I have synthesised a benzimidazole derivative from histidine and o phenylenediamine. product was precipitated with acetone. Theoretical mass expected is 227 Da, But I am getting the mass of 236 and 273 Da as the major relative abundance peaks in LCMS why?
Molecular ion peak is showing a mass of 309 Da why?
Your product would have two or three basic centers which might bind to metal ions, and would be expected to bind extra protons in an aqueous-like solution otherwise (ie: your mass might be +2 or +3 over a neutral structure in any case). Assuming your NMR suggests you have the right product: the +46 is probably a di-sodium salt from when you washed the crude product with brine, or simply salt that got into the mass-spec injector. The 309 might similarly be a di-potassium salt, perhaps. The +9 is harder to explain - best guess would be two protons and a lithium atom, but lithium is a less commonly used salt, so less common contaminant in mass spec in general.
Best suggestion: try to de-salt your compound, and make sure the mass spec is really clean, then try the analysis again.
If you find that LCMS is inconclusive in confirming your expected product, i think you should refer to NMR to give you clear answer about your product structure
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