalized to the 'mass of the ion'.
>>
>> Steve Stein
>> -----Original Message-----
>> From: Gerhard Mayer [mailto:Ger...@ru...]
>> Sent: Monday, February 18, 2013 4:07 AM
>> To: psi...@li...;
>> psi...@li...; Mass spectrometry standard
>> development
>> Subject: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo
>>
>> Dear proteomics community,
>>
>> attached there's the release candidate 3.46.0_rc3 of the psi-ms.obo file.
>>
>> As I notticed now, we have already a term (MS:1000138) for the 'percent collision energy'.
>> Also some new terms for describing SRM transitions are added now.
>>
>>
>> Changed CV terms in version 3.46.0_rc3 of psi-ms.obo:
>> =====================================================
>> ************ 1) Changed the definition from
>> ************    "Collision energy required to fragment an ion
>> represented as a percent value." to
>> ************    "Energy for an ion experiencing collision with a
>> stationary gas particle resulting in dissociation of the ion in
>> percent, normalized to the mass of the ion."
>> ************ 2) Added the has_units relationship [Term]
>> id: MS:1000138
>> name: percent collision energy
>> def: "Energy for an ion experiencing collision with a stationary gas
>> particle resulting in dissociation of the ion in percent, normalized
>> to the mass of the ion." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000045 ! collision energy
>> relationship: has_units UO:0000187 ! percent
>>
>>
>> ************ Changed name from "selected ion m/z" to "selected peptide
>> ion m/z" (to make it more clear for use in SRM) [Term]
>> id: MS:1000744
>> name: selected peptide ion m/z
>> def: "Mass-to-charge ratio of the ion selected for fragmentation."
>> [PSI:MS]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000455 ! ion selection attribute
>> relationship: has_units MS:1000040 ! m/z
>>
>>
>> ************ 1) Changed the definition from
>> ************    "The intensity of the product ion." to
>> ************    "The intensity of a single product ion."
>> ************    to make clear the difference to the new term "average
>> product ion intensity" (MS:1002226)
>> ************ 2) Added the float value type [Term]
>> id: MS:1001226
>> name: product ion intensity
>> def: "The intensity of a single product ion." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> synonym: "fragment ion intensity" EXACT []
>> is_a: MS:1001221 ! fragmentation information
>> relationship: has_units MS:1000131 ! number of detector counts
>> relationship: has_units MS:1000132 ! percent of base peak
>> relationship: has_units MS:1000814 ! counts per second
>> relationship: has_units MS:1000905 ! percent of base peak times 100
>>
>>
>>
>> New CV terms in version 3.46.0_rc3 of psi-ms.obo:
>> =================================================
>> [Term]
>> id: MS:1002218
>> name: percent collision energy ramp start
>> def: "Collision energy at the start of the collision energy ramp in
>> percent, normalized to the mass of the ion." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000138 ! percent collision energy
>> relationship: has_units UO:0000187 ! percent
>>
>> [Term]
>> id: MS:1002219
>> name: percent collision energy ramp end
>> def: "Collision energy at the end of the collision energy ramp in
>> percent, normalized to the mass of the ion." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000138 ! percent collision energy
>> relationship: has_units UO:0000187 ! percent
>>
>> [Term]
>> id: MS:1002220
>> name: MRMaid
>> def: "A web-based SRM assay design tool whose transitions are generated
>> by mining the millions of identified peptide spectra held in the EBI's
>> PRIDE database." [PSI:PI]
>> is_a: MS:1000871 ! SRM software
>>
>> [Term]
>> id: MS:1002221
>> name: MRMaid:peptide score
>> def: "Score in MRMaid to indicate the expected performance of the
>> peptide in SRM." [PSI:PI]
>> is_a: MS:1001143 ! search engine specific score for peptides
>> is_a: MS:1001153 ! search engine specific score
>>
>> [Term]
>> id: MS:1002222
>> name: transition attribute
>> def: "Attribute associated with a SRM transition." [PSI:MS]
>> is_a: MS:1000547 ! object attribute
>> relationship: part_of MS:1000908 ! transition
>>
>> [Term]
>> id: MS:1002223
>> name: peptide ion probability
>> def: "Probability of detecting peptide when parent protein is present."
>> [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1002222 ! transition attribute
>>
>> [Term]
>> id: MS:1002224
>> name: product ion probability
>> def: "Probability of detecting product ion when parental peptide ion is
>> present." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1002222 ! transition attribute
>>
>> [Term]
>> id: MS:1002225
>> name: product ion observed times
>> def: "The times the specific product ion has been observed in a series
>> of experiments." [PSI:PI]
>> xref: value-type:xsd\:int "The allowed value-type for this CV term."
>> is_a: MS:1002222 ! transition attribute
>>
>> [Term]
>> id: MS:1002226
>> name: average product ion intensity
>> def: "Average value of product ion intensity in a collection of
>> identified spectra." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1001226 ! product ion intensity
>>
>> [Term]
>> id: MS:1002227
>> name: product ion intensity standard deviation
>> def: "Standard deviation of product ion intensity in a collection of
>> identified spectra." [PSI:PI]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1001226 ! product ion intensity
>>
>> Best Regards,
>> Gerhard
>>
> ------------------------------------------------------------------------------
> The Go Parallel Website, sponsored by Intel - in partnership with Geeknet,
> is your hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials, tech docs,
> whitepapers, evaluation guides, and opinion stories. Check out the most
> recent posts - join the conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> ------------------------------------------------------------------------------
> The Go Parallel Website, sponsored by Intel - in partnership with Geeknet,
> is your hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials, tech docs,
> whitepapers, evaluation guides, and opinion stories. Check out the most
> recent posts - join the conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev


-- 
---
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
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Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] Update "Current and future support for mzML" table

[pierre-alain b. <pie...@is...>]

HI Steffen,
The page is updated, thanks for the info.
Haven't changed the table for now. But would be nice to add a bit more 
info as sou suggest.

Pierre-Alain


On 19.02.2013 16:34, Steffen Neumann wrote:
> Hi,
>
> Now that the psidev.info website has been transitioned,
> I'd propose to add more software to
> http://www.psidev.info/mzML (scroll down to the end)
> and possibly make this table a bit more prominent.
>
> I also suggest to distinguish between end-user software
> and frameworks / toolkits / parsers targeting developers.
>
> >From my side I'd offer the two entries below.
>
> This request comes out of the COSMOS initiative,
> where we try to increase the adoption of mzML
> in the metabolomics area, specifically for GC-MS.
>
> Yours,
> Steffen
>
> -------------------------------------------------------------------
>
> mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
> http://bioconductor.org/packages/release/bioc/html/mzR.html
>
> "mzR provides a unified API to the common file formats and parsers
> available for mass spectrometry data. It comes with a wrapper for the
> ISB random access parser for mass spectrometry mzXML, mzData and mzML
> files. The package contains the original code written by the ISB, and a
> subset of the proteowizard library for mzML. The netCDF reading code has
> previously been used in XCMS."
>
> Authors: Bernd Fischer, Steffen Neumann, Laurent Gatto
>
> -------------------------------------------------------------------
>
> pymzML: an interface between Python and mzML Mass spectrometry Files
> https://github.com/pymzml/pymzML
>
> "Python module to interface mzML data in Python based on cElementTree
> with additional tools for MS-informatics."
>
> Authors: T. Bald, J. Barth, A. Niehues, M. Specht, M. Hippler, C. Fufezan
>
> -------------------------------------------------------------------
>
>

[Psidev-ms-dev] Update "Current and future support for mzML" table

[Steffen N. <sne...@ip...>]

Hi,

Now that the psidev.info website has been transitioned, 
I'd propose to add more software to
http://www.psidev.info/mzML (scroll down to the end)
and possibly make this table a bit more prominent.

I also suggest to distinguish between end-user software 
and frameworks / toolkits / parsers targeting developers.

>From my side I'd offer the two entries below.

This request comes out of the COSMOS initiative, 
where we try to increase the adoption of mzML 
in the metabolomics area, specifically for GC-MS.

Yours,
Steffen

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

mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
http://bioconductor.org/packages/release/bioc/html/mzR.html

"mzR provides a unified API to the common file formats and parsers
available for mass spectrometry data. It comes with a wrapper for the
ISB random access parser for mass spectrometry mzXML, mzData and mzML
files. The package contains the original code written by the ISB, and a
subset of the proteowizard library for mzML. The netCDF reading code has
previously been used in XCMS."

Authors: Bernd Fischer, Steffen Neumann, Laurent Gatto 

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

pymzML: an interface between Python and mzML Mass spectrometry Files
https://github.com/pymzml/pymzML

"Python module to interface mzML data in Python based on cElementTree
with additional tools for MS-informatics."

