Data-driven mass spectrometry methods (DDA) and data-independent methods (DIA) used in the analysis of biological material

Abstract

Mass spectrometry is an important tool in proteomic, metabolomic and lipidomic analysis. To fully use its potential, it is crucial to select and configure the appropriate analytical approach. For untargeted research, there are two main strategies available: data-dependent analysis (DDA) and data-independent analysis (DIA). Both methods differ in the way the analysis is carried out and in the degree of coverage of the obtained data, which is why each of them can be used in various types of research. The DDA method is based on continuous scanning of the analyzed ions, as a result of which the precursors with the highest intensity are fragmented in the MS2 mode. On the other hand, DIA, due to the use of combined ranges of precursor ion isolation, allows for a deeper analysis of the analyzed compounds. Both approaches also have modifications that improve their operation and enable obtaining more valuable data. Methods combining both techniques are also appearing on the horizon, such as DDIA, which uses the advantages of both methods, opening new analytical possibilities.