Evaluating basic parameters affecting interference in isobaric labelling studies of complex unfractionated samples

摘要

Using SPS-MS3 removes most of the peptide interference at the expense of losing some peptide identifications. Utilizing fewer notches during SPS-MS3 can reduce interference. Selecting 5 notches seems to reduce interference by ～7% while minimizing signal-to-noise loss. Utilizing the smallest IW2 (0.4 m/z) reduces peptide interference. While signal-to-noise is reduced by decreasing IW2, the loss in signal-to-noise is not as severe as when reducing the number of notches. Experiments were performed on a complex unfractionated sample.