Fig. 5

Performance of the Labrador spectral assay library measuring tissue and plasma. Number of (a) identified peptides and (b) identified proteins obtained from six different canine tissues acquired by DIA with gradients of different lengths (11, 22, 45, 90 min). Depicted is the median value of three technical replicates for each tissue and its standard variation. (c) The plot depicts for each gradient length the identified protein groups (1%FDR) in kidney tissue ranked by their abundance highlighting the dynamic range of proteins that can be quantified. Each gradient length (11, 22, 45, 90 min) is represented by a different color. (d) Distribution of the coefficient of variation (CV) of proteins identified in three replicates of kidney tissue (1%FDR) acquired with gradients of different length. Different gradient lengths are color coded. The first and third quartile are marked by a box with whisker indicating the minimum / maximum value and the solid line indicating the median % CV of 10.6% for the 11 minutes, 7.1% for 22 minutes, 6.7% for 45 minutes and 7.0% CV for the 90 minutes gradient. (e) The plot depicts the number of proteins in the annotated canine proteome and in the developed DIA library as well as the number of proteins identified in the DIA analysis in tissues, in kidney tissue and in plasma using a 90 minutes gradient. (f) Principal Component Analysis (PCA) of six tissue and one plasma sample acquired by DIA in three replicates with a 90 minutes gradient. The axes show the variability explained by each component with PC1 representing the most variation in the dataset followed by PC2.