Lung Cancer Proteome Spectral Library for Data-Independent Acquisition Mass Spectrometer

Data-independent acquisition (DIA) mass spectrometry (MS) data acquisition and targeted data extraction has become a promising strategy with enhanced identification coverage and consistent quantitation across multiple samples. However, coverage at the genome-depth still awaits to be improved. Here, we established a high quality proteome reference library from five lung cancer cell lines varying in epidermal growth factor (EGFR) mutation status and twenty two pooled patient-derived lung tumor tissues samples. By using high pH reverse phase (HpRP) fractionation, we were able to achieve 12,344 protein groups (223,091 unique peptide sequences, 344,430 precursors) from 191 data dependent acquisition (DDA) raw files acquired over similar chromatographic and Orbitrap Fusion Lumos MS platform, at 1% PSM and protein level false discovery rate (FDR). Application to tissue and cell line derived peptides also showed deep profiling of library based DIA. The established spectra library provides a useful resource for deep quantitative sensitive proteome profiling of clinical samples.