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MICommunity / psidev

@Deprecated please use https://github.com/HUPO-PSI Code exported from http://sourceforge.net/p/psidev/cvs/
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Succinyl Lysine derivatization #534

Open SourceForge-exporter opened 9 years ago

SourceForge-exporter commented 9 years ago

MOD:01314 represents the reagent-labeling experiment with succinic anhydride using "natural abundance" succinic anhydride. MOD:01315 is the same experiment as MOD:01314 where 1H4 is replaced with 2H4 MOD:01316 is the same experiment as MOD:01314 where 12C4 is replaced with 13C4

Therefore

MOD:01314 should NOT be is_a MOD:01426, it should be is_a MOD:00848
MOD:01315 should be is_a MOD:01426 MOD:01316 should be is_a MOD:01426

Reported by: pmthomas

SourceForge-exporter commented 9 years ago

MOD:01314 4x(1)H,4x(12)C-labeled N6-succinyl-L-lysine is_a MOD:01819 N6-succinyl-L-lysine which is the natural isotope abundance form and has "Source: natural" while MOD:01314 is specifically the isotope labeled form. And since all specifically isotope labeled forms are regarded as artificial, it has "Source: artifact". Likewise, MOD:01315 and MOD:01316 are specifically isotope labeled forms, and so all are MOD:01426 isotope tagged reagent derivatized residue. The difference between MOD:01314 and MOD:01819 is that the average mw's are 228.11 and 228.25 respectively (MOD:01819 includes the natural abundance heavier isotopes in the average but not the most common isotope calculation, while MOD:01314 uses the most common light isotopes for both). Usually I will not be creating duplicate entries for the "natural" most common isotope form, but this was either something done in UniMod or a request. In MS work the average mw is never measured, only the combinatorial isotope masses --- if you have sufficient resolution.

Original comment by: jsgaravelli