psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] Release candidate 4.0.13_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics and metabolomics community,

attached there's the release candidate 4.0.13_rc1 of the psi-ms.obo file.
It contains terms for defining adduct ions and for ion mobility mass 
spectrometry (IM-MS).


New CV terms in version 4.0.13_rc1 of psi-ms.obo:
=================================================
************ new terms for adduct ions
[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:1002807
name: positive mode adduct ion
def: "Adduct ion with positive ionization." [PSI:MS]
is_a: MS:1000353 ! adduct ion

[Term]
id: MS:1002808
name: negative mode adduct ion
def: "Adduct ion with negative ionization." [PSI:MS]
is_a: MS:1000353 ! adduct ion

[Term]
id: MS:1002809
name: adduct ion attribute
def: "Attribute describing an adduct formation." [PSI:PI]
is_a: MS:1000547 ! object attribute

[Term]
id: MS:1002810
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:1002809 ! adduct ion attribute

[Term]
id: MS:1002811
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:1002809 ! adduct ion attribute

[Term]
id: MS:1002812
name: Regular expression for adduct ion formula
def: 
"(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])." 
[PSI:PI]
is_a: MS:1002479 ! regular expression

[Term]
id: MS:1002813
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:1002809 ! adduct ion attribute
relationship: has_regexp MS:1002812 ! 
(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])


************ new terms for IM-MS
[Term]
id: MS:1002814
name: volt-second per square centimeter
def: "An electrical mobility unit that equals the speed [cm/s] an ion 
reaches when pulled through a gas by a Voltage[V] over a certain 
distance [cm]." [PSI:PI]
synonym: "Vs/cm^2" EXACT []
is_a: UO:0000000 ! unit

[Term]
id: MS:1002815
name: inverse reduced ion mobility
def: "Ion mobility measurement for an ion or spectrum of ions as 
measured in an ion mobility mass spectrometer. This might refer to the 
central value of a bin into which all ions within a narrow range of 
mobilities have been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1000503 ! scan attribute
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

[Term]
id: MS:1002816
name: mean ion mobility array
def: "Array of drift times or inverse reduced ion mobilities, averaged 
from a matrix of binned m/z and ion mobility values, corresponding to a 
spectrum of individual peaks encoded with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

[Term]
id: MS:1002817
name: Bruker TDF format
def: "Bruker TDF raw file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002818
name: Bruker TDF nativeID format
def: "Native format defined by frame=xsd:nonNegativeInteger 
scan=xsd:nonNegativeInteger." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1002819
name: Bruker TDF nativeID format, combined spectra
def: "Bruker TDF comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

************ some concrete ion species
************ are there other concrete ions species, which should be 
included here?
[Term]
id: MS:1002820
name: M+H ion
def: "M+H ion from positive ion mode (M in the property ionMass denotes 
the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
property_value: ionMass: "M + 1.007276" xsd:string
is_a: MS:1002807 ! positive mode adduct ion

[Term]
id: MS:1002821
name: M-H ion
def: "M-H ion from negative ion mode (M in the property ionMass denotes 
the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
property_value: ionMass: "M - 1.007276" xsd:string
is_a: MS:1002808 ! negative mode adduct ion



Changed CV terms in version 4.0.13_rc1 of psi-ms.obo:
=====================================================
************ Reactivated the obsolete term 'adduct ion'
[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

Best Regards,
Gerhard

-- 

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

*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 
<http://www.medizinisches-proteom-center.de/>

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

[mayerg97 <ger...@ru...>]

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
>>>>
>>>
>>> -----------------------------------------------------------------
>>> -------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>>
>>>
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>> -- 
>> --------------------------------------------------------------------
>> 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 
<http://www.medizinisches-proteom-center.de/>

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

[Witting, M. Dr. <mic...@he...>]

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
> > >
> >
> >
> > -----------------------------------------------------------------
> > -------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> >
> >
> > _______________________________________________
> > Psidev-ms-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> -- 
> --------------------------------------------------------------------
> 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
-- 

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
 

Helmholtz Zentrum Muenchen
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
Ingolstaedter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen
Registergericht: Amtsgericht Muenchen HRB 6466
USt-IdNr: DE 129521671

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

[Neumann, S. <sne...@ip...>]

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 
> > > 
> > 
> > 
> > -----------------------------------------------------------------
> > -------------
> > Check out the vibrant tech community on one of the world's most 
> > engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> > 
> > 
> > _______________________________________________
> > Psidev-ms-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>  
> -- 
> --------------------------------------------------------------------
> 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
-- 

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] List of ion species, anyone ?

[Schober, D. <dsc...@ip...>]

Dear all,

  First, my admittedly picky view on the matter, having my formal 
ontology hat on (which I wear less and less often these days) ...

Aside my usual ontological aversions against epistemic intrusion a la 
M+3H *ion* /is_a/ *search input details* (rather than a molecule/ion), I 
think the presented pattern will do, given the pragmatic mz CV design. 
Another design principle I am not really comfortable with is that the 
essentials of a class are captured in the definition by selected 
extrinsic rather than essential intrinsic properties, i.e. in this case 
that Ion classes like "positive mode adduct ion type" are defined via 
the mode of an Instrument-run that detected them ("Adduct ion type from 
positive ion mode."). A more intrinsic definition would be via the 
ionisation level of the adduct itself.

These are just comments, and Gerhard knows the CV structure and design 
principles much better.

Best regards,

    Daniel Schober


Am 09.06.2017 um 10:41 schrieb mayerg97:
> 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%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051
>>     <http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org!http://sdm.link/slashdot
>>
>>
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> -- 
>
> *--------------------------------------------------------------------*
>
> *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 
> <http://www.medizinisches-proteom-center.de/>
>

-- 

Dr. Daniel Schober
Senior Ontologist, Data manager

Leibniz Institute of Plant Biochemistry, http://www.IPB-Halle.de
Dept. for Stress and Developmental Biology Bioinformatics & Mass Spectrometry
Weinberg 3 Tel. +49 (0) 345 5582 - 1476
06120 Halle

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

[mayerg97 <ger...@ru...>]

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%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051
>     <http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051>
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

-- 

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

*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 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] New version 4.0.12 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 4.0.12 of the psi-ms.obo file.
It contains new terms for Agilent instruments.


