Figure 2
LTQ-FT data for the peptide at m/z 494.29 (ILDLIESGK). The figure shows an example of data-dependent acquisition on the LTQ-FT. (a) SIM scan of the doubly charged peptide at 494.29, observed in the total ion chromatogram. (b) The peptide is selected for fragmentation and MS2 acquisition, and (c) the most intense daughter-ion is selected for a new round of fragmentation MS3. Partial data obtained in the MS3 is used to confirm sequence observed in the MS2 and, consequently, improves the probability score for the identified sequence.