MSLibrarian

MSLibrarian is an open-source R software package that provides a new workflow and tool for optimizing predicted spectral libraries in data-independent acquisition-mass spectrometry (DIA-MS) proteomics. It addresses the limitations of library-free approaches based on in silico prediction, which often result in reduced coverage and sensitivity due to large library sizes and deviations from experimental data.

Key features of MSLibrarian include:

1. Integration of spectrum-centric DIA data interpretation using the DIA-Umpire approach to inform and calibrate the in silico predicted library and analysis approach.

2. Optimization of intensity prediction parameters through predicted vs. observed comparisons.

3. Calibration of retention time prediction for deviating chromatographic setups.

4. Optimization of library scope and sample representativeness.

Benchmarking experiments using a ground-truth-embedded experiment of species-mixed proteins and quantitative ratio-validation confirmed improvements of up to 13% on the peptide level and 8% on the protein level at equivalent false discovery rate (FDR) control and validation criteria.