New CV terms in version 4.0.12 of psi-ms.obo:
=============================================
[Term]
id: MS:1002783
name: 6550 iFunnel Q-TOF LC/MS
def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002784
name: 6550A iFunnel Q-TOF LC/MS
def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002785
name: 6520B Q-TOF LC/MS
def: "The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002786
name: 6530A Q-TOF LC/MS
def: "The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002787
name: 6530B Q-TOF LC/MS
def: "The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002788
name: 6538 Q-TOF LC/MS
def: "The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002789
name: 6540 Q-TOF LC/MS
def: "The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002790
name: 6542 Q-TOF LC/MS
def: "The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002791
name: 6545 Q-TOF LC/MS
def: "The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002792
name: 6560 Q-TOF LC/MS
def: "The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002793
name: 6570 Q-TOF LC/MS
def: "The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002794
name: 6120B Quadrupole LC/MS
def: "The 6120B Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a single quadrupole mass 
spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002795
name: 6150 Quadrupole LC/MS
def: "The 6150 Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a single quadrupole mass 
spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002796
name: 6224 Time-of-Flight LC/MS
def: "The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography 
instrument combined with a Agilent time of flight mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002797
name: 6230A Time-of-Flight LC/MS
def: "The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography 
instrument combined with a Agilent time of flight mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002798
name: 6230B Time-of-Flight LC/MS
def: "The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography 
instrument combined with a Agilent time of flight mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002799
name: 6430 Triple Quadrupole LC/MS
def: "The 6430 Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a Agilent triple quadrupole mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002800
name: 6495A Triple Quadrupole LC/MS
def: "The 6495A Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a Agilent triple quadrupole mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002801
name: 6495B Triple Quadrupole LC/MS
def: "The 6495B Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a Agilent triple quadrupole mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002802
name: 7000A Triple Quadrupole GC/MS
def: "The 7000A Quadrupole GC/MS system is a Agilent gas chromatography 
instrument combined with a Agilent triple quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002803
name: 7000B Triple Quadrupole GC/MS
def: "The 7000B Quadrupole GC/MS system is a Agilent gas chromatography 
instrument combined with a Agilent triple quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002804
name: 7800 Quadrupole ICP-MS
def: "The 7800 Quadrupole ICP-MS system is a Agilent inductively couple 
plasma instrument combined with a Agilent quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002805
name: 8800 Triple Quadrupole ICP-MS
def: "The 8800 Quadrupole ICP-MS system is a Agilent inductively couple 
plasma instrument combined with a Agilent quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model


Changed CV terms in version 4.0.12 of psi-ms.obo:
=================================================
************ 6120 --> 6120A
[Term]
id: MS:1000469
name: 6120A Quadrupole LC/MS
def: "The 6120A Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a single quadrupole mass 
spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 
quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan 
speed and utilizes multiple signal acquisition." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

************ 6520 --> 6520A
[Term]
id: MS:1000677
name: 6520A Quadrupole Time-of-Flight LC/MS
def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer. This time of flight mass spectrometer has a m/z range of 
50-12000, mass accuracy of less than 2 ppm and resolution greater than 
26,000 at m/z 2722. It has multiple ion sources and can be used with 
multimode ion sources." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

Best Regards,
Gerhard

-- 

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

*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 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] REMINDER: HUPO PSI recommendation document (file format proBAM), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Proteomics community,

 

this is a reminder, that the 60-days public comments 

and external review phase ends in two weeks on 31st May!

 

See below for details of your contribution.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de

 



 

Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Donnerstag, 30. März 2017 09:50
An: 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'ps...@eb...'
<ps...@eb...>; 'psi...@eb...' <psi...@eb...>
Betreff: HUPO PSI recommendation document (file format proBAM), 60-days
public review

 

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

http://www.psidev.info for an overview of activities).

 

A recommendation document specifying the proBAM file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBAM-in-docproc

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 31st May 2017).

 

The format represents output from proteogenomic studies,

mapping the MS-based proteomics PSM information to 

the genome. Background: The proBAM format builds upon the structure of the

original SAM/BAM format (http://samtools.github.io/hts-specs/SAMv1.pdf)

by extending it with other mandatory fields to accommodate unique features

on MS-based proteomics peptide-spectrum matches (PSMs) information.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBAM-in-docproc) 

or send them directly to martin.eisenacher: at : rub.de for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de

 



 

Re: [Psidev-ms-dev] Release candidate 4.0.12_rc2 of psi-ms.obo

[Neumann, S. <sne...@ip...>]

Hi,

out of curiosity, does the MS know which LC it is coupled to ?

Is the difference between "6530A Q-TOF LC/MS" and "6530B Q-TOF LC/MS"
in the MS or LC side ? And what is it called if I shoehorn 
A Waters UPLC in front of it ? 

What I am trying to say is that unless these instrument models 
are in one box, or at least such that e.g. Proteoziward msconvert 
can distinguish them, it might be good to have separate Terms 
for the LC and MS parts of the setup. 

Just my 2c,
Yours,
Steffen






On Wed, 2017-05-10 at 12:47 +0200, mayerg97 wrote:
> Dear proteomics community,
> 
> attached there's the release candidate 4.0.12_rc2 of the psi-ms.obo
> file.
> It contains new terms for Agilent instruments.
> 
> New CV terms in version 4.0.12_rc2 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1002783
> name: 6550 iFunnel Q-TOF LC/MS
> def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002784
> name: 6550A iFunnel Q-TOF LC/MS
> def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002785
> name: 6520B Q-TOF LC/MS
> def: "The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002786
> name: 6530A Q-TOF LC/MS
> def: "The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002787
> name: 6530B Q-TOF LC/MS
> def: "The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002788
> name: 6538 Q-TOF LC/MS
> def: "The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002789
> name: 6540 Q-TOF LC/MS
> def: "The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002790
> name: 6542 Q-TOF LC/MS
> def: "The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002791
> name: 6545 Q-TOF LC/MS
> def: "The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002792
> name: 6560 Q-TOF LC/MS
> def: "The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002793
> name: 6570 Q-TOF LC/MS
> def: "The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002794
> name: 6120B Quadrupole LC/MS
> def: "The 6120B Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a single quadrupole mass
> spectrometer from the 6100 Series of Agilent mass spectrometers."
> [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002795
> name: 6150 Quadrupole LC/MS
> def: "The 6150 Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a single quadrupole mass
> spectrometer from the 6100 Series of Agilent mass spectrometers."
> [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002796
> name: 6224 Time-of-Flight LC/MS
> def: "The 6224 Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002797
> name: 6230A Time-of-Flight LC/MS
> def: "The 6230A Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002798
> name: 6230B Time-of-Flight LC/MS
> def: "The 6230B Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002799
> name: 6430 Triple Quadrupole LC/MS
> def: "The 6430 Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a Agilent triple quadrupole
> mass spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002800
> name: 6495A Triple Quadrupole LC/MS
> def: "The 6495A Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a Agilent triple quadrupole
> mass spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002801
> name: 6495B Triple Quadrupole LC/MS
> def: "The 6495B Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a Agilent triple quadrupole
> mass spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002802
> name: 7000A Triple Quadrupole GC/MS
> def: "The 7000A Quadrupole GC/MS system is a Agilent gas
> chromatography instrument combined with a Agilent triple quadrupole
> mass spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002803
> name: 7000B Triple Quadrupole GC/MS
> def: "The 7000B Quadrupole GC/MS system is a Agilent gas
> chromatography instrument combined with a Agilent triple quadrupole
> mass spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002804
> name: 7800 Quadrupole ICP-MS
> def: "The 7800 Quadrupole ICP-MS system is a Agilent inductively
> couple plasma instrument combined with a Agilent quadrupole mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002805
> name: 8800 Triple Quadrupole ICP-MS
> def: "The 8800 Quadrupole ICP-MS system is a Agilent inductively
> couple plasma instrument combined with a Agilent quadrupole mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> 
> 
> Changed CV terms in version 4.0.12_rc2 of psi-ms.obo:
> =====================================================
> ************ 6120 --> 6120A
> [Term]
> id: MS:1000469
> name: 6120A Quadrupole LC/MS
> def: "The 6120A Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a single quadrupole mass
> spectrometer from the 6100 Series of Agilent mass spectrometers. 6120
> quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan
> speed and utilizes multiple signal acquisition." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> ************ 6520 --> 6520A
> [Term]
> id: MS:1000677
> name: 6520A Quadrupole Time-of-Flight LC/MS
> def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer. This time of flight mass spectrometer has a m/z range
> of 50-12000, mass accuracy of less than 2 ppm and resolution greater
> than 26,000 at m/z 2722. It has multiple ion sources and can be used
> with multimode ion sources." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> Best Regards,
> Gerhard
> -- 
> --------------------------------------------------------------------
> 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
> -------------------------------------------------------------------
> -----------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] Release candidate 4.0.12_rc2 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 4.0.12_rc2 of the psi-ms.obo file.
It contains new terms for Agilent instruments.