Authors: T. Bald, J. Barth, A. Niehues, M. Specht, M. Hippler, C. Fufezan

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


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

[Stein, S. E. Dr. <ste...@ni...>]

Hi Matt,

That Thermo value is inherently 'proprietary' - it is an instrument setting without clear physical meaning. By default is it usually set to 35% for ion trap fragmentation and generally has little effect on fragmentation. It is very important (and has a different meaning) for HCD. If you want to avoid instrument specific parameters - I suggest that you leave it out.

We find that two different instruments with the same Normalized CE can have quite different collision energies. Collision voltage is the proper measure of collision energy for HCD (or QTOF or QQQ) fragmentation of an ion (actual Energy depends on charge). I point out that if the charge is unknown, so is the collision energy - the voltage is always known and reported by the instrument.

ss


-----Original Message-----
From: Matt Chambers [mailto:mat...@gm...] 
Sent: Monday, February 18, 2013 4:32 PM
To: psi...@li...
Subject: Re: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

Hi Steve,

When possible, I'd prefer staying away from vendor-specific terms (especially trademarked ones) simply because it prevents potential downstream problems with intellectual property, i.e. one vendor trying to display trademarked CV params of another vendor. Genericizing this as a concept seems straightforward. In fact, this is term 138: it seems we'd already done so a long time ago and forgotten about it, thanks for digging it up Gerhard!

When I read Thermo's brochure on NCE it seems pretty clear to me that it's a function of m/z (not mass, sorry) of the ion being dissociated; what am I missing?

PSB 104. Normalized Collision Energy(TM) Technology https://static.thermoscientific.com/images/D13507~.pdf

If the definition is bad about the gas phase, should we just ditch that part or how should it be improved?

Thanks,
-Matt


On 2/18/2013 12:46 PM, Stein, Stephen E. Dr. wrote:
> I am concerned with:
> id: MS:1000138
> name: percent collision energy
> def: "Energy for an ion experiencing collision with a stationary gas 
> particle resulting in dissociation of the ion in percent, normalized 
> to the mass of the ion." [PSI:PI]
>
> Assuming this is for a Thermo instrument, the correct term is "Normalized Collision Energy". Thermo algorithms use this value to adjust actual energies to try to equally fragment all ions, regardless of m/z and, for HCD, charge state. Thermo seems to pick a 100% value and sets actual energies as a percent of this. Actual collision energies are the fundamental, transferrable quantities. For HCD these values are output with each spectrum.
>
> I suggest calling this parametert 'Normalized Collision Energy - a Thermo proprietary term. A definition might be 'Thermo-specific instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions.
>
> Someone from Thermo might do better.
>
> Sorry, gas molecules are not 'particles', nor are they 'stationary'. Nor is the energy normalized to the 'mass of the ion'.
>
> Steve Stein
> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Monday, February 18, 2013 4:07 AM
> To: psi...@li...; 
> psi...@li...; Mass spectrometry standard 
> development
> Subject: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo
>
> Dear proteomics community,
>
> attached there's the release candidate 3.46.0_rc3 of the psi-ms.obo file.
>
> As I notticed now, we have already a term (MS:1000138) for the 'percent collision energy'.
> Also some new terms for describing SRM transitions are added now.
>
>
> Changed CV terms in version 3.46.0_rc3 of psi-ms.obo:
> =====================================================
> ************ 1) Changed the definition from
> ************    "Collision energy required to fragment an ion
> represented as a percent value." to
> ************    "Energy for an ion experiencing collision with a
> stationary gas particle resulting in dissociation of the ion in 
> percent, normalized to the mass of the ion."
> ************ 2) Added the has_units relationship [Term]
> id: MS:1000138
> name: percent collision energy
> def: "Energy for an ion experiencing collision with a stationary gas 
> particle resulting in dissociation of the ion in percent, normalized 
> to the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000045 ! collision energy
> relationship: has_units UO:0000187 ! percent
>
>
> ************ Changed name from "selected ion m/z" to "selected peptide 
> ion m/z" (to make it more clear for use in SRM) [Term]
> id: MS:1000744
> name: selected peptide ion m/z
> def: "Mass-to-charge ratio of the ion selected for fragmentation." 
> [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000455 ! ion selection attribute
> relationship: has_units MS:1000040 ! m/z
>
>
> ************ 1) Changed the definition from
> ************    "The intensity of the product ion." to
> ************    "The intensity of a single product ion."
> ************    to make clear the difference to the new term "average
> product ion intensity" (MS:1002226)
> ************ 2) Added the float value type [Term]
> id: MS:1001226
> name: product ion intensity
> def: "The intensity of a single product ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> synonym: "fragment ion intensity" EXACT []
> is_a: MS:1001221 ! fragmentation information
> relationship: has_units MS:1000131 ! number of detector counts
> relationship: has_units MS:1000132 ! percent of base peak
> relationship: has_units MS:1000814 ! counts per second
> relationship: has_units MS:1000905 ! percent of base peak times 100
>
>
>
> New CV terms in version 3.46.0_rc3 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1002218
> name: percent collision energy ramp start
> def: "Collision energy at the start of the collision energy ramp in
> percent, normalized to the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000138 ! percent collision energy
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002219
> name: percent collision energy ramp end
> def: "Collision energy at the end of the collision energy ramp in
> percent, normalized to the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000138 ! percent collision energy
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002220
> name: MRMaid
> def: "A web-based SRM assay design tool whose transitions are generated
> by mining the millions of identified peptide spectra held in the EBI's
> PRIDE database." [PSI:PI]
> is_a: MS:1000871 ! SRM software
>
> [Term]
> id: MS:1002221
> name: MRMaid:peptide score
> def: "Score in MRMaid to indicate the expected performance of the
> peptide in SRM." [PSI:PI]
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1002222
> name: transition attribute
> def: "Attribute associated with a SRM transition." [PSI:MS]
> is_a: MS:1000547 ! object attribute
> relationship: part_of MS:1000908 ! transition
>
> [Term]
> id: MS:1002223
> name: peptide ion probability
> def: "Probability of detecting peptide when parent protein is present."
> [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002222 ! transition attribute
>
> [Term]
> id: MS:1002224
> name: product ion probability
> def: "Probability of detecting product ion when parental peptide ion is
> present." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002222 ! transition attribute
>
> [Term]
> id: MS:1002225
> name: product ion observed times
> def: "The times the specific product ion has been observed in a series
> of experiments." [PSI:PI]
> xref: value-type:xsd\:int "The allowed value-type for this CV term."
> is_a: MS:1002222 ! transition attribute
>
> [Term]
> id: MS:1002226
> name: average product ion intensity
> def: "Average value of product ion intensity in a collection of
> identified spectra." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001226 ! product ion intensity
>
> [Term]
> id: MS:1002227
> name: product ion intensity standard deviation
> def: "Standard deviation of product ion intensity in a collection of
> identified spectra." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001226 ! product ion intensity
>
> Best Regards,
> Gerhard
>

------------------------------------------------------------------------------
The Go Parallel Website, sponsored by Intel - in partnership with Geeknet, 
is your hub for all things parallel software development, from weekly thought 
leadership blogs to news, videos, case studies, tutorials, tech docs, 
whitepapers, evaluation guides, and opinion stories. Check out the most 
recent posts - join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

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

Hi Steve,

When possible, I'd prefer staying away from vendor-specific terms (especially trademarked ones) 
simply because it prevents potential downstream problems with intellectual property, i.e. one vendor 
trying to display trademarked CV params of another vendor. Genericizing this as a concept seems 
straightforward. In fact, this is term 138: it seems we'd already done so a long time ago and 
forgotten about it, thanks for digging it up Gerhard!

When I read Thermo's brochure on NCE it seems pretty clear to me that it's a function of m/z (not 
mass, sorry) of the ion being dissociated; what am I missing?

PSB 104. Normalized Collision Energy(TM) Technology
https://static.thermoscientific.com/images/D13507~.pdf

If the definition is bad about the gas phase, should we just ditch that part or how should it be 
improved?

