Table 3.

An overview of the studies (n=11) that examined the proteome profile in human MS brain tissue.

Authors	Patients	Quality (PMD)	Methodology	Key findings
Newcombe et al. (70)	- 3 WM lesions and adjacent NAWM from 3 blocks of 1 MS patient - 3 blocks of control CM from 2 controls	PMD: 8-15h	LC-MS/MS (MALDI-ToF) with reduction of abundant cytoskeletal proteins	- Cluster analysis based on 109 proteins showed three clusters: WM, NAWM and lesion. - WM samples or lesion samples could cluster with NAWM, but MS lesion and WM samples did not cluster together
Han et al. (71)	- 2 Active, 2 chronic active and 2 chronic lesions of fresh-frozen from 6 MS patients - Normal WM from 2 controls	PMD: 4-24h	LCM, LC-MS/MS (ESI)	- Number of unique proteins in the major lesion types: 158 for active, 416 for chronic active and 236 for chronic lesions. - Revealed 5 proteins involved in coagulation unique for chronic active lesions: tissue factor, PCI, thrombospondin, fibronectin and vitronectin.
Fissolo et al. (72)	- 8 samples from 8 MS patients	PMD: 8-38h	LC-MS/MS (ESI) with antibodies against HLAs	- Identified processed peptides presented on MHC I and II molecules from MS brains as self-antigens of diverse MBP peptides as well as GFAP, NFL, APOD, APOE, ferritin, transferrin - By characterizing the MHC ligandome of MS brain tissue, they identified 118 amino acid sequences from self-proteins from MHC I and 191 from MHC II molecules.
Ly et al. (73)	- 12 chronic active lesions, 8 chronic periplaque WM (PPWM), 12 late reyelinating lesions (LRM), 11 LRM PPWM from 3 MS patients (areas within same category were pooled within patient samples) - 6 WM areas from 4 controls	PMD: 8-58h	LCM, LC-MS/MS (ESI) with iTRAQ labelling	- Myelin-associated glycoprotein was significantly downregulated in chronic demyelinated lesions compared to late remyelinated lesions, NAWM and WM. - The number of protein identifications obtained from chronic lesions was significantly higher than in all other lesional/NAWM areas. - Contactin was downregulated in the NAWM surrounding chronic lesions compared to WM. - GFAP was upregulated in chronic lesions compared to NAWM and DWM. - HAPLN2 was downregulated in late remyelinated lesions and NAWM vs WM. - Upregulation of PRX-6 in chronic lesions vs chronic NAWM.
Broadwater et al. (74)	- parietal, Brodmann areas 1-3, frontal cortex and Brodmann area from 8 MS brains and 8 control brains	PMD: 3-30h	LC-MS/MS (SELDI-ToF)	- 4 proteins differentially expressed: COX5b, brain specific creatine kinase, hemoglobin-b-chain and MBP.
Brown et al. (75)	- 5 postmortem cortical MS tissue - 5 cortical areas from control brains	PMD: 3-23h	LC-MS/MS (ESI)	- 15 proteins including hemoglobin β subunit (Hbb) were identified. - Hbb was enriched in pyramidal neurons in internal layers of the cortex, and interacted with subunits of ATP synthase, histones, and a histone lysine demethylase.
Syed et al. (76)	- 3 chronic active, 3 active lesions, 2 peri-lesional WM and 1 NAWM from MS	PMD: 7-22h	LCM, LC-MS/MS (ESI)	- Ephrin3, an oligodendrocyte differentiation inhibitor, was expressed in demyelinated WM lesions.
Maccarrone et al. (77)	Discovery cohort: - NAWM, NAGM, and lesions with different extent of remyelination from 1 SPMS Validation cohort: - 12 PMS blocks	PMD: 8-24h	MALDI-IMS LC-MS/MS (ESI)	- Lesions with low remyelination had compounds of molecular weights smaller than 5300 Da, whereas completely remyelination had molecular weights of more than 15200 Da. - Tymosin beta-4 was highly expressed in demyelinated lesion rim.
Qendro et al. (68)	- brain lesions of 2 acute MS patients	PMD: 4-24h	LC-MS/MS (ESI) Peptide microarray Exom sequencing	- Mutated forms of proteolipid protein 1 (PLP1).
Faigle et al. (78)	- GM samples from 6 controls and 6 MS cases, WM samples from 3 controls and 9 MS cases.	PMD: 5-22h	LC-MS/MS (ESI)	- Identification of novel citrullinated peptides and already described citrullinated proteins: MBP, GFAP, and vimentin. - Modified proteins in MS WM was higher than control tissue and increased citrullination in WM compared to GM.
Böttcher et al. (79)	10 WM lesions and 10 NAWM from PMS 8 WM from controls	PMD: 4:21-10:20h	Single-cell mass cytometry with CyTOF of isolated microglia	- decreased abundance of homeostatic microglial markers, while increased expression of APC-, phagocytosis-, inflammatory- and apoptosis-related markers in active lesions. - TNFhi microglial cluster was higher in NAWM compared to active lesion - monocyte-derived macrophages were scarce in active lesions