Table 1.
Gender, age and neuropsychological characteristics of the representative study group.
Table 2.
CSF and routine laboratory analysis for the representative study group analyzed in the present study.
Fig 1.
Box plots of LFQ intensities and peptide retention times.
Log2 of the LFQ intensities of all proteins, which were quantified in 100% of the samples, are shown in A (red box plots). The data were not further normalized or transformed once the values from MaxQuant were obtained. B shows the log2 of peptide retention times for every LC-MS/MS run (green box plots).
Fig 2.
A: Two variables, time point (T0, T24 and T48) and human subject (red figures represent female subjects, and blue figures represent male subjects), can characterize every sample in this study, and for every human subject, three samples were obtained. In this study, the inter- and intraindividual variability of the CSF were analyzed. Hereby, the intraindividual variability is defined as the variation within one human subject between the three time points (yellow circle), and the interindividual variability is defined as the variation between all subjects at T0 (green circle). B: The workflow included CSF sampling, sample preparation, tryptic digestion, LC-MS/MS with LFQ and data analysis. We identified 1,284,850 spectra, which resulted in 5601 peptides and 791 protein groups.
Fig 3.
Intra- and interindividual variability.
A: This figure provides twelve Venn diagrams, one for each human subject. Only proteins that were found with at least 2 unique peptides in one of three samples were counted. The three time points are represented by different colors. Proteins that were identified in all three samples are shown in the middle overlap. Each overlap between two circles gives the number of proteins that were identified in these two samples. B: CVt values were calculated for all 216 proteins of the CSF core proteome and were plotted against their abundance rank. Proteins with CVt > 10% are colored in red, and those with CVt < 10% are colored green. C: CVg values were calculated for all 216 proteins of the CSF core proteome and were plotted against their abundance rank. Proteins with CVg > 20% are colored red, and those with CVg < 20% are colored green.
Fig 4.
LFQ intensity-based heatmap of the top 50 proteins.
LFQ intensity-based heatmap of the top 50 proteins. Top 50 proteins were defined by their mean LFQ intensity of all samples. In each column, the LFQ intensity for one sample is visualized. The color range of LFQ intensity extends from 1e8 (green) over 1e9 (yellow) and 1e10 (red) to 1e11 (dark red).
Table 3.
Protein biomarker candidates with their CVs and RCVs.