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Significance was assessed using ANOVA resulting in 210 significantly changing proteins, and 193 of these proteins were associated with a gene symbol and could be used for enrichment calculations with the pathogen interactor lists.
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These dynamically variable and changing proteins were chosen for further evaluation due to the likelihood of them being biologically relevant.
The list of significantly (p < 0.05) changing proteins was triaged further by manual inspection of spectra and data, proteins showing consistent changes across patients and low variation in the technical replicates of the pooled standards were prioritised.
This analysis showed that most of significantly changing proteins had log2 ratios −2 < x > +2, and therefore these values were used as an arbitrary cutoff for significance of regulation.
The latter list of 66 changing proteins upon iron treatment was further confirmed in an independent MRM-like quantitative approach called SWATH MS2 [ 36]. (For all quantitative details see Table S3 and S4).
In the list of 144 significantly changing proteins in AD platelet membrane fractions, we found five additional proteins that have been identified as potential biomarkers or have a function homologous to such a protein (Table 3).
Furthermore, the effects of SB on platelets such as changing protein levels and changing intracellular Ca (2+) level, ROS level as well as cell size were observed with or without pre-treatment of platelets using an antibody against integrin α2β1.
These defects can exert their deleterious impact through changing protein stability and causing the protein to be more susceptible for degradation; changing the protein's functional site residues; or changing the affinity controlling protein-protein interactions [ 10].
The protein measurement is intended only as an indication of changing protein concentrations and not intended as a strict protein quantification.
In these cases, non-3n indels may not have significant effects in changing protein abundance, and thus may be tolerated by selection.
Significantly (p < 0.01) changing protein spots (107) and the corresponding genes were clustered using a hierarchical clustering with average linkage method and correlation as distance metric.
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