Re: [Psidev-pi-dev] [Psidev-ms-dev] PSI-MS: reporter ion cv terms

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

Hi Gerhard, many thanks for adjusting this. Regarding the reporter ions,
what does “mass resp. type” mean? If there is a value that must be
supplied, the term name and definition really should be about that value.

Thanks,

Eric



*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Tuesday, May 24, 2016 6:56 AM
*To:* Harald Barsnes; psi...@li...;
psi...@li...; psi...@li...
*Subject:* Re: [Psidev-ms-dev] PSI-MS: reporter ion cv terms



Hi all,

how about the following terms?

************ New terms for neutral losses
[Term]
id: MS:1002668
name: HPO3 neutral loss
def: "Neutral loss of phosphite." [PSI:PI]
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search

[Term]
id: MS:1002669
name: CH4OS neutral loss
def: "Neutral loss of methanesulfenic acid." [PSI:PI]
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search

[Term]
id: MS:1002670
name: C3H9N neutral loss
def: "Neutral loss of C3H9N." [PSI:PI]
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search

************ New terms for reporter ions. The mass resp. type can be
specified in the value slot.
[Term]
id: MS:1002671
name: frag: iTRAQ 4plex reporter ion
def: "Standard reporter ion for iTRAQ 4Plex." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002672
name: frag: iTRAQ 8plex reporter ion
def: "Standard reporter ion for iTRAQ 8Plex." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002673
name: frag: TMT reporter ion
def: "Standard reporter ion for TMT." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002674
name: frag: TMT ETD reporter ion
def: "Standard reporter ion for TMT ETD." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

Best regards,
Gerhard

Am 24.05.2016 um 12:55 schrieb Harald Barsnes:


Hi Gerhard,

Thanks for adding the neutral losses CV terms. Would be great if you could
also add CV terms for the following reporter ions.


iTRAQ 4plex:

Name: frag: iTRAQ 4plex 114 reporter ion
Description: Standard reporter ion for iTRAQ 4Plex 114.

Name: frag: iTRAQ 4plex 115 reporter ion
Description: Standard reporter ion for iTRAQ 4Plex 115.

Name: frag: iTRAQ 4plex 116 reporter ion
Description: Standard reporter ion for iTRAQ 4Plex 116.

Name: frag: iTRAQ 4plex 117 reporter ion
Description: Standard reporter ion for iTRAQ 4Plex 117.


iTRAQ 8plex:

Name: frag: iTRAQ 8plex 113 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 113.

Name: frag: iTRAQ 8plex 114 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 114.

Name: frag: iTRAQ 8plex 115 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 115.

Name: frag: iTRAQ 8plex 116 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 116.

Name: frag: iTRAQ 8plex 117 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 117.

Name: frag: iTRAQ 8plex 118 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 118.

Name: frag: iTRAQ 8plex 119 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 119.

Name: frag: iTRAQ 8plex 121 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 121.


TMT:

Name: frag: TMT 126 reporter ion
Description: Standard reporter ion for TMT 126.

Name: frag: TMT 127N reporter ion
Description: Standard reporter ion for TMT 127N.

Name: frag: TMT 127C reporter ion
Description: Standard reporter ion for TMT 127C.

Name: frag: TMT 128N reporter ion
Description: Standard reporter ion for TMT 128N.

Name: frag: TMT 128C reporter ion
Description: Standard reporter ion for TMT 128C.

Name: frag: TMT 128N reporter ion
Description: Standard reporter ion for TMT 128N.

Name: frag: TMT 128C reporter ion
Description: Standard reporter ion for TMT 128C.

Name: frag: TMT 130N reporter ion
Description: Standard reporter ion for TMT 130N.

Name: frag: TMT 130C reporter ion
Description: Standard reporter ion for TMT 130C.

Name: frag: TMT 131 reporter ion
Description: Standard reporter ion for TMT 131.

Name: frag: TMT 126 ETD reporter ion
Description: Standard reporter ion for TMT 126 ETD.

Name: frag: TMT 127N ETD reporter ion
Description: Standard reporter ion for TMT 127N ETD.

Name: frag: TMT 127C ETD reporter ion
Description: Standard reporter ion for TMT 127C ETD.

Name: frag: TMT 128N ETD reporter ion
Description: Standard reporter ion for TMT 128N ETD.

Name: frag: TMT 128C ETD reporter ion
Description: Standard reporter ion for TMT 128C ETD.

Name: frag: TMT 129N ETD reporter ion
Description: Standard reporter ion for TMT 129N ETD.

Name: frag: TMT 129C ETD reporter ion
Description: Standard reporter ion for TMT 129C ETD.

Name: frag: TMT 130N ETD reporter ion
Description: Standard reporter ion for TMT 130N ETD.

Name: frag: TMT 130C ETD reporter ion
Description: Standard reporter ion for TMT 130C ETD.

Name: frag: TMT 131 ETD reporter ion
Description: Standard reporter ion for TMT 131 ETD.


All should be children of MS:1002307 (fragmentation ion type).


Thanks in advance.

Best regards,
Harald



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