New CV terms in version 4.0.12_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002783
name: 6550 iFunnel Q-TOF LC/MS
def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002784
name: 6550A iFunnel Q-TOF LC/MS
def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002785
name: 6520B Q-TOF LC/MS
def: "The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002786
name: 6530A Q-TOF LC/MS
def: "The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002787
name: 6530B Q-TOF LC/MS
def: "The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002788
name: 6538 Q-TOF LC/MS
def: "The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002789
name: 6540 Q-TOF LC/MS
def: "The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002790
name: 6542 Q-TOF LC/MS
def: "The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002791
name: 6545 Q-TOF LC/MS
def: "The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002792
name: 6560 Q-TOF LC/MS
def: "The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002793
name: 6570 Q-TOF LC/MS
def: "The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002794
name: 6120B Quadrupole LC/MS
def: "The 6120B Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a single quadrupole mass 
spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002795
name: 6150 Quadrupole LC/MS
def: "The 6150 Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a single quadrupole mass 
spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002796
name: 6224 Time-of-Flight LC/MS
def: "The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography 
instrument combined with a Agilent time of flight mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002797
name: 6230A Time-of-Flight LC/MS
def: "The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography 
instrument combined with a Agilent time of flight mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002798
name: 6230B Time-of-Flight LC/MS
def: "The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography 
instrument combined with a Agilent time of flight mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002799
name: 6430 Triple Quadrupole LC/MS
def: "The 6430 Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a Agilent triple quadrupole mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002800
name: 6495A Triple Quadrupole LC/MS
def: "The 6495A Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a Agilent triple quadrupole mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002801
name: 6495B Triple Quadrupole LC/MS
def: "The 6495B Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a Agilent triple quadrupole mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002802
name: 7000A Triple Quadrupole GC/MS
def: "The 7000A Quadrupole GC/MS system is a Agilent gas chromatography 
instrument combined with a Agilent triple quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002803
name: 7000B Triple Quadrupole GC/MS
def: "The 7000B Quadrupole GC/MS system is a Agilent gas chromatography 
instrument combined with a Agilent triple quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002804
name: 7800 Quadrupole ICP-MS
def: "The 7800 Quadrupole ICP-MS system is a Agilent inductively couple 
plasma instrument combined with a Agilent quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002805
name: 8800 Triple Quadrupole ICP-MS
def: "The 8800 Quadrupole ICP-MS system is a Agilent inductively couple 
plasma instrument combined with a Agilent quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model



Changed CV terms in version 4.0.12_rc2 of psi-ms.obo:
=====================================================
************ 6120 --> 6120A
[Term]
id: MS:1000469
name: 6120A Quadrupole LC/MS
def: "The 6120A Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a single quadrupole mass 
spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 
quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan 
speed and utilizes multiple signal acquisition." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

************ 6520 --> 6520A
[Term]
id: MS:1000677
name: 6520A Quadrupole Time-of-Flight LC/MS
def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer. This time of flight mass spectrometer has a m/z range of 
50-12000, mass accuracy of less than 2 ppm and resolution greater than 
26,000 at m/z 2722. It has multiple ion sources and can be used with 
multimode ion sources." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

Best Regards,
Gerhard

-- 

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

*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 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] Release candidate 4.0.12_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 4.0.12_rc1 of the psi-ms.obo file.
It contains two new terms for Agilent instruments.

New CV terms in version 4.0.12_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002783
name: 6550 iFunnel Q-TOF LC/MS
def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002784
name: 6550A iFunnel Q-TOF LC/MS
def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

Best Regards,
Gerhard

-- 

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

*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 
<http://www.medizinisches-proteom-center.de/>

Re: [Psidev-ms-dev] Possible inconsistency between XSD and documentation

[Race, A. <Ala...@un...>]

Hi Eric,
Sorry for the late reply. Thanks for looking into this. Unfortunately I couldn’t attend the workshop, but I look forward to hearing the outcome of the discussions.

Regards,

Alan

From: Eric Deutsch [mailto:ede...@sy...]
Sent: 08 April 2017 15:02
To: Mass spectrometry standard development <psi...@li...>
Cc: Eric Deutsch <ede...@sy...>
Subject: Re: [Psidev-ms-dev] Possible inconsistency between XSD and documentation

Hi Alan, thank you very much for your several emails about mzML. I’ve not had a chance to study the issues that you point out yet, but I am currently organizing the topics to discuss and address at the PSI workshop later this month, and your issues will be addressed there. Will you be joining us for the workshop?

Regards,
Eric


From: Race, Alan [mailto:Ala...@un...<mailto:Ala...@un...>]
Sent: Monday, April 03, 2017 5:52 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Possible inconsistency between XSD and documentation

Dear all,
I looked into this a little further and there seem to be a few missing reference definitions within the XSD file that could help in the validation of mzML files. Please find attached a patch file for your consideration that includes the proposed changes for adding the missing definitions.

Thanks,

Alan

From: Race, Alan
Sent: 29 March 2017 11:48
To: 'Mass spectrometry standard development' <psi...@li...<mailto:psi...@li...>>
Subject: Possible inconsistency between XSD and documentation

Hello,
I have possibly noticed an inconsistency between the mzML1.1.0.xsd and the documentation as it appears here: http://www.peptideatlas.org/tmp/mzML1.1.0.html#run

The selector for the keyref KEYREF_DEFAULTICREF states that the defaultInstrumentConfigurationRef attribute is found on the spectrumList and the chromatogramList tags, however the documentation states that it should be on the run tag.

