Mass spectrometry-based proteomics identify novel serum osteoarthritis biomarkers

Table 3 Principal component analysis-pairwise differential expression

	OA-obese/control		OA-non-obese/control
Protein (gene designation)	z-score/log₂(ratio)/q-value	Regulation	z-score/log₂(ratio)/q-value	Regulation
C-reactive protein (CRP)	4.21/3.47/ 0.05	↑	3.35/ 2.72/ 0.04	↑
Lysozyme C (LYZ)	3.94/3.29/0.0002	↑	4.45/ 3.40/ 0.03	↑
Cartilage acidic protein 1 (CRTAC1)	2.47/ 2.27/ 0.01	↑	3.19/ 2.62/ 0.003	↑
Prostaglandin-H2 D-isomerase (PTGDS)	2.57/ 2.34/0.0002	↑	*2.57/ 2.23/0.054***	↑
Immunoglobulin delta chain C region (IGHD)	5.91/ 4.65/0.04	↑	1.28/ 1.43/ 0.74	-
Lysine-specific demethylase4C/4E/4B (KDM4C/4B/4E)	2.01/ 1.96/ 0.01	↑	NA
KH-Type Splicing Regulatory Protein (KHSRP)	2.07/ 2.00/ 0.10	-	2.80/2.37/0.04	↑
Immunoglobulin heavy variable 3-35 (IGHV3-35)	1.71/ 1.75/0.34	-	3.15/ 2.59/ 0.02	↑
Protein S100A9 (S100A9)	1.13/ 1.34/ 0.17	-	2.05/ 1.91/ 0.02	↑
Fibrillin-1 (FBN1)	NA		2.99/ 2.49/ 0.02	↑
Adiponectin (ADIPOQ)	-3.57/ -1.91/ 0.04	↓	-2.73/-1.06/ 0.17	-
Actins (ACTA1/ACTC1/ACTG2/ACTA2)	-3.83/ -2.08/0.04	↓	-2.00/ -0.61/ 0.16	-

Serum samples were obtained from control (n=8), osteoarthritis (OA)-obese (n=10), and OA-non-obese (n=10) individuals, prepared for mass spectrometry (MS) and analyzed by principal component analysis (PCA). The intensity values for each protein and for each sample were obtained from the MS analysis output, and the mean of the intensity values was calculated for each protein (for the protein, refer to Table S2). The ratio of the means intensity values was used to calculate the z-score and Limma q-value for each protein. A protein was considered upregulated if the z-score was >1.96, the log₂(ratio) >0 and the Limma q-value <0.05; inversely, a protein was considered downregulated with a z-score <1.96, a log₂(ratio) <0 and a Limma q-value <0.05. The values of statistically differentially regulated proteins are indicated in bold and the value in italic indicates a strong trend towards statistical difference. Of note, all the proteins reported in this table have MS/MS sequences in addition to being in the library
- indicates proteins with no differential regulation; NA (not applicable) refers to proteins for which there were too many missing values to assign a final score

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