Fig. 4

Peptide identifications from non-selected precursors. With larger MME tolerances, here ±5 Da plus isotope error, X!Tandem identified co-eluting peptides with lower (a) or higher (b) m/z than the selected precursor but within the precursor isolation window. In A, a peptide with monoisotopic m/z 842.5 was identified (with PeptideProphet probability cutoff p = 0.989) instead of a peptide (or signal) at m/z 845.3 triggering the MS/MS event. In B, a peptide with m/z 814.0 is identified (with p = 0.992) instead of a peptide at m/z 811.5. Both precursors were the ninth to be acquired out of ten sorted by intensity for their corresponding MS scans, more than 1.5 s after the MS scans themselves, and both precursors disappear into the background in the subsequent MS scans. These are two examples of almost 100 such PSMs in the E. coli ion trap dataset