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

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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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