Fig 1.
Violin plots with data points showing the total protein extracted by using the modular automated protocol on P. putida and R. toruloides from different amounts of biomass (n = 47).
D1 and D7 samples correspond to repeat analysis of a single culture of each organism seven days apart to demonstrate the inter-day variability of the protocol.
Fig 2.
Reproducibility of the modular automated sample preparation workflow as measured by label-free LC-MS/MS shotgun proteomics analysis.
(A) Violin plots showing the coefficient of variation of MS1 ion intensity quantification for over 900 and 1000 proteins from P. putida and R. toruloides, respectively (n = 47). The violin plots display the kernel density estimation of the CV and inside each violin plot is a box plot summarizing ranges (IQR, whiskers, outlier points) and individual medians (solid lines). The LCMS analysis raw data have been deposited to the ProteomeXchange Consortium data depository at http://www.proteomexchange.org/. They are publicly accessible with the dataset identifier PXD029122 and 10.6019/PXD029122.
Fig 3.
Scatter plot display of the CV% for each protein (y-axis) vs the mean MS1 ion intensity detected for each protein (x-axis).