Table II The influence of the dynamic exclusion window (DEW) on the number of peptides identified in a shotgun LC-MS analysis. A DEW time of 15 s yielded the highest total number of identifications. Use of the trace-peak method (TPM) to sequence precursors at peak intensity resulted in fewer identifications
DEWTotal number of scansNumber of MS/MS scansNumber of peptides
90 s75,57657,76735,623
30 s83,46067,71738,617
15 s91,84977,57038,788
5 s111,28197,47930,606
TPM70,00950,72732,979