Method optimization is crucial for
successful mass spectrometry
(MS) analysis. However, extensive method assessments, altering various
parameters individually, are rarely performed due to practical limitations
regarding time and sample quantity. To maximize sample space for optimization
while maintaining reasonable instrumentation requirements, a definitive
screening design (DSD) is leveraged for systematic optimization of
data-independent acquisition (DIA) parameters to maximize crustacean
neuropeptide identifications. While DSDs require several injections,
a library-free methodology enables surrogate sample usage for comprehensive
optimization of MS parameters to assess biomolecules from limited
samples. We identified several parameters contributing significant
first- or second-order effects to method performance, and the DSD
model predicted ideal values to implement. These increased reproducibility
and detection capabilities enabled the identification of 461 peptides,
compared to 375 and 262 peptides identified through data-dependent
acquisition (DDA) and a published DIA method for crustacean neuropeptides,
respectively. Herein, we demonstrate a DSD optimization workflow,
using standard material, not reliant on spectral libraries for the
analysis of any low abundance molecules from previous samples of limited
availability. This extends the DIA method to low abundance isoforms
dysregulated or only detectable in disease samples, thus improving
characterization of previously inaccessible biomolecules, such as
neuropeptides. Data are available via ProteomeXchange with identifier
PXD038520.