LTQ FT MS Accurate Mass and SRM Data Dependent Exclusion MSn Measurements for Structure Determination of FK228 and Its Metabolites

MS2 fragments are produced by cleavage of all protonated molecules at the lone electron pairs of heteroatoms or the π electrons of double bonds of FK228. Usually, data dependent MS3 measurement cleaves only MS2 fragment of highest intensity that normally does not contain important metabolic sites. New SRM (selected reaction monitoring) data dependent exclusion MSn measurement makes it possible to obtain MS3 fragmentation data for all MS2 fragments, useful for structural determination of FK228 and its metabolites using ESI ion trap. The two different fragmentation pathways of FK228, of which fragment ions had the different elemental composition, were estimated. The accurate masses of FK228 fragment ions Fa1 (or Fb1) and Fa2 (or Fb2) were measured by LTQ FT MS to compare with those calculated exact masses. The fragmentation pathway of formers was correct as the result. LTQ FT MS accurate mass and SRM data dependent exclusion MSn measurements are required for the structure determination of FK228 and its metabolites.