Hybrid Data Acquisition and Processing Strategies with Increased Throughput and Selectivity: pSMART Analysis for Global Qualitative and Quantitative Analysis

Data-dependent acquisition (DDA)
and data-independent acquisition
strategies (DIA) have both resulted in improved understanding of proteomics
samples. Both strategies have advantages and disadvantages that are
well-published, where DDA is typically applied for deep discovery
and DIA may be used to create sample records. In this paper, we present
a hybrid data acquisition and processing strategy (pSMART) that combines
the strengths of both techniques and provides significant benefits
for qualitative and quantitative peptide analysis. The performance
of pSMART is compared to published DIA strategies in an experiment
that allows the objective assessment of DIA performance with respect
to interrogation of previously acquired MS data. The results of this
experiment demonstrate that pSMART creates fewer decoy hits than a
standard DIA strategy. Moreover, we show that pSMART is more selective,
sensitive, and reproducible than either standard DIA or DDA strategies
alone.