Thanks,
-Matt


On 2/18/2013 12:46 PM, Stein, Stephen E. Dr. wrote:
> I am concerned with:
> id: MS:1000138
> name: percent collision energy
> def: "Energy for an ion experiencing collision with a stationary gas
> particle resulting in dissociation of the ion in percent, normalized to
> the mass of the ion." [PSI:PI]
>
> Assuming this is for a Thermo instrument, the correct term is "Normalized Collision Energy". Thermo algorithms use this value to adjust actual energies to try to equally fragment all ions, regardless of m/z and, for HCD, charge state. Thermo seems to pick a 100% value and sets actual energies as a percent of this. Actual collision energies are the fundamental, transferrable quantities. For HCD these values are output with each spectrum.
>
> I suggest calling this parametert 'Normalized Collision Energy - a Thermo proprietary term. A definition might be 'Thermo-specific instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions.
>
> Someone from Thermo might do better.
>
> Sorry, gas molecules are not 'particles', nor are they 'stationary'. Nor is the energy normalized to the 'mass of the ion'.
>
> Steve Stein
> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Monday, February 18, 2013 4:07 AM
> To: psi...@li...; psi...@li...; Mass spectrometry standard development
> Subject: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo
>
> Dear proteomics community,
>
> attached there's the release candidate 3.46.0_rc3 of the psi-ms.obo file.
>
> As I notticed now, we have already a term (MS:1000138) for the 'percent collision energy'.
> Also some new terms for describing SRM transitions are added now.
>
>
> Changed CV terms in version 3.46.0_rc3 of psi-ms.obo:
> =====================================================
> ************ 1) Changed the definition from
> ************    "Collision energy required to fragment an ion
> represented as a percent value." to
> ************    "Energy for an ion experiencing collision with a
> stationary gas particle resulting in dissociation of the ion in percent,
> normalized to the mass of the ion."
> ************ 2) Added the has_units relationship
> [Term]
> id: MS:1000138
> name: percent collision energy
> def: "Energy for an ion experiencing collision with a stationary gas
> particle resulting in dissociation of the ion in percent, normalized to
> the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000045 ! collision energy
> relationship: has_units UO:0000187 ! percent
>
>
> ************ Changed name from "selected ion m/z" to "selected peptide
> ion m/z" (to make it more clear for use in SRM)
> [Term]
> id: MS:1000744
> name: selected peptide ion m/z
> def: "Mass-to-charge ratio of the ion selected for fragmentation." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000455 ! ion selection attribute
> relationship: has_units MS:1000040 ! m/z
>
>
> ************ 1) Changed the definition from
> ************    "The intensity of the product ion." to
> ************    "The intensity of a single product ion."
> ************    to make clear the difference to the new term "average
> product ion intensity" (MS:1002226)
> ************ 2) Added the float value type
> [Term]
> id: MS:1001226
> name: product ion intensity
> def: "The intensity of a single product ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> synonym: "fragment ion intensity" EXACT []
> is_a: MS:1001221 ! fragmentation information
> relationship: has_units MS:1000131 ! number of detector counts
> relationship: has_units MS:1000132 ! percent of base peak
> relationship: has_units MS:1000814 ! counts per second
> relationship: has_units MS:1000905 ! percent of base peak times 100
>
>
>
> New CV terms in version 3.46.0_rc3 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1002218
> name: percent collision energy ramp start
> def: "Collision energy at the start of the collision energy ramp in
> percent, normalized to the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000138 ! percent collision energy
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002219
> name: percent collision energy ramp end
> def: "Collision energy at the end of the collision energy ramp in
> percent, normalized to the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000138 ! percent collision energy
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002220
> name: MRMaid
> def: "A web-based SRM assay design tool whose transitions are generated
> by mining the millions of identified peptide spectra held in the EBI's
> PRIDE database." [PSI:PI]
> is_a: MS:1000871 ! SRM software
>
> [Term]
> id: MS:1002221
> name: MRMaid:peptide score
> def: "Score in MRMaid to indicate the expected performance of the
> peptide in SRM." [PSI:PI]
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1002222
> name: transition attribute
> def: "Attribute associated with a SRM transition." [PSI:MS]
> is_a: MS:1000547 ! object attribute
> relationship: part_of MS:1000908 ! transition
>
> [Term]
> id: MS:1002223
> name: peptide ion probability
> def: "Probability of detecting peptide when parent protein is present."
> [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002222 ! transition attribute
>
> [Term]
> id: MS:1002224
> name: product ion probability
> def: "Probability of detecting product ion when parental peptide ion is
> present." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002222 ! transition attribute
>
> [Term]
> id: MS:1002225
> name: product ion observed times
> def: "The times the specific product ion has been observed in a series
> of experiments." [PSI:PI]
> xref: value-type:xsd\:int "The allowed value-type for this CV term."
> is_a: MS:1002222 ! transition attribute
>
> [Term]
> id: MS:1002226
> name: average product ion intensity
> def: "Average value of product ion intensity in a collection of
> identified spectra." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001226 ! product ion intensity
>
> [Term]
> id: MS:1002227
> name: product ion intensity standard deviation
> def: "Standard deviation of product ion intensity in a collection of
> identified spectra." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001226 ! product ion intensity
>
> Best Regards,
> Gerhard
>

Re: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

[Stein, S. E. Dr. <ste...@ni...>]

I am concerned with:
id: MS:1000138
name: percent collision energy
def: "Energy for an ion experiencing collision with a stationary gas 
particle resulting in dissociation of the ion in percent, normalized to 
the mass of the ion." [PSI:PI]

Assuming this is for a Thermo instrument, the correct term is "Normalized Collision Energy". Thermo algorithms use this value to adjust actual energies to try to equally fragment all ions, regardless of m/z and, for HCD, charge state. Thermo seems to pick a 100% value and sets actual energies as a percent of this. Actual collision energies are the fundamental, transferrable quantities. For HCD these values are output with each spectrum. 

I suggest calling this parametert 'Normalized Collision Energy - a Thermo proprietary term. A definition might be 'Thermo-specific instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions.

Someone from Thermo might do better.

Sorry, gas molecules are not 'particles', nor are they 'stationary'. Nor is the energy normalized to the 'mass of the ion'.

Steve Stein
-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...] 
Sent: Monday, February 18, 2013 4:07 AM
To: psi...@li...; psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

Dear proteomics community,

attached there's the release candidate 3.46.0_rc3 of the psi-ms.obo file.

As I notticed now, we have already a term (MS:1000138) for the 'percent collision energy'.
Also some new terms for describing SRM transitions are added now.


Changed CV terms in version 3.46.0_rc3 of psi-ms.obo:
=====================================================
************ 1) Changed the definition from
************    "Collision energy required to fragment an ion 
represented as a percent value." to
************    "Energy for an ion experiencing collision with a 
stationary gas particle resulting in dissociation of the ion in percent, 
normalized to the mass of the ion."
************ 2) Added the has_units relationship
[Term]
id: MS:1000138
name: percent collision energy
def: "Energy for an ion experiencing collision with a stationary gas 
particle resulting in dissociation of the ion in percent, normalized to 
the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000045 ! collision energy
relationship: has_units UO:0000187 ! percent


************ Changed name from "selected ion m/z" to "selected peptide 
ion m/z" (to make it more clear for use in SRM)
[Term]
id: MS:1000744
name: selected peptide ion m/z
def: "Mass-to-charge ratio of the ion selected for fragmentation." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000040 ! m/z


************ 1) Changed the definition from
************    "The intensity of the product ion." to
************    "The intensity of a single product ion."
************    to make clear the difference to the new term "average 
product ion intensity" (MS:1002226)
************ 2) Added the float value type
[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100



New CV terms in version 3.46.0_rc3 of psi-ms.obo:
=================================================
[Term]
id: MS:1002218
name: percent collision energy ramp start
def: "Collision energy at the start of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! percent collision energy
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002219
name: percent collision energy ramp end
def: "Collision energy at the end of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! percent collision energy
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002220
name: MRMaid
def: "A web-based SRM assay design tool whose transitions are generated 
by mining the millions of identified peptide spectra held in the EBI's 
PRIDE database." [PSI:PI]
is_a: MS:1000871 ! SRM software

[Term]
id: MS:1002221
name: MRMaid:peptide score
def: "Score in MRMaid to indicate the expected performance of the 
peptide in SRM." [PSI:PI]
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002222
name: transition attribute
def: "Attribute associated with a SRM transition." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000908 ! transition

[Term]
id: MS:1002223
name: peptide ion probability
def: "Probability of detecting peptide when parent protein is present." 
[PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! transition attribute

[Term]
id: MS:1002224
name: product ion probability
def: "Probability of detecting product ion when parental peptide ion is 
present." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! transition attribute

[Term]
id: MS:1002225
name: product ion observed times
def: "The times the specific product ion has been observed in a series 
of experiments." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002222 ! transition attribute

[Term]
id: MS:1002226
name: average product ion intensity
def: "Average value of product ion intensity in a collection of 
identified spectra." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002227
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of 
identified spectra." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001226 ! product ion intensity

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
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

Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

[pierre-alain b. <pie...@is...>]

