Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] List of ion species, anyone ?

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Dear Steffen and Michael,

in principle one could specify the adduct ions more generic, but even 
then the problem remains that one has to adapt the RegEx if one wants to 
cover e.g. other neutral losses.

[Term]
id: MS:1000353
name: adduct ion
def: "Ion formed by the interaction of an ion with one or more atoms or 
molecules to form an ion containing all the constituent atoms of the 
precursor ion as well as the additional atoms from the associated atoms 
or molecules." [PSI:MS]
is_a: MS:1002806 ! ion

[Term]
id: MS:1002806
name: ion
def: "An atomic or molecular species having a net positive or negative 
electric charge." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Ontology

[Term]
id: MS:1002856
name: adduct ion formula
def: "Adduct formation formula specified by the given value." 
[PMID:22111785, DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000353 ! adduct ion
relationship: has_regexp MS:1002857 ! 
(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-]\d{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\]\d{0,1}[+-])

[Term]
id: MS:1002857
name: Regular expression for adduct ion formula
def: 
"(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-]\d{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\]\d{0,1}[+-])" 
[PSI:PI]
is_a: MS:1002479 ! regular expression

[Term]
id: MS:1002858
name: adduct ion attribute
def: "Attribute describing an adduct formation." [PSI:PI]
is_a: MS:1000547 ! object attribute

[Term]
id: MS:1002859
name: adduct ion mass
def: "Mass of an adduct formation specified by the given value." 
[DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002858 ! adduct ion attribute

[Term]
id: MS:1002860
name: adduct ion isotope
def: "Isotope of the matrix molecule M of an adduct formation." 
[PMID:18790129]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002858 ! adduct ion attribute

