Fig. 3
Measuring global protein abundance changes. (a) H. salinarum NRC-1 under standard growth conditions, three biological replicates are depicted in different colors and sampling time points are indicated at 14.3 h, 21.5 h, 28.8 h and 40.8 h; (b) Overlay of total ion current (TIC) of three SWATH-MS runs exemplifying technically reproducibility in data acquisition; (c) Number of unique peptides and (d) number of proteins for each biological replicate and time point identified with Spectronaut. The error bars indicate the variability within three replicates represented as standard error of the mean. These are calculated as the ratio of standard deviation of the number of quantified peptides or proteins observed in each biological replicate to the square-root of the sample size (n = 3). The yellow dots denote the number of identifications in each replicate and highlight consistency in identification at the peptide and protein level; (e) Overlap of identified precursor ions in each MS run determined with Spectronaut (red) and with OneOmics (blue) highlighting comparable identifications with both software tools; (f) Principal Component Analysis (PCA) of H. salinarum NRC-1 protein profiles. DIA/SWATH-MS analysis of total lysate shows that biological and technical replicates cluster tightly while data sampled at different time points separate from each other. PCA was performed within OneOmics. Each marker represents a SWATH-MS run. Marker shapes indicate biological replicates and colors highlight the sampled time points; (g) Heatmap of log2 fold protein abundance changes (LFC) obtained for three time point contrasts using OneOmics software. TP2 (mid-exponential phase), TP3 (late exponential phase), and TP4 (stationary phase) represent contrasts for each one of these time points in respect to early exponential phase (TP1). Data were visualized with ComplexHeatmap; (h) Volcano plots of differentially expressed proteins using OneOmics analyzed data and ggplot2 for visualization. Depicted are proteins satisfying criteria of |log2 (relative change)| ≥ 0.75 and adjusted p-value < 0.05.