Thanks Gerhard,
with a few comments below
Cheers,
Pierre-Alain

On 18.02.2013 10:07, Gerhard Mayer wrote:
> Dear proteomics community,
>
> attached there's the release candidate 3.46.0_rc3 of the psi-ms.obo file.
>
> As I notticed now, we have already a term (MS:1000138) for the 
> 'percent collision energy'.
> Also some new terms for describing SRM transitions are added now.
>
>
> Changed CV terms in version 3.46.0_rc3 of psi-ms.obo:
> =====================================================
> ************ 1) Changed the definition from
> ************    "Collision energy required to fragment an ion 
> represented as a percent value." to
> ************    "Energy for an ion experiencing collision with a 
> stationary gas particle resulting in dissociation of the ion in 
> percent, normalized to the mass of the ion."
> ************ 2) Added the has_units relationship
> [Term]
> id: MS:1000138
> name: percent collision energy
> def: "Energy for an ion experiencing collision with a stationary gas 
> particle resulting in dissociation of the ion in percent, normalized 
> to the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000045 ! collision energy
> relationship: has_units UO:0000187 ! percent
>
>
> ************ Changed name from "selected ion m/z" to "selected peptide 
> ion m/z" (to make it more clear for use in SRM)
> [Term]
> id: MS:1000744
> name: selected peptide ion m/z
> def: "Mass-to-charge ratio of the ion selected for fragmentation." 
> [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000455 ! ion selection attribute
> relationship: has_units MS:1000040 ! m/z
>
Don't like this. Too restrictive for peptides. SRM can be used for other 
molecules as well.
Better use "selected precursor m/z"


>
> ************ 1) Changed the definition from
> ************    "The intensity of the product ion." to
> ************    "The intensity of a single product ion."
> ************    to make clear the difference to the new term "average 
> product ion intensity" (MS:1002226)
> ************ 2) Added the float value type
> [Term]
> id: MS:1001226
> name: product ion intensity
> def: "The intensity of a single product ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> synonym: "fragment ion intensity" EXACT []
> is_a: MS:1001221 ! fragmentation information
> relationship: has_units MS:1000131 ! number of detector counts
> relationship: has_units MS:1000132 ! percent of base peak
> relationship: has_units MS:1000814 ! counts per second
> relationship: has_units MS:1000905 ! percent of base peak times 100
>
>
>
> New CV terms in version 3.46.0_rc3 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1002218
> name: percent collision energy ramp start
> def: "Collision energy at the start of the collision energy ramp in 
> percent, normalized to the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000138 ! percent collision energy
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002219
> name: percent collision energy ramp end
> def: "Collision energy at the end of the collision energy ramp in 
> percent, normalized to the mass of the ion." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000138 ! percent collision energy
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002220
> name: MRMaid
> def: "A web-based SRM assay design tool whose transitions are 
> generated by mining the millions of identified peptide spectra held in 
> the EBI's PRIDE database." [PSI:PI]
> is_a: MS:1000871 ! SRM software
>
> [Term]
> id: MS:1002221
> name: MRMaid:peptide score
> def: "Score in MRMaid to indicate the expected performance of the 
> peptide in SRM." [PSI:PI]
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1002222
> name: transition attribute
> def: "Attribute associated with a SRM transition." [PSI:MS]
> is_a: MS:1000547 ! object attribute
> relationship: part_of MS:1000908 ! transition

Why not "SRM transition attribute"?

>
> [Term]
> id: MS:1002223
> name: peptide ion probability
> def: "Probability of detecting peptide when parent protein is 
> present." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002222 ! transition attribute
Would prefer "Peptide ion detection probability"
peptide ion probability does not mean anything clear and specific to me

>
> [Term]
> id: MS:1002224
> name: product ion probability
> def: "Probability of detecting product ion when parental peptide ion 
> is present." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002222 ! transition attribute
>
Would prefer
name: product ion detection probability
def: "Probability of detecting product ion when precursor ion is 
present." [PSI:PI]
product ion probability does not mean anything specific to me. In 
addition, this is also valid for non-peptide product ion and would fit 
metabolomic use. If you want to be more specific to peptide, use another 
term such as peptide product ion detection probability.

> [Term]
> id: MS:1002225
> name: product ion observed times
> def: "The times the specific product ion has been observed in a series 
> of experiments." [PSI:PI]
> xref: value-type:xsd\:int "The allowed value-type for this CV term."
> is_a: MS:1002222 ! transition attribute
What does this mean here? number of times, retention/elution time(s) Not 
clear to me.
>
> [Term]
> id: MS:1002226
> name: average product ion intensity
> def: "Average value of product ion intensity in a collection of 
> identified spectra." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001226 ! product ion intensity
>
> [Term]
> id: MS:1002227
> name: product ion intensity standard deviation
> def: "Standard deviation of product ion intensity in a collection of 
> identified spectra." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001226 ! product ion intensity
>
> Best Regards,
> Gerhard
>
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

[Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.46.0_rc3 of the psi-ms.obo file.

As I notticed now, we have already a term (MS:1000138) for the 'percent 
collision energy'.
Also some new terms for describing SRM transitions are added now.


Changed CV terms in version 3.46.0_rc3 of psi-ms.obo:
=====================================================
************ 1) Changed the definition from
************    "Collision energy required to fragment an ion 
represented as a percent value." to
************    "Energy for an ion experiencing collision with a 
stationary gas particle resulting in dissociation of the ion in percent, 
normalized to the mass of the ion."
************ 2) Added the has_units relationship
[Term]
id: MS:1000138
name: percent collision energy
def: "Energy for an ion experiencing collision with a stationary gas 
particle resulting in dissociation of the ion in percent, normalized to 
the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000045 ! collision energy
relationship: has_units UO:0000187 ! percent


************ Changed name from "selected ion m/z" to "selected peptide 
ion m/z" (to make it more clear for use in SRM)
[Term]
id: MS:1000744
name: selected peptide ion m/z
def: "Mass-to-charge ratio of the ion selected for fragmentation." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000040 ! m/z


************ 1) Changed the definition from
************    "The intensity of the product ion." to
************    "The intensity of a single product ion."
************    to make clear the difference to the new term "average 
product ion intensity" (MS:1002226)
************ 2) Added the float value type
[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100



New CV terms in version 3.46.0_rc3 of psi-ms.obo:
=================================================
[Term]
id: MS:1002218
name: percent collision energy ramp start
def: "Collision energy at the start of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! percent collision energy
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002219
name: percent collision energy ramp end
def: "Collision energy at the end of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! percent collision energy
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002220
name: MRMaid
def: "A web-based SRM assay design tool whose transitions are generated 
by mining the millions of identified peptide spectra held in the EBI's 
PRIDE database." [PSI:PI]
is_a: MS:1000871 ! SRM software

[Term]
id: MS:1002221
name: MRMaid:peptide score
def: "Score in MRMaid to indicate the expected performance of the 
peptide in SRM." [PSI:PI]
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002222
name: transition attribute
def: "Attribute associated with a SRM transition." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000908 ! transition

[Term]
id: MS:1002223
name: peptide ion probability
def: "Probability of detecting peptide when parent protein is present." 
[PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! transition attribute

[Term]
id: MS:1002224
name: product ion probability
def: "Probability of detecting product ion when parental peptide ion is 
present." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! transition attribute

[Term]
id: MS:1002225
name: product ion observed times
def: "The times the specific product ion has been observed in a series 
of experiments." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002222 ! transition attribute

[Term]
id: MS:1002226
name: average product ion intensity
def: "Average value of product ion intensity in a collection of 
identified spectra." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002227
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of 
identified spectra." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001226 ! product ion intensity

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
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

Re: [Psidev-ms-dev] Release candidate 3.46.0_rc2 of psi-ms.obo

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

Hi Gerhard,

Looks good. We'll let the "normalized" part in the name be implied since it's a percentage. But in 
the definition, maybe something like:
"The energy for an ion experiencing collision with a stationary gas particle resulting in
  dissociation of the ion in percent, normalized to the mass of the ion."

I'm also thinking that the term could derive from collision energy so that people that use the new 
term might still work with older parsers (if by chance they are looking for the term or children of 
the term collision energy instead of only the term itself).

Thanks,
-Matt


On 2/13/2013 10:21 AM, Gerhard Mayer wrote:
> Dear proteomics community,
>
> attached there's the release candidate 3.46.0_rc2 of the psi-ms.obo file.
> It contains new terms for the collision energy given as percentage values.
>
> Changed CV terms in version 3.46.0_rc2 of psi-ms.obo:
> =====================================================
> ************
>
> New CV terms in version 3.46.0_rc2 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1002218
> name: collision energy percentage
> def: "Energy for an ion experiencing collision with a stationary gas particle resulting in
> dissociation of the ion in percent." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000510 ! precursor activation attribute
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002219
> name: collision energy ramp start percentage
> def: "Collision energy at the start of the collision energy ramp in percent." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002218 ! collision energy percentage
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002220
> name: collision energy ramp end percentage
> def: "Collision energy at the end of the collision energy ramp in percent." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002218 ! collision energy percentage
> relationship: has_units UO:0000187 ! percent
>
> [Term]
> id: MS:1002221
> name: MRMaid
> def: "A web-based SRM assay design tool whose transitions are generated by mining the millions of
> identified peptide spectra held in the EBI's PRIDE database." [PSI:PI]
> is_a: MS:1000871 ! SRM software
>
>
> Best Regards,
> Gerhard
>
>
>
> ------------------------------------------------------------------------------
> Free Next-Gen Firewall Hardware Offer
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> and get the hardware for free! Learn more.
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>

[Psidev-ms-dev] Release candidate 3.46.0_rc2 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.46.0_rc2 of the psi-ms.obo file.
It contains new terms for the collision energy given as percentage values.

