High‐performance matrix‐assisted laser desorption/ionization (MALDI) using 7 T Fourier transform mass spectrometry (FTMS) was investigated for peptide amino acid sequence analysis. Two synthetic peptides representative of the type which would be displayed by major histocompatibility complex molecules from tumor cells were investigated by MALDI/FTMS. Molecular ions of the two 9‐amino acids peptides were detected with resolving power of 8000–17 900 and mass measurement accuracy between 8 and 81 ppm for the all 12C isotope ions. An ultra‐high resolution spectrum (RP 300 000) for the molecular ion of one of the two peptides was obtained. Structurally useful sequence information was obtained by use of surface‐induced dissociation (SID) of the molecular ion species. Interestingly, SID of a sodium‐attached peptide molecular ion resulted in the production of numerous sodium‐attached sequence ions.
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