Table 2.

Verification of the validity of quantifications by Normalized Total TIC (MS/MS LFQ).

Protein	Protein ID	Fold Change (MS/MS)	p-value (MS/MS)	Fold Change (WB)	p-value (WB)
Calreticulin	CALR_HUMAN	1	0.89	1.21	0.67
Ras-related protein Rab-7a	RAB7A_HUMAN	1	0.89	0.98	0.97
TAR DNA-binding protein 43	TADBP_HUMAN	0.4	0.038	0.49	0.04
Mitochondrial import receptor subunit TOM22 homolog	TOM22_HUMAN	0.6	0.12	0.48	0.15
Vesicle-associated membrane protein 2	VAMP2_HUMAN	1.5	0.036	2.11	0.029
Vesicle-associated membrane protein-associated protein B/C	VAPB_HUMAN	1.5	0.27	1.25	0.25

A number of proteins were analyzed by Western blot and quantified for comparison to the fold change values determined by MS/MS LFQ. The fold changes and p-values calculated by both methods gave comparable results, providing confidence in the LFQ quantification method used in this study. The data provided here refer to AF22 cells challenged with oAβ relative to untreated AF22 cells. Fold changes determined by MS/MS are described in Table 1 and Supplementary Table S3. Western blots are provided in Supplementary Fig. S2. For MS/MS data: T-test with Benjamini-Hochberg correction, n = 14-16. For WB data: T-test, n = 6-7 per group.