Computational Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage and Applications to 15 Tumors

Efficient
peptide and protein identifications from data-independent
acquisition mass spectrometric (DIA-MS) data typically rely on a project-specific
spectral library with a suitable size. Here, we describe subLib, a
computational strategy for optimizing the spectral library for a specific
DIA data set based on a comprehensive spectral library, requiring
the preliminary analysis of the DIA data set. Compared with the pan-human
library strategy, subLib achieved a 41.2% increase in peptide precursor
identifications and a 35.6% increase in protein group identifications
in a test data set of six colorectal tumor samples. We also applied
this strategy to 389 carcinoma samples from 15 tumor data sets: up
to a 39.2% increase in peptide precursor identifications and a 19.0%
increase in protein group identifications were observed. Our strategy
for spectral library size optimization thus successfully proved to
deepen the proteome coverages of DIA-MS data.