Fig. 3.

Targeted acquisition improves the coverage of CL-modified peptides. A, Diagram of untargeted and targeted acquisition methods. Both method types have precursors selected for MS/MS acquisition in order of MS1 signal intensity, but with a targeted method, the precursors must also be part of a Δ8.0502 Da doublet to be selected. B, A comparison of the number of Δ8.0502 Da doublet features found in the MS1 spectrum of soluble pre-fraction SCX fraction #16, which had corresponding MS/MS scans in the untargeted (TopS) and targeted (MTag, and Incl) acquisition methods, revealed that the MS/MS spectra of a larger number of crosslinker-modified precursors were acquired when targeted methods were used on sample fractions that had not been affinity enriched than on those fractions that had been affinity enriched. C, A comparison of the number of Δ8.0502-Da doublet features found in all SCX fractions that had been affinity enriched showed no benefit of targeted methods over the untargeted method for crosslinker-modified precursor acquisition. Here we show data from only the soluble pre-fraction.