fig2

Figure 2. Comparison of identification and quantification abilities of DDA and DIA-PASEF approaches. Number of peptides identified by DDA and DIA-PASEF (A) mass spectrometry methods. Number of protein groups identified by DDA and DIA-PASEF (B) mass spectrometry methods. Number of quantitated protein groups in any, half, or all (Q0, Q50, and Q100, respectively) samples in each group identified by DDA- or DIA-PASEF (C) mass spectrometry. For each figure panel, facet_grid function in ggplot2 was used to generate different sections; DC groups are at the top and NC at the bottom, while DDA groups are on the left side and DIA on the right side. DDA: Data-dependent acquisition; DIA: data-independent acquisition; PASEF: parallel accumulation-serial fragmentation; DC: differential centrifugation; NC: non-differential centrifugation.