Table 1. Precursor Selection Logic Implemented in Each Data Acquisition Strategy.

precursor selection logic	Strategy 1: conventional DDA	Strategy 2: smart MS2 iterative exclusion of all precursors	Strategy 3: smart MS2 iterative exclusion of identified peptides
intensity-based precursor selection	10 highest intensity eligible precursors from each MS1 scan are selected for MS2 (top 10)
noise filtration	charge and intensity threshold	charge and defined elution profile (isotopic envelope and consecutive scan appearance)
percent chimeric intensity (PCI) filter	N/A	precursor becomes an eligible MS2 candidate if PCI filter threshold is exceeded
intraexperiment (dynamic) exclusion	60 s exclusion after MS2	30 s minimum m/z exclusion extended until end of elution
interexperiment exclusion	N/A	all precursors fragmented in previous experiments	only peptides identified in previous experiments
postacquisition database search	N/A	N/A	X!Tandem (1% FDR)