Table 2. Significantly Different Protein Abundance by Parallel Reaction Monitoring.

A surrogate peptide was used for estimating protein level abundance for targeted proteins. Both 24 h poststroke intervention (n=35) vs nonstroke samples (n=35) and 96 h poststroke intervention (n=20) comparisons describe the log2 fold change of proteins in stroke subjects compared with nonstroke control subjects. Differential abundance was determined for between nonstroke and stroke time points by linear model adjusted for sex and HDL-C. Differential protein abundance for paired samples at 24 and 96 h was determined by paired 2-sided t test. For the paired measures, 3 proteins were not tested due to missing values (LPA, ITIH4, and SAA1). BenjaminiHochberg correction was applied for each comparison, with 38 tests for both nonstroke and stroke time point comparisons, and 35 tests for the paired comparison. Compared with healthy nonstroke HDL proteome, 8 proteins were significantly different in 24 h postintervention stroke patient HDL, and 4 additional proteins were significantly different in 96 h postintervention stroke patient HDL. Three proteins were significantly different from 24 to 96 h measurements.

		24h vs. non-stroke		96h vs. non-stroke		96h vs. 24h (paired)
Protein	Abbrev.	log₂FC	Adj. P value	log₂FC	Adj. P value	log₂FC	Adj. P value
adipocyte plasma membrane-associated protein	APMAP	1.61	4.68E-08	1.84	9.04E-08	0.10	0.750
phosphate inositol-glycan specific phospholipase D	GPLD1	1.47	6.23E-08	1.47	3.94E-06	−0.01	0.963
apolipoprotein E	APOE	0.76	3.51E-04	0.73	0.003	−0.06	0.750
indian hedgehog protein	IHH	−0.59	0.001	−0.68	0.001	−0.12	0.557
inter-alpha-trypsin inhibitor chain H4	ITIH4	−1.12	0.003	−1.03	0.018	−	-
serum amyloid A2	SAA2	2.48	0.010	4.15	0.000	1.62	0.032
apolipoprotein A-IV	APOA4	−0.56	0.028	−0.70	0.013	−0.07	0.848
clusterin	CLU	0.36	0.041	0.42	0.029	−0.02	0.954
anthrax toxin receptor 2	ANTXR2	−0.25	0.253	−0.81	1.77E-04	−0.51	0.015
alpha-1-antitrypsin	SERPINA1	0.21	0.474	0.70	0.013	0.42	0.163
apolipoprotein F	APOF	−0.06	0.765	0.40	0.028	0.41	0.015
serum paraoxonase/arylesterase 1	PON1	0.15	0.253	0.28	0.037	0.16	0.174

Comparison; significance testing. 24 h vs nonstroke; linear model: ≈sample group + sex + HDL-C; 96 h vs nonstroke; linear model: ≈sample group + sex + HDL-C; and 96 vs 24 h; paired 2-sided t test. HDL indicates high-density lipoprotein; ITIH4, inter-alpha-trypsin inhibitor chain H4; and SAA1, serum amyloid A1.