Fig 1.
Workflow of the quantitative analysis of individual variation in normal human urinary and cerebrospinal fluid (CSF) proteomes.
Fig 2.
Technical variation in urinary and CSF proteomes.
The technical variations in male (A) and female (B) urinary proteomes are shown. The technical variations in male (C) and female (D) CSF proteomes are shown. The proteins with median and top 5% technical CVs are annotated in the figures.
Table 1.
The technical, inter-individual and intra-gender variations of the urinary and CSF proteomes.
Fig 3.
Inter-individual variation of urinary and CSF proteomes.
The inter-individual variations of male (A), female (B), and both male and female (C) urinary proteomes are shown. The inter-individual variations of male (D), female (E), and both male and female (F) CSF proteomes are shown. The proteins with median and top 10% inter-individual CVs are annotated in the figures.
Fig 4.
Comparison of the inter-individual variation of urinary and CSF proteomes.
A. Distribution of inter-individual variations of CSF and urine are shown in a box plot. The inter-individual variation of CSF was much lower than that of urine. B. Scatter plots of the inter-individual variation for urine and CSF proteins. The CV determined for the inter-individual variation of CSF is plotted against the inter-individual variation of urine. The spots above the 45° line show a higher CV for urine than CSF, which is true for the vast majority of the spots.
Fig 5.
Inter-gender variation in the urinary and CSF proteomes.
A. Unsupervised hierarchical clustering of triplicate samples from 14 cognitively normal individuals (7 males and 7 females). B. Unsupervised hierarchical clustering of triplicate samples from 14 cognitively normal individuals (7 males and 7 females).
Table 2.
The estimated minimal sample size for quantitative analysis based on the iTRAQ labeling quantification method for urine (A) and CSF (B), where power is the power of the statistical test, α is the significance level, and π refers to the estimated proportion of truly deferentially expressed proteins among all of the identified proteins.
Fig 6.
GO term enrichment analysis of high-CV proteins and low-CV proteins in the urinary and CSF proteomes.
High, mid and low individual CV urinary proteins are classified into cellular component (A), molecular function (B) and biological process (C) categories for human genes. Genes for which no annotations could be assigned were excluded from the analysis for both the ligand and the genome sets. Categories with a constitution of at least 2% are displayed in the bar charts. High, mid and low individual CV CSF proteins are classified into cellular component (D), molecular function (E) and biological process (F) categories for human genes.
Table 3.
Comparison of the inter-individual variations and minimal sample sizes of the urinary and CSF proteomes between this study and previous studies.