Fig. 3
From: Neat plasma proteomics: getting the best out of the worst
Impact of data search strategy. A Number of identified protein groups across 1, 4, 10 and 33 neat plasma samples (mean ± standard deviation) analyzed with DIA-NN v1.8.1 library-free search strategy with and without Match Between Runs (MBR). B Number of identified protein groups across 30 brain biopsy compared with 33 neat plasma (DIA-NN v1.8.1 with MBR). C Number of identified protein groups across 10 injections of different neat plasma (biological variability) and 10 injections of same plasma (technical variability) (mean ± standard deviation) in DDA and DIA acquisition modes (Evo-TTP) and analyzed with DIA-NN v1.8.1 library-free search strategy (with MBR) and Maxquant v2.3.0.0 (with MBR). D Coefficient of variation distribution calculated from LFQ raw intensities (non log transformed) across 10 injections of different neat plasma (biological variability) and 10 injections of same plasma (technical variability) in DDA and DIA acquisition modes and analyzed with DIA-NN v1.8.1 library-free search strategy (with MBR) and Maxquant Maxquant v2.3.0.0 (with MBR)