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Determining the Site of Modification … Part 3

September 8, 2009

Tandem mass spectrometry involves the process of selecting and separating a product ion(s) (or daughter ion(s)) and fragmenting it in a second mass analyzer. This is commonly referred to as MS/MS or MS2. Additional tandem processes can be applied to ions in the MS/MS data to create MS3 data, and so forth.

The metabolites A and B share the same exact mass, and as such, cannot be differentiated by the MS data alone (see Part 1 of this series). The MS/MS data, described in Part 2, offers fragment information that can assist in eliminating one of the candidates. Taking it a step further and thus verifying the candidate metabolite A, ESI+ MS3 data is presented herein.

The fragmentation scheme below shows both the Parent and Metabolite A with the fragment at 121 Da, in bold, fragmenting to create a fragment at 93 Da. This is supported by the nearly-identical MS3 data displayed below.

MS2CompareToAPI_Part3Frag_Sept82009 MS2CompareToAPI_Part3MS3_121_Sept82009

On the right-hand side of the fragmentation scheme, the fragments 106 and 108 Da are expected for the MS3 data of the Parent and Metabolite A, respectively.

MS2CompareToAPI_Part3MS3_134_Sept82009

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