Changed CV terms in version 3.46.0_rc2 of psi-ms.obo:
=====================================================
************

New CV terms in version 3.46.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002218
name: collision energy percentage
def: "Energy for an ion experiencing collision with a stationary gas 
particle resulting in dissociation of the ion in percent." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002219
name: collision energy ramp start percentage
def: "Collision energy at the start of the collision energy ramp in 
percent." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002218 ! collision energy percentage
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002220
name: collision energy ramp end percentage
def: "Collision energy at the end of the collision energy ramp in 
percent." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002218 ! collision energy percentage
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002221
name: MRMaid
def: "A web-based SRM assay design tool whose transitions are generated 
by mining the millions of identified peptide spectra held in the EBI's 
PRIDE database." [PSI:PI]
is_a: MS:1000871 ! SRM software


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
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

Re: [Psidev-ms-dev] Permission to translate your page at http://www.psidev.info/

[Vera D. <ver...@we...>]

*Dear Sir,

A week ago, I have inquired for your permission to translate your web page.
Since I still haven't  got an answer, I would like to emphasize that your
article would be of a great aid to my intention to connect people from
former Yugoslavian countries.

I believe that it offers just the right kind of information for achieving
that goal. Therefore, it would be very kind of you to consider my proposal
and review it.


Yours faithfully,
Vera*

On Wed, Jan 30, 2013 at 5:50 PM, Vera Djuraskovic <
ver...@we...> wrote:

>
> Dear Sir,
>
> I am writing to inquire regarding your web page about mzIdentML where I
> have found a lot of useful information. My name is Vera and I'm currently
> studying at the Faculty of Computer Science in Belgrade.
> Here is the URL of your article: http://www.psidev.info/groups/**
> massspectrometry/tagged?page=1<http://www.psidev.info/groups/massspectrometry/tagged?page=1>
>
> I would like to share it with the people from Former Yugoslav Republics:
> Serbia, Montenegro, Croatia, Slovenia, Macedonia, Bosnia and Herzegovina.
>
> I would be grateful if you could allow me to translate your writing into
> Serbo-Croatian language, that is used in all Former Yugoslav Republics and
> to post it on my website. Hopefully, it will help our people to gather some
> additional knowledge about computing.
>
> I hope to hear from you soon.
>
> Regards,
> Vera Djuraskovic
> veradjuraskovic@**webhostinggeeks.com<ver...@we...>
> http://science.**webhostinggeeks.com/<http://science.webhostinggeeks.com/>
> Tel: +381 64 2107060
>
>
>


-- 

Vera Djuraskovic
ver...@we...
http://science.webhostinggeeks.com/
Tel: +381 64 210 70 60

[Psidev-ms-dev] Still time to participate in the ABRF iPRG study

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

Hi everyone, I just wanted to announce that there is still time to
participate in this year’s ABRF iPRG study. This year we are analyzing a
dataset with paired RNA-seq and proteomics LC-MS/MS data, a workflow that
will surely become more common. Learn from and contribute to this year’s
study.



More information is available at:



http://www.abrf.org/index.cfm/group.show/proteomicsinformaticsresearchgroup.53.htm



http://www.abrf.org/ResearchGroups/ProteomicsInformaticsResearchGroup/Studies/iprg2013_study_participation_final.pdf



Regards,

Eric

[Psidev-ms-dev] Annual PSI workshop registration is open

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

Hi everyone, I am pleased to announce that registration for the annual
Proteomics Standards Initiative (PSI) workshop is now open. This year it
will be held April 15-17 in Liverpool, UK at the University of Liverpool
and is locally organized by Andy Jones.



We welcome back participants from previous years, but also highly encourage
new participation. Come learn about PSI projects and then lend a hand with
the many tasks and discussions that we need to have to further our goals of
open data exchange. The workshop features very few traditional talks, but
rather open discussions and hands-on resolution of open issues.



Some of the issues that will be addressed in parallel sessions at the
workshop:

Molecular Interactions:

- PSICQUIC & PSICQUIC-view (PSI Common Query User Interface)

- PSI-MI 2.5 (Molecular Interactions format)

- JAMI (Java Molecular Interactions common framework)

Mass spectrometry:

- DIA (Data Independent Acquisition) support

- Data compression for the formats

Proteomics Informatics:

- Protein Grouping in mzIdentML

- PTM scoring representation in mzIdentML

- SRM Support in mzQuantML



Workshop registration is free! Registration forms, hotel and travel
information is available at:

http://www.psidev.info/



Register today! We look forward to seeing you in Liverpool!



Please forward this message to any persons or lists that would benefit from
this announcement.



Regards,

Eric

Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD

[Dmitrii T. <Dmi...@ni...>]

Matt,

1. Why HCD is important

For a given precursor ion, HCD seems to be the closest measure of the
precursor ion excitation energy.  That is, ms/ms spectrum is a *function* of
HCD. In other words, MS/MS spectrum of an ion for the same HCD energy is
reproducible.
HCD energy, from my experience in analyzing HCD MS/MS spectra (if I am not
mistaken), is a kind of voltage. Hence it does not depend on the
software-determined precursor ion charge.

On the other hand, for the same NCD, the excitation energy put into the
precursor seems to be varying with the charge assigned by Xcalibur to the
precursor ion. This assigned charge may vary because of software errors; it
may differ from the real charge of the precursor. Therefore, one may observe
noticeable variability of the MS/MS spectrum of a precursor ion for the same
NCD value.

2. IMO, so far HCD energy is Thermo-specific. However, I am not very sure.
As to me, HCD may be output in a separate field in mzML and mzXML format. It
would also be nice to output it into MFG format upon request.

3. My previous e-mail

From: dmi...@gm...
To: spc...@go...
Subject: msconvert: missing HCD energy (eV) in RAW (Thermo) to mzML/mzXML
conversion
Timestamp: 12/18/2012 12:17 PM

Hello,
I would like to report a problem with msconvert.

Brief description
============

msconvert does not extract HCD energy from Thermo RAW files.

Background
==========
HCD energy is *almost* always present in RAW file HCD ms/ms spectra. NCD
"energy" is *always* present in HCD ms/ms spectra. That is, two energies
(NCD and HCD) may be present in a HCD ms/ms spectrum. These two energy
values are usually different. The units of HCD activation energy, according
to RAW file contents, are eV. The units of NCD energy are percent (%).

To derive HCD from NCD, one seems to need the charge used by the instrument
software and m/z of the isolation range center. The actual formulas are
unknown to me. It is also unknown to me if these formulas are the same for,
for example, Orbitrap Velos and Q-Exactive.

I have no information about contents of RAW files with mass spectra
measured on Thermo Exactive (without Q), which may use HCD.


Problems
========
1. HCD energy is not read by msconvert from Thermo RAW files.
2. HCD energy is not output into mzXML or mzML files by msconvert.
3. The fact that the activation method name in mzML file is

<cvParam cvRef="MS" accession="MS:1000422" name="*high-energy
collision-induced dissociation*" value=""/>

is accompanied by NCD value (not HCD value) in erroneous units,
electronvolt,

<cvParam cvRef="MS" accession="MS:1000045" name="*collision energy*" value="
*28.0*" unitCvRef="UO" unitAccession="UO:0000266" unitName="*electronvolt*
"/>

is unfortunate.


How to read HCD energy from a RAW file
===============================
>From my limited experience, there are two methods, usually only one works.

1. In Q-Exactive, Trailer Extra string named  "HCD Energy eV:" may contain
a string like this
"24.243"

2. In Orbitrap Velos, Trailer Extra string named "FT Analyzer Message:" may
look like this
"MCal=29d RF=600V *HCD=35eV* Lock(inj371.1, NOT FOUND, t=1s, +0.067ppm)"
Here HCD value seems to be always an integer. Sometimes the value is zero
due to the rounding. Sometimes it is missing. Therefore, zero cannot be
used to mark the value as missing.

Unfortunately, I do not have information about RAW files produced by other
Thermo instruments that employ HCD activation method.

