PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation

• DOI: 10.1021/acs.jproteome.0c00381
• Publication Date: 2020-09-25T10:20:50Z
• Authors: Xue Cai; Weigang Ge; Xiao Yi; Rui Sun; Jiang Zhu; Cong Lu; Ping Sun; Tiansheng Zhu; Guan Ruan; Chunhui Yuan; Shuang Liang; Mengge Lyu; Shiang Huang; Yi Zhu; Tiannan Guo
• Keywords: Orbitrap; Proteome

The performance of data-independent acquisition (DIA) mass spectrometry (MS) depends on the separation efficiency peptide precursors. In Orbitrap-based spectrometers, precursors is limited by relatively slow scanning rate compared to time flight (TOF)-based MS. Here, we present PulseDIA, a multi-injection gas-phase fractionation (GPF) strategy for enhanced DIA-MS. This achieved equally dividing conventional DIA analysis covering entire range into multiple injections analyses with complementary windows. Using mouse liver digests, PulseDIA method identified up 50% more peptides and 29% protein groups than that same length effective gradient time. Compared GPF, PusleDIA exhibited higher flexibility 18% 8% using two injections. gain per unit was highest in GPF. We further applied profile proteome 18 human tissue samples (benign malignant) from nine cholangiocarcinoma (CCA) patients. 7796 these CCA samples, 14% increase group identification method. missing value matrix dropped 7% DIA. A total 681 significantly altered proteins were detected including several dysregulated proteins, which absent analysis. Taken together, as an DIA-MS improved sensitivity reproducibility.