Parallel accumulation‐serial fragmentation method for in‐depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with nonsmall cell lung cancer

Purpose Advances in mass spectrometry‐based quantitative proteomic analysis have successfully demonstrated the in‐depth detection of protein biomarkers in bronchoalveolar lavage fluid (BALF) from patients with lung cancers. Recently, ion mobility technology was incorporated into the mass spectrometers escalating the sensitivity and throughput. Utilizing these advantages, herein, we employed the parallel accumulation–serial fragmentation (PASEF) implanted in a timsTOF Pro mass spectrometer to examine the alteration of BALF proteomes in patients with nonsmall cell lung cancers (NSCLCs). Experimental design BALF proteins were processed from patients with NSCLC and analyzed in a timsTOF Pro mass spectrometer with the PASEF method using a peptide input of 100 ng. Label‐free mass spectrometry data were analyzed in the FragPipe platform. Results We quantitated over 1400 proteins from a single injection of 100 ng of peptides per sample with a median of ∼2000 proteins. We were able to find a few potential biomarker proteins upregulated in NSCLC. Conclusions and clinical relevance The alterations of the BALF proteome landscape vary among patients with NSCLC as previously observed in patients with small‐cell lung cancers. The PASEF method has significantly enhanced the sensitivity and throughput, demonstrating its effectiveness in clinical research and application.