Changing:

<xs:keyref name="KEYREF_DEFAULTICREF" refer="dx:KEY_IC_ID">
      …
               <xs:selector xpath="./dx:run/dx:spectrumList|./dx:run/dx:chromatogramList" />
      …
</xs:keyref>

To:

<xs:keyref name="KEYREF_DEFAULTICREF" refer="dx:KEY_IC_ID">
      …
               <xs:selector xpath="./dx:run" />
      …
</xs:keyref>

Seems to produce the correct output when validating. In a vaguely related note, and out of curiosity – why does the schema constrict the spectrum ID to the pattern "\S+=\S+( \S+=\S+)*"?

Thanks,

Alan

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

[Reza S. <r7...@gm...>]

Hi all,

We are now working on the mzTab specifications aim to finals it (or near finals) in the next two days. Question of adduct CV was discussed here again. Any follow up on this to make it happened? any volunteers? suggestions?

Best wishes,
Reza

> On 5 Jan 2017, at 20:0mzTab specifucation 8, Joel Rein <Joe...@wa...> wrote:
> 
> 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%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051 <http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "mztab4metabolomics" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to mzt...@go... <mailto:mzt...@go...>.
> To post to this group, send email to mzt...@go... <mailto:mzt...@go...>.
> To view this discussion on the web, visit https://groups.google.com/d/msgid/mztab4metabolomics/a692ea6a-c867-4851-a310-d38b966670a5%40googlegroups.com <https://groups.google.com/d/msgid/mztab4metabolomics/a692ea6a-c867-4851-a310-d38b966670a5%40googlegroups.com?utm_medium=email&utm_source=footer>.
> For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.

Re: [Psidev-ms-dev] mzML validator

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

Hi Dave, you're right, there are two mzML semantic validators listed at
http://www.psidev.info/mzml:

 - mzML semantic validator
<http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/mzML/> created
by Marc Sturm (OpenMS/TOPP <http://www.openms.de>)
http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/mzML/

 - mzML semantic validator
<http://eddie.thep.lu.se/prodac_validator/validator.pl> at ProDaC
http://eddie.thep.lu.se/prodac_validator/validator.pl

But both are not working.



Does anyone out there know if the URLs for these services have moved or
discontinued or just temporarily in need of service?



One can still download and install locally the validators at
http://www.openms.de/

And https://github.com/HUPO-PSI/mzML/tree/master/validator



Thanks,

Eric





-----Original Message-----
From: David Tabb [mailto:dt...@su...]
Sent: Tuesday, April 18, 2017 2:53 AM
To: Eric Deutsch
Subject: mzML validator



Hi, Eric.



I am trying to use mzML as a format to demonstrate XML validation

against standards.  Sadly, it appears that the link to "MS validator" at

http://www.psidev.info/validator is no longer working.  Do you know an

updated URL?



Thanks,

Dave



The integrity and confidentiality of this email is governed by these terms
/ Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos.
http://www.sun.ac.za/emaildisclaimer

[Psidev-ms-dev] New version 4.0.11 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 4.0.11 of the psi-ms.obo file.

It contains new and changed terms for isobaric labelling and
reporter ions used in quantification by isobaric labelling techniques.


New CV terms in version 4.0.11 of psi-ms.obo:
=============================================
************ New terms for isobaric labelling techniques
[Term]
id: MS:1002756
name: iodoTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher sulfhydryl-reactive 
iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002757
name: glyco-TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, 
PMID:22455665]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002758
name: aminoxyTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002759
name: hydrazideTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002760
name: iTRAQH quantitation analysis
def: "Quantification analysis using the carbonyl-reactive isobaric tags 
for relative and absolute quantification hydrazide (iTRAQH) labelling 
workflow." [PSI:PI, PMID:22926130]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002761
name: DiART quantitation analysis
def: "Quantification analysis using the amine-reactive deuterium 
isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, 
PMID:20715779]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002762
name: DiLeu quantitation analysis
def: "Quantification analysis using the amine-reactive dimethyl leucine 
(DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ New terms for TMT 10-plex reagents
[Term]
id: MS:1002763
name: TMT reagent 127N
def: "The name of the sample labelled with the TMT reagent 127N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002764
name: TMT reagent 127C
def: "The name of the sample labelled with the TMT reagent 127C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002765
name: TMT reagent 128N
def: "The name of the sample labelled with the TMT reagent 128N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002766
name: TMT reagent 128C
def: "The name of the sample labelled with the TMT reagent 128C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002767
name: TMT reagent 129N
def: "The name of the sample labelled with the TMT reagent 129N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002768
name: TMT reagent 129C
def: "The name of the sample labelled with the TMT reagent 129C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent
[Term]
id: MS:1002769
name: TMT reagent 130N
def: "The name of the sample labelled with the TMT reagent 130N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002770
name: TMT reagent 130C
def: "The name of the sample labelled with the TMT reagent 130C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

************ New terms for DiART labelling reagents
[Term]
id: MS:1002771
name: DiART reagent
def: "Deuterium isobaric amine reactive tag labeling reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002772
name: DiART reagent 114
def: "The name of the sample labelled with the DiART reagent 114." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002773
name: DiART reagent 115
def: "The name of the sample labelled with the DiART reagent 115." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002774
name: DiART reagent 116
def: "The name of the sample labelled with the DiART reagent 116." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002775
name: DiART reagent 117
def: "The name of the sample labelled with the DiART reagent 117." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002776
name: DiART reagent 118
def: "The name of the sample labelled with the DiART reagent 118." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002777
name: DiART reagent 119
def: "The name of the sample labelled with the DiART reagent 119." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

************ New terms for DiLeu labelling reagents
[Term]
id: MS:1002778
name: DiLeu reagent
def: "Dimethyl leucine labeling reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002779
name: DiLeu reagent 115
def: "The name of the sample labelled with the DiLeu reagent 115." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002780
name: DiLeu reagent 116
def: "The name of the sample labelled with the DiLeu reagent 116." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002781
name: DiLeu reagent 117
def: "The name of the sample labelled with the DiLeu reagent 117." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002782
name: DiLeu reagent 118
def: "The name of the sample labelled with the DiLeu reagent 118." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent


Changed CV terms in version 4.0.11 of psi-ms.obo:
=================================================
************ added is_a: MS:1001833 ! quantitation analysis summary
************ added amine-reactive to the definition
[Term]
id: MS:1001837
name: iTRAQ quantitation analysis
def: "Quantification analysis using the SCIEX amine-reactive isobaric 
tags for relative and absolute quantification (iTRAQ) labelling 
workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in 
the 114-121 m/z range." [PSI:PI, PMID:15385600]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ added amine-reactive to the definition
[Term]
id: MS:1002010
name: TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher amine-reactive 
tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are 
measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ added is_a: MS:1001833 ! quantitation analysis summary
************ and added PMID-reference
[Term]
id: MS:1002212
name: IPTL quantitation analysis
def: "Quantification analysis using a labelling strategy where both 
peptide termini are labelled so that the peptides from different 
labelling schema are isobaric." [PSI:PI, PMID:19655813]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ Changed definition to include glycoTMT, iodoTMT, aminoxyTMT 
or hydrazideTMT
[Term]
id: MS:1002615
name: TMT reagent
def: "Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT 
or hydrazideTMT isobaric labeling." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

************ Changed definition to include iTRAQH
[Term]
id: MS:1002622
name: iTRAQ reagent
def: "Isobaric tag for relative and absolute quantitation (iTRAQ or 
iTRAQH) reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

Best Regards,
Gerhard

-- 

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

*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 
<http://www.medizinisches-proteom-center.de/>

Re: [Psidev-ms-dev] Possible inconsistency between XSD and documentation

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

Hi Alan, thank you very much for your several emails about mzML. I’ve not
had a chance to study the issues that you point out yet, but I am currently
organizing the topics to discuss and address at the PSI workshop later this
month, and your issues will be addressed there. Will you be joining us for
the workshop?