Thank you.

Dmitrii




> -----Original Message-----
> From: Matt Chambers [mailto:mat...@gm...]
> Sent: Tuesday, January 29, 2013 11:21 AM
> To: Mass spectrometry standard development; Rudnick, Paul A;
> Tchekhovskoi, Dmitrii V. Dr.
> Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD
> 
> Paul/Dmitrii, I can't find the email where you told me why you wanted the
> real eV value for HCD. Is
> there a reason it would make sense to have real eV for HCD but not for
CID?
> If not I figure we
> should try to support both eV and NCE (if possible) for both methods.
> 
> I do agree with Eric and Karl that NCE is more important to most users
(even
> less-so-typical ones
> like us don't know how to calculate eV from it!). But moving NCE to a new
> cvParam is disruptive to
> an unknown degree: it's hard to predict what it will break. I suspect the
> answer is "not much" but
> only because most of the people who could be using mzML for extracting
> NCE are actually pulling the
> value straight from the RAW files or some other custom conversion.
> 
> Also, should the new term be Thermo-specific (and a proper noun) or
> should it be a generic
> normalized CE? The normalization concept seems somewhat general,
> Thermo's trademark on "Normalized
> Collision Energy" notwithstanding... :)
> 
> -Matt
> 
> 
> On 1/28/2013 10:06 AM, Eric Deutsch wrote:
> > I would agree with this suggestion; let's just fix the units with a new
cv
> > term for the correct unit and move on. It would be nice to document this
> > in a public way that conversions before XX suffered from the unit
> problem,
> > which was corrected as of XX.
> >
> > Regards,
> > Eric
> >
> >
> > -----Original Message-----
> > From: Karl [mailto:cl...@br...]
> > Sent: Friday, January 25, 2013 12:53 PM
> > To: 'Mass spectrometry standard development'; 'Matthew Chambers'
> > Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs.
HCD
> >
> > Hi Matt,
> >
> > I think it would be unwise to convert from % to eV and keep only the eV
> > value stored in the mzML file. The main reason is that the typical user
of
> > Thermo instruments/data only knows the values expressed as % , even
> though
> > they may not know what units are in use.  So you I think you should
update
> > the units to allow for percent or add a new cvParam that is for
collision
> > energy in units of %.
> >
> > When you say:
> > 	>So basically, every collision energy cvParam ever written for a
> > Thermo mzML file has been wrong. :) I think it is more accurate to say
> > that the units of the cvParam have always been erroneous for Thermo
> > mzML's, the values have always been right.
> >
> > Nonetheless it is interesting that one can now additionally extract the
> > value in units of eV from the scan header for HCD spectra.
> > 	"HCD Energy eV:" line of the scan header  for QExactive
> > instruments
> > 	or the "HCD=" key/value pair of the "FT Analyzer Message:" line of
> > the scan header for Orbitrap Elite and Velos Orbitrap instruments.
> > For CID spectra collected at high resolution in the Orbitrap, the scan
> > header and scan filter still contain only the value in % units
> >
> > --Karl
> >
> >
> >
> > -----Original Message-----
> > From: Shofstahl, Jim [mailto:jim...@th...]
> > Sent: Friday, January 25, 2013 2:01 PM
> > To: Matthew Chambers; psi...@li...
> > Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs.
HCD
> >
> > Matt,
> >
> > I will have to ask some of our hardware/firmware people since I don' t
> > know the answer at this moment.
> >
> > Jim
> >
> > -----Original Message-----
> > From: Matthew Chambers [mailto:mat...@gm...]
> > Sent: Friday, January 25, 2013 10:58 AM
> > To: psi...@li...; Shofstahl, Jim
> > Subject: Collision energy units for Thermo CID vs. HCD
> >
> > Hi all,
> >
> > It's been brought to my attention that since the LCQ the collision
> > energies in the scan filter for Thermo CID instruments has not been
> > reported in electronvolts but as a percentage because it is in fact the
> > "Normalized Collision Energy(tm)" described here:
> > https://static.thermoscientific.com/images/D13507~.pdf
> >
> > Right now EV is the only unit we allow for collision energy in the CV,
but
> > I don't know of a way to convert from NCE to EV! So basically, every
> > collision energy cvParam ever written for a Thermo mzML file has been
> > wrong. :)
> >
> > Jim, do you know how to convert that percentage to EV, or is the
> > conversion formula proprietary? If it's feasible to convert I'd prefer
to
> > do that, but otherwise we may have to add "percentage" to the allowed
> unit
> > types of the cvParam.
> >
> > Newer "HCD" instruments on the other hand report the actual EV in a
> couple
> > different places (while still reporting the NCE in the scan filter):
> > either in the "HCD Energy eV:" line of the scan header or the "HCD="
> > key/value pair of the "FT Analyzer Message:" line of the scan header.
> >
> > Furthermore, I've seen stepped collision energies for HCD like
> > "HCD=24..44eV"; how should that be encoded in mzML?
> >
> > -Matt
> >
> >
--------------------------------------------------------------------------
> > --
> > --
> > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC,
> > Windows 8 Apps, JavaScript and much more. Keep your skills current with
> > LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and
> > experts. ON SALE this month only -- learn more at:
> > http://p.sf.net/sfu/learnnow-d2d
> > _______________________________________________
> > Psidev-ms-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >
> >
> >
--------------------------------------------------------------------------
> > ----
> > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC,
> > Windows 8 Apps, JavaScript and much more. Keep your skills current with
> > LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and
> > experts. ON SALE this month only -- learn more at:
> > http://p.sf.net/sfu/learnnow-d2d
> > _______________________________________________
> > Psidev-ms-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >

Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD

[Paul R. <rud...@ni...>]

Matt -
A good reason to include eV is because that value is removed from the 
equation used to derive it.  In other words, it is unimportant to know 
what happens between the nominal setting and the energy applied as long 
as eV is captured.  We use these values extensively in library 
building.  In fact, it is likely that consensus libraries will not be 
the best solution for collision cell data (e.g., HCD). Instead, 
libraries containing multiple 'best-replicate' spectra covering short eV 
ranges will make better reference data.
Paul
On 1/29/2013 11:20 AM, Matt Chambers wrote:
> Paul/Dmitrii, I can't find the email where you told me why you wanted the real eV value for HCD. Is
> there a reason it would make sense to have real eV for HCD but not for CID? If not I figure we
> should try to support both eV and NCE (if possible) for both methods.
>
> I do agree with Eric and Karl that NCE is more important to most users (even less-so-typical ones
> like us don't know how to calculate eV from it!). But moving NCE to a new cvParam is disruptive to
> an unknown degree: it's hard to predict what it will break. I suspect the answer is "not much" but
> only because most of the people who could be using mzML for extracting NCE are actually pulling the
> value straight from the RAW files or some other custom conversion.
>
> Also, should the new term be Thermo-specific (and a proper noun) or should it be a generic
> normalized CE? The normalization concept seems somewhat general, Thermo's trademark on "Normalized
> Collision Energy" notwithstanding... :)
>
> -Matt
>
>
> On 1/28/2013 10:06 AM, Eric Deutsch wrote:
>> I would agree with this suggestion; let's just fix the units with a new cv
>> term for the correct unit and move on. It would be nice to document this
>> in a public way that conversions before XX suffered from the unit problem,
>> which was corrected as of XX.
>>
>> Regards,
>> Eric
>>
>>
>> -----Original Message-----
>> From: Karl [mailto:cl...@br...]
>> Sent: Friday, January 25, 2013 12:53 PM
>> To: 'Mass spectrometry standard development'; 'Matthew Chambers'
>> Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD
>>
>> Hi Matt,
>>
>> I think it would be unwise to convert from % to eV and keep only the eV
>> value stored in the mzML file. The main reason is that the typical user of
>> Thermo instruments/data only knows the values expressed as % , even though
>> they may not know what units are in use.  So you I think you should update
>> the units to allow for percent or add a new cvParam that is for collision
>> energy in units of %.
>>
>> When you say:
>> 	>So basically, every collision energy cvParam ever written for a
>> Thermo mzML file has been wrong. :) I think it is more accurate to say
>> that the units of the cvParam have always been erroneous for Thermo
>> mzML's, the values have always been right.
>>
>> Nonetheless it is interesting that one can now additionally extract the
>> value in units of eV from the scan header for HCD spectra.
>> 	"HCD Energy eV:" line of the scan header  for QExactive
>> instruments
>> 	or the "HCD=" key/value pair of the "FT Analyzer Message:" line of
>> the scan header for Orbitrap Elite and Velos Orbitrap instruments.
>> For CID spectra collected at high resolution in the Orbitrap, the scan
>> header and scan filter still contain only the value in % units
>>
>> --Karl
>>
>>
>>
>> -----Original Message-----
>> From: Shofstahl, Jim [mailto:jim...@th...]
>> Sent: Friday, January 25, 2013 2:01 PM
>> To: Matthew Chambers; psi...@li...
>> Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD
>>
>> Matt,
>>
>> I will have to ask some of our hardware/firmware people since I don' t
>> know the answer at this moment.
>>
>> Jim
>>
>> -----Original Message-----
>> From: Matthew Chambers [mailto:mat...@gm...]
>> Sent: Friday, January 25, 2013 10:58 AM
>> To: psi...@li...; Shofstahl, Jim
>> Subject: Collision energy units for Thermo CID vs. HCD
>>
>> Hi all,
>>
>> It's been brought to my attention that since the LCQ the collision
>> energies in the scan filter for Thermo CID instruments has not been
>> reported in electronvolts but as a percentage because it is in fact the
>> "Normalized Collision Energy(tm)" described here:
>> https://static.thermoscientific.com/images/D13507~.pdf
>>
>> Right now EV is the only unit we allow for collision energy in the CV, but
>> I don't know of a way to convert from NCE to EV! So basically, every
>> collision energy cvParam ever written for a Thermo mzML file has been
>> wrong. :)
>>
>> Jim, do you know how to convert that percentage to EV, or is the
>> conversion formula proprietary? If it's feasible to convert I'd prefer to
>> do that, but otherwise we may have to add "percentage" to the allowed unit
>> types of the cvParam.
>>
>> Newer "HCD" instruments on the other hand report the actual EV in a couple
>> different places (while still reporting the NCE in the scan filter):
>> either in the "HCD Energy eV:" line of the scan header or the "HCD="
>> key/value pair of the "FT Analyzer Message:" line of the scan header.
>>
>> Furthermore, I've seen stepped collision energies for HCD like
>> "HCD=24..44eV"; how should that be encoded in mzML?
>>
>> -Matt
>>
>> --------------------------------------------------------------------------
>> --
>> --
>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC,
>> Windows 8 Apps, JavaScript and much more. Keep your skills current with
>> LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and
>> experts. ON SALE this month only -- learn more at:
>> http://p.sf.net/sfu/learnnow-d2d
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>>
>> --------------------------------------------------------------------------
>> ----
>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC,
>> Windows 8 Apps, JavaScript and much more. Keep your skills current with
>> LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and
>> experts. ON SALE this month only -- learn more at:
>> http://p.sf.net/sfu/learnnow-d2d
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>

Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD

[Stein, S. E. Dr. <ste...@ni...>]

HCD collision energies determine the degree of fragmentation - they are indirectly related to NCE (depends on m/z, charge and tuning). Spectra radically change with changing HCD energy (which are effectively the same as in QTOF and triple quads). This energy determines the actual translational energy of the ion prior to entry to the collision cell.

Ion Trap Fragmentation (CID on a Thermo) is only weakly dependent on the "collision energy", since once the ion gets enough energy it dissociates regardless of the 'resonant' voltage applied to heat it up. The selection of the actual excitation energy is complex and probably not useful to know. 

-----Original Message-----
From: Matt Chambers [mailto:mat...@gm...] 
Sent: Tuesday, January 29, 2013 11:21 AM
To: Mass spectrometry standard development; Rudnick, Paul A; Tchekhovskoi, Dmitrii V. Dr.
Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD

Paul/Dmitrii, I can't find the email where you told me why you wanted the real eV value for HCD. Is there a reason it would make sense to have real eV for HCD but not for CID? If not I figure we should try to support both eV and NCE (if possible) for both methods.

I do agree with Eric and Karl that NCE is more important to most users (even less-so-typical ones like us don't know how to calculate eV from it!). But moving NCE to a new cvParam is disruptive to an unknown degree: it's hard to predict what it will break. I suspect the answer is "not much" but only because most of the people who could be using mzML for extracting NCE are actually pulling the value straight from the RAW files or some other custom conversion.

Also, should the new term be Thermo-specific (and a proper noun) or should it be a generic normalized CE? The normalization concept seems somewhat general, Thermo's trademark on "Normalized Collision Energy" notwithstanding... :)

-Matt


On 1/28/2013 10:06 AM, Eric Deutsch wrote:
> I would agree with this suggestion; let's just fix the units with a 
> new cv term for the correct unit and move on. It would be nice to 
> document this in a public way that conversions before XX suffered from 
> the unit problem, which was corrected as of XX.
>
> Regards,
> Eric
>
>
> -----Original Message-----
> From: Karl [mailto:cl...@br...]
> Sent: Friday, January 25, 2013 12:53 PM
> To: 'Mass spectrometry standard development'; 'Matthew Chambers'
> Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. 
> HCD
>
> Hi Matt,
>
> I think it would be unwise to convert from % to eV and keep only the 
> eV value stored in the mzML file. The main reason is that the typical 
> user of Thermo instruments/data only knows the values expressed as % , 
> even though they may not know what units are in use.  So you I think 
> you should update the units to allow for percent or add a new cvParam 
> that is for collision energy in units of %.
>
> When you say:
> 	>So basically, every collision energy cvParam ever written for a 
> Thermo mzML file has been wrong. :) I think it is more accurate to say 
> that the units of the cvParam have always been erroneous for Thermo 
> mzML's, the values have always been right.
>
> Nonetheless it is interesting that one can now additionally extract 
> the value in units of eV from the scan header for HCD spectra.
> 	"HCD Energy eV:" line of the scan header  for QExactive instruments
> 	or the "HCD=" key/value pair of the "FT Analyzer Message:" line of 
> the scan header for Orbitrap Elite and Velos Orbitrap instruments.
> For CID spectra collected at high resolution in the Orbitrap, the scan 
> header and scan filter still contain only the value in % units
>
> --Karl
>
>
>
> -----Original Message-----
> From: Shofstahl, Jim [mailto:jim...@th...]
> Sent: Friday, January 25, 2013 2:01 PM
> To: Matthew Chambers; psi...@li...
> Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. 
> HCD
>
> Matt,
>
> I will have to ask some of our hardware/firmware people since I don' t 
> know the answer at this moment.
>
> Jim
>
> -----Original Message-----
> From: Matthew Chambers [mailto:mat...@gm...]
> Sent: Friday, January 25, 2013 10:58 AM
> To: psi...@li...; Shofstahl, Jim
> Subject: Collision energy units for Thermo CID vs. HCD
>
> Hi all,
>
> It's been brought to my attention that since the LCQ the collision 
> energies in the scan filter for Thermo CID instruments has not been 
> reported in electronvolts but as a percentage because it is in fact 
> the "Normalized Collision Energy(tm)" described here:
> https://static.thermoscientific.com/images/D13507~.pdf
>
> Right now EV is the only unit we allow for collision energy in the CV, 
> but I don't know of a way to convert from NCE to EV! So basically, 
> every collision energy cvParam ever written for a Thermo mzML file has 
> been wrong. :)
>
> Jim, do you know how to convert that percentage to EV, or is the 
> conversion formula proprietary? If it's feasible to convert I'd prefer 
> to do that, but otherwise we may have to add "percentage" to the 
> allowed unit types of the cvParam.
>
> Newer "HCD" instruments on the other hand report the actual EV in a 
> couple different places (while still reporting the NCE in the scan filter):
> either in the "HCD Energy eV:" line of the scan header or the "HCD="
> key/value pair of the "FT Analyzer Message:" line of the scan header.
>
> Furthermore, I've seen stepped collision energies for HCD like 
> "HCD=24..44eV"; how should that be encoded in mzML?
>
> -Matt
>
> ----------------------------------------------------------------------
> ----
> --
> --
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, 
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills 
> current with LearnDevNow - 3,200 step-by-step video tutorials by 
> Microsoft MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
> ----------------------------------------------------------------------
> ----
> ----
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, 
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills 
> current with LearnDevNow - 3,200 step-by-step video tutorials by 
> Microsoft MVPs and experts. ON SALE this month only -- learn more at:
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Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD

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

Paul/Dmitrii, I can't find the email where you told me why you wanted the real eV value for HCD. Is 
there a reason it would make sense to have real eV for HCD but not for CID? If not I figure we 
should try to support both eV and NCE (if possible) for both methods.

I do agree with Eric and Karl that NCE is more important to most users (even less-so-typical ones 
like us don't know how to calculate eV from it!). But moving NCE to a new cvParam is disruptive to 
an unknown degree: it's hard to predict what it will break. I suspect the answer is "not much" but 
only because most of the people who could be using mzML for extracting NCE are actually pulling the 
value straight from the RAW files or some other custom conversion.

