Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] CV term for isotopomers

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Hi Gerhard,
Fine to define a generic term to describe such MS signal.
But there are a few problems/questions here: There is a need to consider the correct definitions of the molecular species and the need to differentiate the description of the molecular species from the MS signals that represent these molecular species

1)      Definitions of molecular species: isotopologue and isotopomer (see IUPAC gold book : https://goldbook.iupac.org/html/I/I03351.html and https://goldbook.iupac.org/html/I/I03352.html) are terms that define specific molecular species:

-          If you want to describe is the possibility to differentiate an isotope from another, where the number of isotopic atoms differ (same chemical structure (example C2H5ON) but another isotopic atom distribution: 12C2 H5 O 14N2   vs.   13C1 12C1 H5 O 14N   vs.   12C2 H5 O 15N) In that case these are isotopologues. They also do not have, in most of the cases, the exact same mass. Please note that isotopologue has also a definition based on identity of mass number (same total number of protons and neutrons, but differently distributed in the atoms).

-          In contrast, two isotopomers have the same number of each isotopic atom but differ in the position, such as in constitutional isomers ( example ethanol : H3(13C)-(12C)H2OH vs H3(12C)-(13C)H2OH) or isotopic stereomers ((R)- and (S)-CH3CHDOH), which share an exact same mass.

2)      MS signals do represent molecular ions, but are not molecular ions themselves. In that respect, the term isotopomer has to be different from isotopomer MS signal. What you want to describe here are MS signals representing isomers (isotopomers, isotopologues, mix of them). Therefore there is a need to use isotopomer MS signal  and isotopologue MS signal  (no need to specify that they are ion signals).

3)      A MS signal at M+1 (nominal mass of the monoisotopic form + 1Da, low res instruments) is often a mix of isotopologues and isotopomers (one 13C OR one 15N OR one 2H (deuterium) distributed on the ion/molecule). In that case the signal cannot discriminate. Both strict terms isotopomer and isotopologue are not full correct. One should use the term isobar (same mass number). Only if the signals can be discriminated at very high resolving power instruments (which can discriminate the isobars 12C15N from 13C14N one can specify them as different isotopologues)

4)      In all cases the definition field of the PSI-MS CV term must not be restricted to quantified peak as it is proposed. This term isotopomer describes a (group of) molecules or a (group of) ion(s). This  should be available for quant as well as for ID. It should only represent a descriptor of what isotopomer is considered in a data analysis process. Please remove the restriction to quant in the definition of the terms here

My proposal:   use three terms for the definition of the molecular species MS signals: isotopic ion MS peak, isotopomer MS peak, isotopologue MS peak, and create also terms for the definition of the molecular species themselves.

id: MS:nnnnnnn
name: isotopic ion MS peak
def: " A MS peak that represents one or more isotopic ions. The value slot contains description of the represented isotope set , e.g. 'M+1 peak'." [PSI:PI]." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

id: MS:nnnnnnn
name: isotopomer MS peak
def: " The described isotopomer MS signal. The value slot contains description of the represented isotopomer, e.g. '13C peak' or '15N peak'." [PSI:PI]." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
is_a: MS:nnnnnnn ! isotopic ion MS signal

id: MS:nnnnnnn
name: isotopologue MS peak
def: " The described isotopologue MS signal. The value slot contains description of the represented isotopologue , e.g. '13C1 peak' or '15N1 peak'." [PSI:PI]." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
is_a: MS:nnnnnnn ! isotopic ion MS signal

id: MS:1002955
name: isotopomer
def: " An isomer that differ from another only in the spatial distribution of the constitutive isotopic atoms." [PSI:PI]." [https://goldbook.iupac.org/html/I/I03352.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
is_a: MS:nnnnnnn ! isomer

id: MS:nnnnnnn
name: isotopologue
def: " A molecular entity that differs only in isotopic composition (number of isotopic substitutions),." [PSI:PI]." [https://goldbook.iupac.org/html/I/I03351.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
is_a: MS:nnnnnnn ! isomer

id: MS:nnnnnnn
name: isomer
def: " One of several species (or molecular entities ) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae " [PSI:PI]." [https://goldbook.iupac.org/html/I/I03289.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

Pierre-Alain

De : mayerg97 via Psidev-pi-dev <psi...@li...>
Envoyé : vendredi 8 juin 2018 12:32
À : psi...@li...
Cc : psi...@li...; Mass spectrometry standard development <psi...@li...>; jones, Andy <And...@li...>
Objet : Re: [Psidev-pi-dev] [Psidev-ms-vocab] CV term for isotopomers

Hi all,

I would propose to add a generic term with a string value like e.g.

[Term]
id: MS:1002955
name: isotopomer
def: "The quantified isotopomer. The value slot contains the quantified peak, e.g. '13C peak' or '15N peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

Cheers,
Gerhard
Am 06.06.2018 um 17:21 schrieb Jones, Andy:
Hi all,

I have a potential term request for mzTab-M in this section, where we allow the exporter to state if quant is being provided for an assumed peak other than the monoisotopic one (for quant approaches that are not de-isotoping features). I don't see any such term already in PSI-MS, does this seem sensible to add, or should we just add a specification for a number e.g. +1, +2 (relative to the monoisotopic peak). I recognize that for very-high res instruments one might be able to resolve separately a 13C and a 15N peak, I think this is done here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838547/. For these kinds of approaches, it would seem useful to be able to state some other knowledge about the peak being quantified.

Let me know any thoughts!
Best wishes
Andy

6.4.5. isotopomer
Description:

If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here e.g. "+1", "+2", "13C peak" using cvParams, otherwise (i.e. for approaches where SMF rows are de-isotoped features) this MUST be null.

Type:

Parameter

Is Nullable:

TRUE

Example:

SFH SMF_ID ... isotopomer ...
SMF 1 ... [MS,MS:1000XX,"13C peak", ]...

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Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER

PhD student

Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

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