Regards,

Eric





*From:* Race, Alan [mailto:Ala...@un...]
*Sent:* Monday, April 03, 2017 5:52 AM
*To:* Mass spectrometry standard development
*Subject:* Re: [Psidev-ms-dev] Possible inconsistency between XSD and
documentation



Dear all,

I looked into this a little further and there seem to be a few missing
reference definitions within the XSD file that could help in the validation
of mzML files. Please find attached a patch file for your consideration
that includes the proposed changes for adding the missing definitions.



Thanks,



Alan



*From:* Race, Alan
*Sent:* 29 March 2017 11:48
*To:* 'Mass spectrometry standard development' <
psi...@li...>
*Subject:* Possible inconsistency between XSD and documentation



Hello,

I have possibly noticed an inconsistency between the mzML1.1.0.xsd and the
documentation as it appears here:
http://www.peptideatlas.org/tmp/mzML1.1.0.html#run



The selector for the keyref KEYREF_DEFAULTICREF states that the
defaultInstrumentConfigurationRef attribute is found on the spectrumList
and the chromatogramList tags, however the documentation states that it
should be on the run tag.



Changing:



<xs:keyref name="KEYREF_DEFAULTICREF" refer="dx:KEY_IC_ID">

      …

               <xs:selector
xpath="./dx:run/dx:spectrumList|./dx:run/dx:chromatogramList" />

      …

</xs:keyref>



To:



<xs:keyref name="KEYREF_DEFAULTICREF" refer="dx:KEY_IC_ID">

      …

               <xs:selector xpath="./dx:run" />

      …

</xs:keyref>



Seems to produce the correct output when validating. In a vaguely related
note, and out of curiosity – why does the schema constrict the spectrum ID
to the pattern "\S+=\S+( \S+=\S+)*"?



Thanks,



Alan

Re: [Psidev-ms-dev] Possible inconsistency between XSD and documentation

[Race, A. <Ala...@un...>]

Dear all,
I looked into this a little further and there seem to be a few missing reference definitions within the XSD file that could help in the validation of mzML files. Please find attached a patch file for your consideration that includes the proposed changes for adding the missing definitions.

Thanks,

Alan

From: Race, Alan
Sent: 29 March 2017 11:48
To: 'Mass spectrometry standard development' <psi...@li...>
Subject: Possible inconsistency between XSD and documentation

Hello,
I have possibly noticed an inconsistency between the mzML1.1.0.xsd and the documentation as it appears here: http://www.peptideatlas.org/tmp/mzML1.1.0.html#run

The selector for the keyref KEYREF_DEFAULTICREF states that the defaultInstrumentConfigurationRef attribute is found on the spectrumList and the chromatogramList tags, however the documentation states that it should be on the run tag.

Changing:

<xs:keyref name="KEYREF_DEFAULTICREF" refer="dx:KEY_IC_ID">
      ...
               <xs:selector xpath="./dx:run/dx:spectrumList|./dx:run/dx:chromatogramList" />
      ...
</xs:keyref>

To:

<xs:keyref name="KEYREF_DEFAULTICREF" refer="dx:KEY_IC_ID">
      ...
               <xs:selector xpath="./dx:run" />
      ...
</xs:keyref>

Seems to produce the correct output when validating. In a vaguely related note, and out of curiosity - why does the schema constrict the spectrum ID to the pattern "\S+=\S+( \S+=\S+)*"?

Thanks,

Alan

[Psidev-ms-dev] Release candidate 4.0.11_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 4.0.11_rc1 of the psi-ms.obo file.

It contains new and changed terms for isobaric labelling and
reporter ions used in quantification by isobaric labelling techniques.


New CV terms in version 4.0.11_rc1 of psi-ms.obo:
=================================================
************ New terms for isobaric labelling techniques
[Term]
id: MS:1002756
name: iodoTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher sulfhydryl-reactive 
iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002757
name: glyco-TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, 
PMID:22455665]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002758
name: aminoxyTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002759
name: hydrazideTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002760
name: iTRAQH quantitation analysis
def: "Quantification analysis using the carbonyl-reactive isobaric tags 
for relative and absolute quantification hydrazide (iTRAQH) labelling 
workflow." [PSI:PI, PMID:22926130]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002761
name: DiART quantitation analysis
def: "Quantification analysis using the amine-reactive deuterium 
isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, 
PMID:20715779]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002762
name: DiLeu quantitation analysis
def: "Quantification analysis using the amine-reactive dimethyl leucine 
(DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ New terms for TMT 10-plex reagents
[Term]
id: MS:1002763
name: TMT reagent 127N
def: "The name of the sample labelled with the TMT reagent 127N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002764
name: TMT reagent 127C
def: "The name of the sample labelled with the TMT reagent 127C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002765
name: TMT reagent 128N
def: "The name of the sample labelled with the TMT reagent 128N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002766
name: TMT reagent 128C
def: "The name of the sample labelled with the TMT reagent 128C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002767
name: TMT reagent 129N
def: "The name of the sample labelled with the TMT reagent 129N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002768
name: TMT reagent 129C
def: "The name of the sample labelled with the TMT reagent 129C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent
[Term]
id: MS:1002769
name: TMT reagent 130N
def: "The name of the sample labelled with the TMT reagent 130N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002770
name: TMT reagent 130C
def: "The name of the sample labelled with the TMT reagent 130C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

************ New terms for DiART labelling reagents
[Term]
id: MS:1002771
name: DiART reagent
def: "Deuterium isobaric amine reactive tag labeling reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002772
name: DiART reagent 114
def: "The name of the sample labelled with the DiART reagent 114." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002773
name: DiART reagent 115
def: "The name of the sample labelled with the DiART reagent 115." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002774
name: DiART reagent 116
def: "The name of the sample labelled with the DiART reagent 116." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002775
name: DiART reagent 117
def: "The name of the sample labelled with the DiART reagent 117." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002776
name: DiART reagent 118
def: "The name of the sample labelled with the DiART reagent 118." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002777
name: DiART reagent 119
def: "The name of the sample labelled with the DiART reagent 119." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