Best regards,
Gerhard Mayer

Am 14.06.2017 um 15:24 schrieb Witting, Michael, Dr. via Psidev-ms-vocab:
> Hi Gerd, Hi Steffen,
>
> and if we are currently talking about such things: What about isotopes? We
> might think about something like M+1, M+2, M+3 with a value that can specify
> more exact which isotope, if you have the resolution e.g. M+1 could be 13C
> or 15N or M+2, 13C2 or 34S.
>
> Best regards,
>
> Michael
>
> -----Ursprüngliche Nachricht-----
> Von: Neumann, Steffen [mailto:sne...@ip...]
> Gesendet: Mittwoch, 14. Juni 2017 15:20
> An: psi...@li...; ger...@ru...;
> psi...@li...; psi...@li...;
> joe...@wa...; mzt...@go...
> Cc: mic...@he...; Schober, Daniel
> Betreff: Re: [Psidev-ms-dev] List of ion species, anyone ?
>
> Hi Gerd,
>
> Michael Witting and I also had already started a simple list, but a problem
> might be that there will always be one ion type missing.
> It also depends on the sample and analytical conditions, e.g. M+3H would be
> fairly uncommon.
>
> Michael has a good set of literature describing adducts, and Tobias Kind in
> UC Davies has a nice collection at
> http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator
>
> In the R package CAMERA (see below) we defined them in a combinatorial way,
> and comes up with ~134 combinations (considering neutral losses common in
> metabolomics).
> So in addition to a fixed list, it would be great to have more generic
> annotation terms. like
>
> [Term]
> id: MS:10028XX
> name: adduct ion formula
> def: "Adduct formation with specified ion." [PSI:MS]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002806 ! adduct ion type
>
> And we'd need examples how to put the generic adduct ion into the
> value="..." of the cvParam something like
>
> 	"+3H", "+Cl", "-H"
>
> and similar we want to annotate cluster ions like
>
> 	"M", "2M"
>
> and neutral losses
>
> 	"-H20", "-H20-H20", "-C6H10O5"
>
> So both a short list of "common" (in metabolomics/proteomics) ion species
> plus some more generic approach make sense, striking a balance between
> simplicity and general applicability.
>
>
> Yours,
> Steffen
>
> library(CAMERA)
> r <- new("ruleSet");
> r2 <- setDefaultLists(r) ;
> r3 <- readLists(r2) ;
> r4 <- setDefaultParams(r3) ;
> r5 <- generateRules(r4)
> r5@rules["name"]
>
>                  name
> 1             [M+H]+
> 2           [M+2H]2+
> 3           [M+3H]3+
> 4         [M+H+Na]2+
> 5          [M+H+K]2+
> 6            [M+Na]+
> ...
> 42    [2M+2Na+K-H]2+
> 43    [2M+3Na+K-H]3+
> 44    [2M+Na+2K-H]2+
> 45   [2M+2Na+2K-H]3+
> 47        [2M+2K-H]+
> ...
> 93        [M+H-NH3]+
> 94      [M+2H-NH3]2+
> 95      [M+3H-NH3]3+
> 96        [M+H-H20]+
> 97      [M+2H-H20]2+
> 98      [M+3H-H20-H20]3+
> 99        [M+H-CH4]+
> 100     [M+2H-CH4]2+
> 101     [M+3H-CH4]3+
> ...
> 128 [M+3H-C6H10O4]3+
> 129   [M+H-C6H10O5]+
> ...
> 134  [M+3H-C6H8O6]3+
>
>
>
>
> On Fri, 2017-06-09 at 10:41 +0200, mayerg97 wrote:
>> Hi Joel and Steffen,
>> dear metabolomics and proteomics community,
>>
>> would the following terms fit for you purposes?
>>
>> [Term]
>> id: MS:1002806
>> name: adduct ion type
>> def: "Adduct ion type resulting from ionization in ESI-MS or other
>> soft ionization techniques." [PSI:MS]
>> is_a: MS:1001249 ! search input details
>>
>> [Term]
>> id: MS:1002807
>> name: positive mode adduct ion type
>> def: "Adduct ion type from positive ion mode." [PSI:MS]
>> is_a: MS:1002806 ! adduct ion type
>>
>> [Term]
>> id: MS:1002808
>> name: negative mode adduct ion type
>> def: "Adduct ion type from negative ion mode." [PSI:MS]
>> is_a: MS:1002806 ! adduct ion type
>>
>> [Term]
>> id: MS:1002809
>> name: M+3H ion
>> def: "M+3H ion in positive ion mode (M in the property ionMass
>> denotes the mass of the neutral molecule)." [http://fiehnlab.ucdavis.
>> edu/staff/kind/Metabolomics/MS-Adduct-Calculator,
>> http://dx.doi.org/10.1016/S1044-0305(99)00089-6]
>> property_value: ionMass: "M/3 + 1.007276" xsd:string
>> is_a: MS:1002807 ! positive mode adduct ion type
>>
>> ... analogous for the other positive mode adduct ions
>>
>> [Term]
>> id: MS:10028xy
>> name: M-3H ion
>> def: "M-3H ion in negative ion mode (M in the property ionMass
>> denotes the mass of the neutral molecule)." [http://fiehnlab.ucdavis.
>> edu/staff/kind/Metabolomics/MS-Adduct-Calculator,
>> http://dx.doi.org/10.1016/S1044-0305(99)00089-6]
>> property_value: ionMass: "M/3 - 1.007276 " xsd:string
>> is_a: MS:1002808 ! negative mode adduct ion type
>>
>> ... analogous for the other negative mode ions
>>
>> Best regards,
>> Gerhard Mayer
>>
>> Am 05.01.2017 um 13:08 schrieb Joel Rein:
>>> Hi Steffen,
>>>
>>> I'd be very keen to see such a list developed/help with the RFC.
>>> I think Tobias Kind's list (http://fiehnlab.ucdavis.edu/staff/kind/
>>> Metabolomics/MS-Adduct-Calculator/) would be a useful list to
>>> include.
>>>
>>> Cheers,
>>> Joel
>>>
>>> On Wednesday, January 4, 2017 at 8:06:12 PM UTC, Steffen Neumann
>>> wrote:
>>>> Hi,
>>>>
>>>> are there any efforts to collect ion species for psi-ms.obo,
>>>> such as [M+H]+ or [M-Cl]- ?
>>>>
>>>> I was able to find "(M+H)+" in [1], but nothing in psi-ms.obo.
>>>> I know a few groups interested in such a list, and would be
>>>> happy to collect terms and send a proposal to Gerhard for
>>>> inclusion.
>>>>
>>>> If there are no proposals or suggestions, I would start-off
>>>> the stuff Michael Witting has collected, and come back with an
>>>> RFC.
>>>>
>>>> Yours,
>>>> Steffen
>>>>
>>>>
>>>> [1] http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2
>>>> F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051
>>>>
>>>
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>> -- 
>> --------------------------------------------------------------------
>> Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER
>> PhD student
>> Medizinisches Proteom-Center
>> DEPARTMENT Medical Bioinformatics
>> Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
>> Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554
>> E-mail ger...@ru...
>> www.medizinisches-proteom-center.de

-- 

*--------------------------------------------------------------------*

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
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