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

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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
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-- 

IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
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