************ New terms for DiLeu labelling reagents
[Term]
id: MS:1002778
name: DiLeu reagent
def: "Dimethyl leucine labeling reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002779
name: DiLeu reagent 115
def: "The name of the sample labelled with the DiLeu reagent 115." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002780
name: DiLeu reagent 116
def: "The name of the sample labelled with the DiLeu reagent 116." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002781
name: DiLeu reagent 117
def: "The name of the sample labelled with the DiLeu reagent 117." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002782
name: DiLeu reagent 118
def: "The name of the sample labelled with the DiLeu reagent 118." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent


Changed CV terms in version 4.0.11_rc1 of psi-ms.obo:
=====================================================
************ added is_a: MS:1001833 ! quantitation analysis summary
************ added amine-reactive to the definition
[Term]
id: MS:1001837
name: iTRAQ quantitation analysis
def: "Quantification analysis using the SCIEX amine-reactive isobaric 
tags for relative and absolute quantification (iTRAQ) labelling 
workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in 
the 114-121 m/z range." [PSI:PI, PMID:15385600]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ added amine-reactive to the definition
[Term]
id: MS:1002010
name: TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher amine-reactive 
tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are 
measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ added is_a: MS:1001833 ! quantitation analysis summary
************ and added PMID-reference
[Term]
id: MS:1002212
name: IPTL quantitation analysis
def: "Quantification analysis using a labelling strategy where both 
peptide termini are labelled so that the peptides from different 
labelling schema are isobaric." [PSI:PI, PMID:19655813]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ Changed definition to include glycoTMT, iodoTMT, aminoxyTMT 
or hydrazideTMT
[Term]
id: MS:1002615
name: TMT reagent
def: "Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT 
or hydrazideTMT isobaric labeling." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

************ Changed definition to include iTRAQH
[Term]
id: MS:1002622
name: iTRAQ reagent
def: "Isobaric tag for relative and absolute quantitation (iTRAQ or 
iTRAQH) reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent


Best Regards,
Gerhard

-- 

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

*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 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] New version 4.0.10 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 4.0.10 of the psi-ms.obo file.

It contains corrections for the names of is_a relationships for several 
terms,
which result from our ontology reorganisation last summer.

Thanks Hannes, for pointing out these inconsistencies.


New CV terms in version 4.0.10 of psi-ms.obo:
=============================================
************ No new terms


Changed CV terms in version 4.0.10 of psi-ms.obo:
=================================================
************ is_a: MS:1001105 ! peptide result details
************ replaced by
************ is_a: MS:1001105 ! peptide sequence-level identification 
attribute
[Term]
id: MS:1001114
name: retention time(s)
def: "OBSOLETE Retention time of the spectrum from the source file." 
[PSI:PI]
comment: This term was made obsolete because scan start time 
(MS:1000016) should be used instead.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
is_obsolete: true

************ is_a: MS:1001092 ! peptide identification confidence metric
************ replaced by
************ is_a: MS:1001092 ! peptide sequence-level identification 
statistic
[Term]
id: MS:1001191
name: p-value
def: "OBSOLETE Quality estimation by p-value." [PSI:PI]
comment: This term was made obsolete because now is split into peptide 
and protein terms.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
is_a: MS:1001198 ! protein identification confidence metric
is_obsolete: true

************ is_a: MS:1001116 ! single protein result details
************ replaced by
************ MS:1001116 ! single protein identification statistic
[Term]
id: MS:1001198
name: protein identification confidence metric
def: "Identification confidence metric for a protein." [PSI:PI]
is_a: MS:1001116 ! single protein identification statistic

************ is_a: MS:1001143 ! search engine specific score for PSMs
************ replaced by
************ is_a: MS:1001143 ! PSM-level search engine specific statistic
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more 
specific terms for PSM-level FDRScore (1002355), distinct peptide-level 
FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein 
group-level FDRScore (MS:1002374).
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
is_obsolete: true

************ is_a: MS:1001116 ! single protein result details
************ replaced by
************ is_a: MS:1001116 ! single protein identification statistic
[Term]
id: MS:1002268
name: Byonic:Best LogProb
def: "Best (most negative) log p-value of an individual PSM." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002109 ! lower score better

************ is_a: MS:1002405 ! protein cluster details
************ replaced by
************ is_a: MS:1002405 ! protein group-level result list attribute
[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which 
must match the number of clusters that pass the threshold in the file." 
[PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002405 ! protein group-level result list attribute

************ is_a: MS:1002358 ! search engine specific score for 
distinct peptides
************ replaced by
************ is_a: MS:1002358 ! search engine specific peptide 
sequence-level identification statistic
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in 
the CV.
is_a: MS:1002358 ! search engine specific peptide sequence-level 
identification statistic
is_obsolete: true

************ is_a: MS:1001143 ! search engine specific score for PSMs
************ replaced by
************ is_a: MS:1001143 ! PSM-level search engine specific statistic
************ in the following six OpenXQuest terms
[Term]
id: MS:1002681
name: OpenXQuest:combined score
def: "OpenXQuest's combined score for a cross-link spectrum match." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002682
name: OpenXQuest:xcorr xlink
def: "OpenXQuest's cross-correlation of cross-linked ions subscore." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002683
name: OpenXQuest:xcorr common
def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002684
name: OpenXQuest:match-odds
def: "OpenXQuest's match-odds subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002685
name: OpenXQuest:intsum
def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002686
name: OpenXQuest:wTIC
def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ is_a: MS:1001073 ! database type
************ replaced by
************ is_a: MS:1001073 ! database type amino acid
[Term]
id: MS:1002752
name: database type spectral library
def: "Database containing spectra." [PSI:PI]
is_a: MS:1001073 ! database type amino acid

************ Removed
************ is_a: MS:1001153 ! search engine specific score
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more 
specific terms for PSM-level FDRScore (1002355), distinct peptide-level 
FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein 
group-level FDRScore (MS:1002374).
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_obsolete: true

Best Regards,
Gerhard

-- 

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

*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 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] HUPO PSI recommendation document (file format proBAM), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

http://www.psidev.info for an overview of activities).

 

A recommendation document specifying the proBAM file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBAM-in-docproc

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 31st May 2017).

 

The format represents output from proteogenomic studies,

mapping the MS-based proteomics PSM information to 

the genome. Background: The proBAM format builds upon the structure of the

original SAM/BAM format (http://samtools.github.io/hts-specs/SAMv1.pdf)

by extending it with other mandatory fields to accommodate unique features

on MS-based proteomics peptide-spectrum matches (PSMs) information.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBAM-in-docproc) 

or send them directly to martin.eisenacher: at : rub.de for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de

 



 

[Psidev-ms-dev] Release candidate 4.0.10_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 4.0.10_rc1 of the psi-ms.obo file.

It contains corrections for the names of is_a relationships for several 
terms,
which result from our ontology reorganisation last summer.

Thanks Hannes, for pointing out these inconsistencies.


