Fig. 2

Comparison of the MP proteomes in SLE and HC. a Fold-change, abundance, and statistical difference of all proteins (n = 1098) identified in the SLE-MP versus HC-MP cohort. Protein abundances for all proteins (n = 505) with q < 0.05 are divided into 3 ranges (between 13,550 and 38,700 and values either below or above this range. Significant entries (n = 15) in the SLE group which have zero median IBAQ values (intensity-based absolute quantification analysis) are included as open symbols. X-axis is the SLE/HC average intensity (LFQ) value ratio depicted as Log₂(SLE/HC). Y-axis is −log(q). Vertical lines mark twice up- or downregulation, while values above the horizontal line all are below q = 0.05, i.e. are statistically significant. Areas of the plot containing the serum amyloid A (SAA1, SAA2) and galectin-3 binding (G3BP) proteins and a number of immunoglobulins and complement proteins (Ig + C) are indicated. The two insets show the position in the plots of 4 chosen categories of proteins: platelet membrane and mitochondrial proteins which are highly significantly decreased in SLE-MPs and glycolytic and pentose pathway enzymes and small GTPases and their regulators that are highly upregulated in SLE-MPs. b Relative protein abundance based on the abundance ranking in SLE samples) and SLE/HC ratios (log(2) Y-axis) for chosen categories of proteins. Acute phase proteins and galectin-3 binding protein (G3BP) have been labelled: SAA1, SAA2, serum amyloid A protein, isoform 1 and 2, respectively; ORM, orosomucoid isoforms; HPX, hemopexin; FGA, FGB, FGG, fibrinogen α, β, and γ chains, respectively