Fig. 1.

The four major categories of mass spectroscopy methods for protein analysis. All mass spectroscopy (MS) methods fall into one of the four quadrants, defined based on the degree of multiplexing samples (x-axis) and the number of peptides fragmented and analyzed per secondary MS scan (y-axis). Higher degrees of multiplexing favor higher throughput of analysis (Framework for multiplicative scaling of single-cell proteomics, 2023). DDA, data-dependent acquisition (an approach that fragments one peptide sequence at a time); DIA, data-independent acquisition (an approach that fragments multiple peptide sequences at a time); LF, label free; plexDIA, DIA analysis of sample multiplexed with nonisobaric mass tags; TMT, tandem mass tags.