New CV terms in version 4.0.10_rc1 of psi-ms.obo:
=================================================
************ No new terms


Changed CV terms in version 4.0.10_rc1 of psi-ms.obo:
=====================================================
************ is_a: MS:1001105 ! peptide result details
************ replaced by
************ is_a: MS:1001105 ! peptide sequence-level identification 
attribute
[Term]
id: MS:1001114
name: retention time(s)
def: "OBSOLETE Retention time of the spectrum from the source file." 
[PSI:PI]
comment: This term was made obsolete because scan start time 
(MS:1000016) should be used instead.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
is_obsolete: true

************ is_a: MS:1001092 ! peptide identification confidence metric
************ replaced by
************ is_a: MS:1001092 ! peptide sequence-level identification 
statistic
[Term]
id: MS:1001191
name: p-value
def: "OBSOLETE Quality estimation by p-value." [PSI:PI]
comment: This term was made obsolete because now is split into peptide 
and protein terms.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
is_a: MS:1001198 ! protein identification confidence metric
is_obsolete: true

************ is_a: MS:1001116 ! single protein result details
************ replaced by
************ MS:1001116 ! single protein identification statistic
[Term]
id: MS:1001198
name: protein identification confidence metric
def: "Identification confidence metric for a protein." [PSI:PI]
is_a: MS:1001116 ! single protein identification statistic

************ is_a: MS:1001143 ! search engine specific score for PSMs
************ replaced by
************ is_a: MS:1001143 ! PSM-level search engine specific statistic
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more 
specific terms for PSM-level FDRScore (1002355), distinct peptide-level 
FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein 
group-level FDRScore (MS:1002374).
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
is_obsolete: true

************ is_a: MS:1001116 ! single protein result details
************ replaced by
************ is_a: MS:1001116 ! single protein identification statistic
[Term]
id: MS:1002268
name: Byonic:Best LogProb
def: "Best (most negative) log p-value of an individual PSM." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002109 ! lower score better

************ is_a: MS:1002405 ! protein cluster details
************ replaced by
************ is_a: MS:1002405 ! protein group-level result list attribute
[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which 
must match the number of clusters that pass the threshold in the file." 
[PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002405 ! protein group-level result list attribute

************ is_a: MS:1002358 ! search engine specific score for 
distinct peptides
************ replaced by
************ is_a: MS:1002358 ! search engine specific peptide 
sequence-level identification statistic
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in 
the CV.
is_a: MS:1002358 ! search engine specific peptide sequence-level 
identification statistic
is_obsolete: true

************ is_a: MS:1001143 ! search engine specific score for PSMs
************ replaced by
************ is_a: MS:1001143 ! PSM-level search engine specific statistic
************ in the following six OpenXQuest terms
[Term]
id: MS:1002681
name: OpenXQuest:combined score
def: "OpenXQuest's combined score for a cross-link spectrum match." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002682
name: OpenXQuest:xcorr xlink
def: "OpenXQuest's cross-correlation of cross-linked ions subscore." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002683
name: OpenXQuest:xcorr common
def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002684
name: OpenXQuest:match-odds
def: "OpenXQuest's match-odds subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002685
name: OpenXQuest:intsum
def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002686
name: OpenXQuest:wTIC
def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ is_a: MS:1001073 ! database type
************ replaced by
************ is_a: MS:1001073 ! database type amino acid
[Term]
id: MS:1002752
name: database type spectral library
def: "Database containing spectra." [PSI:PI]
is_a: MS:1001073 ! database type amino acid

************ Removed
************ is_a: MS:1001153 ! search engine specific score
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more 
specific terms for PSM-level FDRScore (1002355), distinct peptide-level 
FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein 
group-level FDRScore (MS:1002374).
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_obsolete: true

Best Regards,
Gerhard

-- 

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

*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 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] Possible inconsistency between XSD and documentation

[Race, A. <Ala...@un...>]

Hello,
I have possibly noticed an inconsistency between the mzML1.1.0.xsd and the documentation as it appears here: http://www.peptideatlas.org/tmp/mzML1.1.0.html#run

The selector for the keyref KEYREF_DEFAULTICREF states that the defaultInstrumentConfigurationRef attribute is found on the spectrumList and the chromatogramList tags, however the documentation states that it should be on the run tag.

Changing:

<xs:keyref name="KEYREF_DEFAULTICREF" refer="dx:KEY_IC_ID">
      ...
               <xs:selector xpath="./dx:run/dx:spectrumList|./dx:run/dx:chromatogramList" />
      ...
</xs:keyref>

To:

<xs:keyref name="KEYREF_DEFAULTICREF" refer="dx:KEY_IC_ID">
      ...
               <xs:selector xpath="./dx:run" />
      ...
</xs:keyref>

Seems to produce the correct output when validating. In a vaguely related note, and out of curiosity - why does the schema constrict the spectrum ID to the pattern "\S+=\S+( \S+=\S+)*"?

Thanks,

Alan

[Psidev-ms-dev] [BioSharing] Record Maintenance

[<bio...@gm...>]

<p>Dear Dear BioSharing maintainer/contact,<br/><br>We are contacting you on behalf of BioSharing, an ELIXIR-UK node resource based at the University of Oxford, UK, that manually curates inter-related records on data standards, databases and data policies in the life, biomedical and environmental sciences.<br/><br>Over the last 8 months we have manually curated/reviewed every standard and database record in BioSharing as part of our curation drive.<br/><br>We note that you are listed as a contact for the following record(s). We would be grateful if you could take a look at these records and not only assess them for accuracy but also consider claiming them. This will allow you to edit these records and correct any inaccuracies and update them as necessary. All edits will be reviewed by a BioSharing engineer to ensure they conform to our curation guidelines:<ul><li>mzData (<a href="https://biosharing.org/bsg-s000582">https://biosharing.org/bsg-s000582</a>)</li><li>Transition Markup Language (<a href="https://biosharing.org/bsg-s000113">https://biosharing.org/bsg-s000113</a>)</li></ul></p><br><p>If you are not the appropriate contact, could we please ask you to forward this email to the appropriate person/group. We would be grateful if the appropriate person could look over the record and check the details therein to ensure it is an accurate representation of your resource.<br/><br>One of the features that makes BioSharing so powerful is the ability for users to 'claim' records. This allows a user to maintain the BioSharing record for their resource themselves, so they can edit the record and update it whenever they please. Claiming is essentially a one-off vetting of the record, as the BioSharing team can take care of the record maintenance and will only email maintainers if there is a query with the resource record that they cannot solve themselves. Another advantage of claiming the record is that any changes to that record, or linking to that record from other records, will result in an email being sent to you, allowing you to validate any changes. Records can be maintained by an individual, a number of individuals, or a group email account.<br/><br>We work with journal and funder data editors to help them pick the right resources to recommend for use by authors and fundees. Claiming your record will ensure you resource is represented correctly and increase the chances of your resource being selected for endorsement.<br><br><br/>Many thanks in advance for your time and assistance.<br>Please do not hesitate to contact us at <bio...@li...> should you have any queries.<br/><br>Yours sincerely,<br>The BioSharing team</p>

[Psidev-ms-dev] New version 4.0.9 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 4.0.9 of the psi-ms.obo file.

It contains new terms for binary data arrays and their compression
and for spectral library searches.


