Figures 1, 2 & 3: Identified unique proteins, peptides and average Full Width at Half Maximum (FWHM) from 80 ng HeLa Tryptic Digest injection on an Aurora Elite™ 15 cm x 75 μm column using different gradient lengths. Samples were run on a Waters ACQUITY UPLC M-Class coupled to a Bruker timsTOF Pro, dia-PASEF acquisition. Data analysed using DIA-NN.

Figure 4: Yeast tryptic digest was spiked into a HeLa tryptic digest (200 ng) in different ratios (Sample A – 45 ng; Sample B – 15 ng). Samples were run on a Waters ACQUITY UPLC M-Class coupled to a Bruker timsTOF Pro, dia-PASEF acquisition using an Aurora 15 cm x 75 μm column. Data analysed using DIA-NN. Each point represents a unique protein with ratios calculated between the A and B samples. Figure 5: Boxplot demonstrating average ratio and interquartile range of data. Expected ratios are indicated with dashed lines.