Table 1:

Proteomic Studies in Schizophrenia.

	cohort	region	extracts	Proteomic method	# altered proteins	altered proteins	Protein groups/pathways
Whole cells
Clark et al., 2006	10 SCZ1 10 CTRL1	ACC	whole cell	2D-E MALDI-TOF MS	SCZ −36	Table 4 in Clark et al., 2006	synaptic, signaling, metabolic and oxidative stress, trafficking, cytoskeletal and glial-specific proteins
Clark et al., 2007	10 SCZ1 10 CTRL1	ACC	whole cell	2D-E MALDI-TOF MS	SCZ - 27	Table 3 in Clark et al., 2007	functionally classified as metabolism, cytoskeleton, synapse
Sivagnanasu et al., 2007	10 SCZ1 10 CTRL1	CC genu	whole cell	2D-E Maldi-TOF	SCZ −34 21 altered L/R hemisphere	Table 2 in Sivagnasundaram et al., 2007	Human Proteome Database cytoskeletal structure and function, neuroprotective function and energy metabolism
Pennington et al., 2008a	35 SCZ2 35 BPD2 35 CTRL2	DLPFC	whole cell	2D DIGE 2D linear Ion trap	SCZ −9 BPD - 45 Both - 6	PASCIN 1 DYN NF-L	SCZ: synaptic proteins (7 of the 15) in septin family
Martins-de-Souza et al., 2010	11 SCZ3 (6F/5M) 8 CTRL4 (2F/6M)	ACC	whole cell	2D-E MALDI-TOF MS	SCZ - 28 Males 11 Females 7	WB validation – SCZ-CTRL DPYSL2, CRYABPRDX6 WB validation –M/F GLUL	Human Protein Reference Database Communication/signal transduction Metabolism/energy
Saia-Cereda et al., 2105	9 SCZ3 5 CTRL4	CC	Cytoplasmic	LTQ orbitrap XL spectral counting	SCZ - 65	Table 2 in Saia-Cereda et al., 2015	Ingenuity: energy metabolism, cell communication and signaling and cell growth and maintenance
MacDonald et al., 2015	22 SCZ5 23 CTRL5	AC Gray matter	whole cell	LC-SRM/MS	SCZ- 155	Table 2 in MacDonald et al., 2015	DAVID: Glutamate signaling pathway Co-expression network analysis Clathrin coated vesicle membrane, NADH binding
Saia-Cereda et al., 2106	5 SCZ6 5 CTRL4	CC	whole cell	2D-RP/RP multiplexed (DIA)	SCZ - 56 differentially phosphorylated - 68	Tables 2 and 3 in Saia-Cereda et al., 2016	Ingenuity: Phosphorylation CTNF pathway incl. PI3K, mTOR ephrinB
Whole cell laser dissected
Pennington et al., 2008b	12 SCZ2 13 CTRL2	Insular cortex layer 2	whole cell Laser dissected	2D-DIGE 2D linear ion trap	in SCZ or BPD or both - 19	Table 2 in Pennington et al., 2008b WB validation: DRP-2 a-synuclein	Most affected categories: cell communication/signal transduction protein metabolism
Focking et al., 2011	20 SCZ2 20 BPD2 20 CTRL2	Mid-HC cornu ammonis regions 2 and 3	whole cell Laser dissected	2D-DIGE mass spectrometry	common to more than one HC region SCZ - 32 BPD - 38	WB Validation: PCMT1, SPTAN1, ARMCX1, ANXA6 SEPT11, FSCN1	Ingenuity (SCZ) Cellular assembly and organization Cellular compromise Cell morphology Cell signaling Cell to cell signaling and interaction
Nuclear
Saia-Cereda et al., 2107	12 SCZ3 8 CTRL4	CC (white matter) ATL (gray matter)	Nuclear enrichment	2D-E LTQ orbitrap	SCZ Nuclear proteins CC – 552 ATL – 224	Table 2 in Saia-Cereda et al., 2017	Reactome for proteins commonly regulated between the two regions: Cellular stress response Heat shock proteins STRING:Nuclear protein specific: CC-calcium-calmodulin ATL spliceosome
Membrane
Behan et al., 2009	Proteomic studies : pooled samples 10 SCZ2 10 BPD2 10 CTRL2 Validation Studies: 20 subjects/grp2 10 subjects/ group7	DLPFC	Proteomics: membrane microdomains Validations: whole cell	2D-DIGE RP-LC-MS/MS	in one or both disorders −16	WB Validation Incr. BPD and SCZ in: Stanley Brains STXBP1, BASP1 LAMP Harvard Brains STXBP1, BASP1	NA
Synaptic
Smalla et al., 2008	8 SCZ8 8 CTRL8	DLPFC	synaptic structures	2D-E MALDI-TOF	SCZ – 41	WB validation: Prohibitin common alteration between SCZ AND ketamine treated rats	NA
Velasquez et al., 2017	8 SCZ6 8 CTRLS4 pooled	PFC	synaptosomes	iTRAQ LTQ orbitrap Q-Exactive	SCZ iTRAQ −12 label free −55	Limbic system associated protein Alpha-calcium/calmodulin-dependent protein kinase II confirmed by PRM	DAVID and Reactome: Dysregulated by both methods: synaptic activity signaling pathways associated with calcium
Post synaptic density
Focking, Lopez, et al., 2015	20 SCZ2 20 CTRL2 2 sample pooled	ACC	PSD	label free LC-MS Q Exactive	SCZ-143 (25 after correction for FDR)	WB validation: AP2B1 DNM1 MAPK3 SYNPO	DAVID NIH: KEGG Endocytosis Calcium signaling Long-term potentiation (FDR signif) Neurotrophin signaling (FDR signif)

¹NSW Tissue Resource Centre (University of Sydney, NSW, Australia),

²Stanley Brain Collection,

³Norbaden, Germany,

⁴Heidelberg Germany,

⁵University of Pittsburgh,

⁶State Mental Hospital Weisloch, Germany,

⁷Harvard,

⁸New Magdeberg Brain Collection. Abbreviations: SCZ, Schizophrenia; BPD, Bipolar Disorder; CTRL, Control; DLPFC, Dorsolateral Prefrontal Cortex; ACC, anterior cingulate cortex; AC, auditory cortex; CC, corpus collosum; HC, hippocampus; ATL, anterior temporal lobe.