New CV terms in version 4.0.9 of psi-ms.obo:
============================================
[Term]
id: MS:1002742
name: noise array
def: "A data array of noise values." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002743
name: sampled noise m/z array
def: "A data array of parallel, independent m/z values for a sampling of 
noise across a spectrum (typically much smaller than MS:1000514, the m/z 
array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1002744
name: sampled noise intensity array
def: "A data array of intensity values for the amplitude of noise 
variation superposed on the baseline (MS:1002745) across a spectrum (for 
use with MS:1002743, sampled noise m/z array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000131 ! number of detector counts

[Term]
id: MS:1002745
name: sampled noise baseline array
def: "A data array of baseline intensity values (the intensity in the 
absence of analytes) for a sampling of noise across a spectrum (for use 
with MS:1002743, sampled noise m/z array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002746
name: MS-Numpress linear prediction compression followed by zlib compression
def: "Compression using MS-Numpress linear prediction compression and 
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002747
name: MS-Numpress positive integer compression followed by zlib compression
def: "Compression using MS-Numpress positive integer compression and 
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002748
name: MS-Numpress short logged float compression followed by zlib 
compression
def: "Compression using MS-Numpress short logged float compression and 
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002749
name: Mascot:IntegratedSpectralLibrarySearch
def: "Means that Mascot has integrated the search results of database 
and spectral library search into a single data set." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1002750
name: NIST MSPepSearch
def: "Search tool of the NIST (National Institute of Standrads and 
Technology) for spectral library searches." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002751
name: NIST MSP format
def: "MSP text format defined by the NIST." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002752
name: database type spectral library
def: "Database containing spectra." [PSI:PI]
is_a: MS:1001073 ! database type

[Term]
id: MS:1002753
name: value between 0 and 1000 inclusive
def: "Value range for scores." [PSI:PI]
is_a: MS:1002304 ! domain range

[Term]
id: MS:1002754
name: MSPepSearch:score
def: "MSPepSearch score (0 for entirely dissimilar and 1000 for 
identical observed spectrum and library spectrum." [PSI:PI]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002753 ! value between 0 and 1000 inclusive

[Term]
id: MS:1002755
name: combined ms-ms + spectral library search
def: "A combined MS2 (with fragment ions) and spectral library search." 
[PSI:PI]
is_a: MS:1001080 ! search type


Changed CV terms in version 4.0.9 of psi-ms.obo:
================================================
************ Changed web link to the new GitHub adress 
https://github.com/ms-numpress/ms-numpress
[Term]
id: MS:1002312
name: MS-Numpress linear prediction compression
def: "Compression using MS-Numpress linear prediction compression." 
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002313
name: MS-Numpress positive integer compression
def: "Compression using MS-Numpress positive integer compression." 
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002314
name: MS-Numpress short logged float compression
def: "Compression using MS-Numpress short logged float compression." 
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

Best Regards,
Gerhard

-- 

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

*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 
<http://www.medizinisches-proteom-center.de/>

Re: [Psidev-ms-dev] Release candidate 4.0.9_rc1 of psi-ms.obo

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

Thank you Gerhard. This is pretty good. I think I would like a little more
clarification on the noise terms. Some suggestions in red:



id: MS:1002742
name: noise array
def: "A data array of noise values." [PSI:MS]

id: MS:1002743
name: sampled noise m/z array
def: "A data array of parallel, independent m/z values for a sampling of
noise across a spectrum (typically much smaller than MS:1000514, the m/z
array)." [PSI:MS]

id: MS:1002744
name: sampled noise intensity array
def: "A data array of intensity values for the amplitude of noise variation
superposed on the baseline (MS:1002745) across a spectrum (for use with
MS:0002743, sampled noise m/z array)." [PSI:MS]

id: MS:1002745
name: sampled noise baseline array
def: "A data array of baseline intensity values (the intensity in the
absence of analytes) for a sampling of noise across a spectrum (for use
with MS:0002743, sampled noise m/z array)." [PSI:MS]

Does that clarify the intent accurately?



Thanks,

Eric





*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Tuesday, March 21, 2017 6:29 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] Release candidate 4.0.9_rc1 of psi-ms.obo



Dear proteomics community,

attached there's the release candidate 4.0.9_rc1 of the psi-ms.obo file.

It contains new terms for binary data arrays and their compression
and for spectral library searches.


New CV terms in version 4.0.9_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002742
name: noise array
def: "A data array of noise values." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002743
name: sampled noise m/z array
def: "A data array of parallel, independent m/z values for a sampling of
noise across a spectrum (typically much smaller than MS:1000514, the m/z
array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1002744
name: sampled noise intensity array
def: "A data array of intensity values for a sampling of noise across a
spectrum (for use with MS:0000000, sampled noise m/z array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000131 ! number of detector counts

[Term]
id: MS:1002745
name: sampled noise baseline array
def: "A data array of signal baseline values (the signal in the absence of
analytes) for a sampling of noise across a spectrum (for use with
MS:0000000, sampled noise m/z array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002746
name: MS-Numpress linear prediction compression followed by zlib compression
def: "Compression using MS-Numpress linear prediction compression and
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002747
name: MS-Numpress positive integer compression followed by zlib compression
def: "Compression using MS-Numpress positive integer compression and zlib."
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002748
name: MS-Numpress short logged float compression followed by zlib
compression
def: "Compression using MS-Numpress short logged float compression and
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002749
name: Mascot:IntegratedSpectralLibrarySearch
def: "Means that Mascot has integrated the search results of database and
spectral library search into a single data set." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1002750
name: NIST MSPepSearch
def: "Search tool of the NIST (National Institute of Standrads and
Technology) for spectral library searches." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002751
name: NIST MSP format
def: "MSP text format defined by the NIST." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002752
name: database type spectral library
def: "Database containing spectra." [PSI:PI]
is_a: MS:1001073 ! database type

[Term]
id: MS:1002753
name: value between 0 and 1000 inclusive
def: "Value range for scores." [PSI:PI]
is_a: MS:1002304 ! domain range

[Term]
id: MS:1002754
name: MSPepSearch:score
def: "MSPepSearch score (0 for entirely dissimilar and 1000 for identical
observed spectrum and library spectrum." [PSI:PI]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002753 ! value between 0 and 1000 inclusive

[Term]
id: MS:1002755
name: combined ms-ms + spectral library search
def: "A combined MS2 (with fragment ions) and spectral library search."
[PSI:PI]
is_a: MS:1001080 ! search type


Changed CV terms in version 4.0.9_rc1 of psi-ms.obo:
====================================================
************ Changed web link to the new GitHub adress
https://github.com/ms-numpress/ms-numpress
[Term]
id: MS:1002312
name: MS-Numpress linear prediction compression
def: "Compression using MS-Numpress linear prediction compression." [
https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002313
name: MS-Numpress positive integer compression
def: "Compression using MS-Numpress positive integer compression." [
https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002314
name: MS-Numpress short logged float compression
def: "Compression using MS-Numpress short logged float compression." [
https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

Best Regards,
Gerhard

-- 

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

*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