Data Acquisition Strategy for Mass Spectrometers Applied to Bottom-up-Based Protein Identification

The high complexity of the proteome has brought great challenges to mass spectrometry-based protein identification. The technical requirements continuously forward the development of mass spectrometry. The advance in hardware and software of instrument platform provides more choices and supports for protein identification. However, it is necessary to design high-quality data acquisition strategy, which is heavily dependent on the specific biological problem and the sample, to make the best use of the performance of the instrument. Here, the data acquisition strategies that have been developed for mass spectrometers in high throughput protein identification were reviewed. The simple repetitions, ion exclusion, ion inclusion, online intelligent data acquisition and segmented scanning technology for Bottom-up strategy were highlighted, and the impact of these strategies on the protein identification was concerned. Finally, the advantages and disadvantages of various strategies were summarized, and the future directions of developing the data acquisition strategy for mass spectrometers were discussed.