Table 1.
Mass spectrometry participant demographics.
Table 2.
Targeted immunoassays participant demographics.
Fig 1.
Schematic to illustrate the timing and location of the sural nerve injury and tissue collection.
Fig 2.
Flowchart to illustrate the steps of mass spectrometry (data acquisition), and the statistical analysis (post-acquisition analysis).
Fig 3.
Quality control checks of mass spectrometry data.
A-C. Pooled coefficient of variance (PCV), pooled median absolute deviation (PMAD), and pooled estimate of variance (PEV) were all small in these analyses. Small numbers here are ideal since they show low variation of the sample replicates. D. Cor graph compares the pairwise sample correlations of the treatment groups of the normalization methods. The high intragroup correlation values here are desirable since they show high correlation of the replicates within a treatment group.
Fig 4.
Clear Proteomic Changes Between Naïve and Injured Nerve.
A. Overall proteomic expression was altered after nerve injury based on Pearson r correlation. The Pearson’s correlation R-value for each sample, correlated with every other sample is displayed in a correlation matrix of naïve and injured samples (matrix scale orange R = 1: Perfect correlation, green R = -1: Perfect anti-correlation). B. Lin’s CCC demonstrated strong homogeneity among samples within the pre- and post-injury groups C. The volcano plot shows proteins that were downregulated (blue) and upregulated (red) after injury. For the volcano plot, the p-value cutoff was 1E-10 and the Z (Log2(FC)) cutoff (log2 scale) was |4|.
Table 3.
The top significantly upregulated (GO) pathways after injury.
Table 4.
The top significantly downregulated (GO) pathways after injury.
Fig 5.
Changes in growth factors after injury based on the GO pathway “Growth Factor Activity”.
A. Mass Spectrometry: Analysis of all the protein products that were significantly upregulated or downregulated (q-value ≤ 0.05 and Z ≥ |2|, range: -3 to 3). B. Immunoassay: Mean (triangle) differences, between naïve and injured tissue samples, and 95% CI for EPO, PDGF-AA and–BB, VEGF, BDNF, NGFR, beta-NGF, CDNF, and GDNF. Red markers represent mean difference CIs that were above zero and gray ones represent mean difference CIs that include zero.
Fig 6.
Changes in myelination after injury based on the GO pathway “Myelination”.
Analysis of all the protein products that were significantly upregulated or downregulated from the GO pathway (q-value ≤ 0.05 and Z ≥ |2| (log2), range -3 to 3.
Fig 7.
Changes in Schwann cell phenotype after injury based on the GO pathway “Schwann cell differentiation”.
A. Mass spectrometry: All the proteins that were significantly upregulated or downregulated (q-value ≤ 0.05 and Z ≥ |2|, range -3 to 3). B. Immunoassay: The mean difference of c-JUN and its activated form phospho c-JUN content, in the naïve and injured tissue and 95% CI bands. Red markers represent mean difference CI that was above zero and gray one represent mean difference CI that included zero. C. Graph of mass spectrometry analysis of all the protein products that were significantly upregulated or downregulated from the GO pathway, “EMT”.
Fig 8.
Anti-apoptosis factor changes after injury based on the GO pathway, “Negative Regulation of Apoptotic Processes”.
Mass spectrometry analysis of all the protein products that were significantly upregulated or downregulated (q-value ≤ 0.05 and Z ≥ |2|, range -3 to 3). Immunoassay: Quantified NRF2 and BCL-6 changes after injury. The NRF2 graph (gray markers) shows the mean difference 95% CI that includes zero, and the BCL6 graph (red markers) represent mean difference 95% CI that is above zero.
Fig 9.
Axonal response after injury Graph of mass spectrometry analysis of all the protein products that were significantly upregulated or downregulated from the GO pathway, “Response to Axonal Injury” (q-value ≤ 0.05 and Z ≥ |2| (log2), range -2.5 to 2.5).