Also, should the new term be Thermo-specific (and a proper noun) or should it be a generic 
normalized CE? The normalization concept seems somewhat general, Thermo's trademark on "Normalized 
Collision Energy" notwithstanding... :)

-Matt


On 1/28/2013 10:06 AM, Eric Deutsch wrote:
> I would agree with this suggestion; let's just fix the units with a new cv
> term for the correct unit and move on. It would be nice to document this
> in a public way that conversions before XX suffered from the unit problem,
> which was corrected as of XX.
>
> Regards,
> Eric
>
>
> -----Original Message-----
> From: Karl [mailto:cl...@br...]
> Sent: Friday, January 25, 2013 12:53 PM
> To: 'Mass spectrometry standard development'; 'Matthew Chambers'
> Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD
>
> Hi Matt,
>
> I think it would be unwise to convert from % to eV and keep only the eV
> value stored in the mzML file. The main reason is that the typical user of
> Thermo instruments/data only knows the values expressed as % , even though
> they may not know what units are in use.  So you I think you should update
> the units to allow for percent or add a new cvParam that is for collision
> energy in units of %.
>
> When you say:
> 	>So basically, every collision energy cvParam ever written for a
> Thermo mzML file has been wrong. :) I think it is more accurate to say
> that the units of the cvParam have always been erroneous for Thermo
> mzML's, the values have always been right.
>
> Nonetheless it is interesting that one can now additionally extract the
> value in units of eV from the scan header for HCD spectra.
> 	"HCD Energy eV:" line of the scan header  for QExactive
> instruments
> 	or the "HCD=" key/value pair of the "FT Analyzer Message:" line of
> the scan header for Orbitrap Elite and Velos Orbitrap instruments.
> For CID spectra collected at high resolution in the Orbitrap, the scan
> header and scan filter still contain only the value in % units
>
> --Karl
>
>
>
> -----Original Message-----
> From: Shofstahl, Jim [mailto:jim...@th...]
> Sent: Friday, January 25, 2013 2:01 PM
> To: Matthew Chambers; psi...@li...
> Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD
>
> Matt,
>
> I will have to ask some of our hardware/firmware people since I don' t
> know the answer at this moment.
>
> Jim
>
> -----Original Message-----
> From: Matthew Chambers [mailto:mat...@gm...]
> Sent: Friday, January 25, 2013 10:58 AM
> To: psi...@li...; Shofstahl, Jim
> Subject: Collision energy units for Thermo CID vs. HCD
>
> Hi all,
>
> It's been brought to my attention that since the LCQ the collision
> energies in the scan filter for Thermo CID instruments has not been
> reported in electronvolts but as a percentage because it is in fact the
> "Normalized Collision Energy(tm)" described here:
> https://static.thermoscientific.com/images/D13507~.pdf
>
> Right now EV is the only unit we allow for collision energy in the CV, but
> I don't know of a way to convert from NCE to EV! So basically, every
> collision energy cvParam ever written for a Thermo mzML file has been
> wrong. :)
>
> Jim, do you know how to convert that percentage to EV, or is the
> conversion formula proprietary? If it's feasible to convert I'd prefer to
> do that, but otherwise we may have to add "percentage" to the allowed unit
> types of the cvParam.
>
> Newer "HCD" instruments on the other hand report the actual EV in a couple
> different places (while still reporting the NCE in the scan filter):
> either in the "HCD Energy eV:" line of the scan header or the "HCD="
> key/value pair of the "FT Analyzer Message:" line of the scan header.
>
> Furthermore, I've seen stepped collision energies for HCD like
> "HCD=24..44eV"; how should that be encoded in mzML?
>
> -Matt
>
> --------------------------------------------------------------------------
> --
> --
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC,
> Windows 8 Apps, JavaScript and much more. Keep your skills current with
> LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and
> experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
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> Psidev-ms-dev mailing list
> Psi...@li...
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>
>
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> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC,
> Windows 8 Apps, JavaScript and much more. Keep your skills current with
> LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and
> experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
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>

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.46.0_rc1 of psi-ms.obo

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

Thanks as always, Gerhard!

The definition of the collision energy percentage seems like it could be
improved. There's no mention of the percentage and what it's a percentage
of. I cannot come up with something better offhand, but will ask around.
But maybe there are some gurus out there receiving who really understand
what the number that these Thermo machines are reporting means and can
write an eloquent definition that makes it clear for us all??

Thanks,
Eric


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Tuesday, January 29, 2013 5:54 AM
To: psi...@li...;
psi...@li...; psi...@li...
Subject: [Psidev-ms-vocab] Release candidate 3.46.0_rc1 of psi-ms.obo

Dear proteomics community,

attached there's the release candidate 3.46.0_rc1 of the psi-ms.obo file.
It contains new terms for the collision energy given as percentage values.

I also added the list of all purgatory terms (see Word document). If there
are no counter-arguments, I propose to make all these purgatory terms
obsoleted in one of the future versions of our CV.

Changed CV terms in version 3.46.0_rc1 of psi-ms.obo:
=====================================================
************ No changed terms


New CV terms in version 3.46.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002218
name: collision energy percentage
def: "Energy for an ion experiencing collision with a stationary gas
particle resulting in dissociation of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002219
name: collision energy ramp start percentage
def: "Collision energy at the start of the collision energy ramp."
[PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002218 ! collision energy percentage
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002220
name: collision energy ramp end percentage
def: "Collision energy at the end of the collision energy ramp." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002218 ! collision energy percentage
relationship: has_units UO:0000187 ! percent

Best Regards,
Gerhard

--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik
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

Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD

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

I would agree with this suggestion; let's just fix the units with a new cv
term for the correct unit and move on. It would be nice to document this
in a public way that conversions before XX suffered from the unit problem,
which was corrected as of XX.

Regards,
Eric


-----Original Message-----
From: Karl [mailto:cl...@br...]
Sent: Friday, January 25, 2013 12:53 PM
To: 'Mass spectrometry standard development'; 'Matthew Chambers'
Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD

Hi Matt,

I think it would be unwise to convert from % to eV and keep only the eV
value stored in the mzML file. The main reason is that the typical user of
Thermo instruments/data only knows the values expressed as % , even though
they may not know what units are in use.  So you I think you should update
the units to allow for percent or add a new cvParam that is for collision
energy in units of %.

When you say:
	>So basically, every collision energy cvParam ever written for a
Thermo mzML file has been wrong. :) I think it is more accurate to say
that the units of the cvParam have always been erroneous for Thermo
mzML's, the values have always been right.

Nonetheless it is interesting that one can now additionally extract the
value in units of eV from the scan header for HCD spectra.
	"HCD Energy eV:" line of the scan header  for QExactive
instruments
	or the "HCD=" key/value pair of the "FT Analyzer Message:" line of
the scan header for Orbitrap Elite and Velos Orbitrap instruments.
For CID spectra collected at high resolution in the Orbitrap, the scan
header and scan filter still contain only the value in % units

--Karl



-----Original Message-----
From: Shofstahl, Jim [mailto:jim...@th...]
Sent: Friday, January 25, 2013 2:01 PM
To: Matthew Chambers; psi...@li...
Subject: Re: [Psidev-ms-dev] Collision energy units for Thermo CID vs. HCD

Matt,

I will have to ask some of our hardware/firmware people since I don' t
know the answer at this moment.

Jim

-----Original Message-----
From: Matthew Chambers [mailto:mat...@gm...]
Sent: Friday, January 25, 2013 10:58 AM
To: psi...@li...; Shofstahl, Jim
Subject: Collision energy units for Thermo CID vs. HCD

Hi all,

It's been brought to my attention that since the LCQ the collision
energies in the scan filter for Thermo CID instruments has not been
reported in electronvolts but as a percentage because it is in fact the
"Normalized Collision Energy(tm)" described here:
https://static.thermoscientific.com/images/D13507~.pdf

Right now EV is the only unit we allow for collision energy in the CV, but
I don't know of a way to convert from NCE to EV! So basically, every
collision energy cvParam ever written for a Thermo mzML file has been
wrong. :)

Jim, do you know how to convert that percentage to EV, or is the
conversion formula proprietary? If it's feasible to convert I'd prefer to
do that, but otherwise we may have to add "percentage" to the allowed unit
types of the cvParam.

Newer "HCD" instruments on the other hand report the actual EV in a couple
different places (while still reporting the NCE in the scan filter):
either in the "HCD Energy eV:" line of the scan header or the "HCD="
key/value pair of the "FT Analyzer Message:" line of the scan header.

Furthermore, I've seen stepped collision energies for HCD like
"HCD=24..44eV"; how should that be encoded in mzML?

-Matt

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experts. ON SALE this month only -- learn more at:
http://p.sf.net/sfu/learnnow-d2d
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Windows 8 Apps, JavaScript and much more. Keep your skills current with
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