Fig. 1: Overview of the PYE sample set and the study design. | Nature Communications

Fig. 1: Overview of the PYE sample set and the study design.

From: Multicenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set

Fig. 1: Overview of the PYE sample set and the study design.The alternative text for this image may have been generated using AI.

a Left panel: The PYE sample set was centrally prepared and consists of six different samples. A tryptic digest of human plasma (orange) serves as background. Varying spike-ins of tryptic E. coli (green) and yeast proteomes (violet) mimic differentially regulated proteins between samples with the denominations A and B enabling the evaluation of label-free quantification in a plasma background. Exact sample compositions are provided in the black boxes (percent of total protein mass). To resemble the challenges of protein dynamic range in clinical plasma samples, sample set PYE1 was further diluted with tryptic human plasma reducing the proportion of tryptic E. coli and yeast proteomes in the sample sets PYE3 and PYE9. Middle panel: PYE samples were shipped for LC-MS analysis to twelve different sites of the MSCoreSys network. Right panel: Subsequent raw data and statistical analyses of all acquired data sets were conducted centrally. b Overview of instrumentation and LC-MS setups used in the round robin study. Parts of a partially generated in Biorender (https://BioRender.com/9vhkffx, https://creativecommons.org/licenses/by-sa/4.0/ for R logo).

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