Supplementary Data for Quantitative Changes in the Mitochondrial Proteome from Subjects with Mild Cognitive Impairment, Early Stage and Late Stage Alzheimer’s disease Table 1 - 112 unique, non-redundant proteins identified and quantified in at least two of the three analytical replicates for all three disease stages. Table 2 - MCI mitochondrial samples, Protein Summary Table 3 - MCI mitochondrial samples, Experiment 1 Table 4 - MCI mitochondrial samples, Experiment 2 Table 5 - MCI mitochondrial samples, Experiment 3 Table 6 - EAD Mitochondrial Study, Protein Summary Table 7 - EAD Mitochondrial Study, Experiment 1 Table 8 - EAD Mitochondrial Study, Experiment 2 Table 9 - EAD Mitochondrial Study, Experiment 3 Table 10 - LAD Mitochondrial Study, Protein Summary Table 11 - LAD Mitochondrial Study, Experiment 1 Table 12 - LAD Mitochondrial Study, Experiment 2 Table 13 - LAD Mitochondrial Study, Experiment 3 Supplemental Table 1. 112 unique, non-redundant proteins identified and quantified in at least two of the three analytical replicates for all three disease stages. Description Data MCI EAD LAD AATM_HUMAN (P00505) Aspartate aminotransferase, mitochondrial precursor (EC Mean 1.43 1.70 1.31 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transaminase 2) [MASS=47475] SEM 0.07 0.09 0.09 Count 3.00 3.00 3.00 ACON_HUMAN (Q99798) Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) Mean 1.24 1.61 1.19 (Citrate hydro-lyase) (Aconitase) [MASS=85425] SEM 0.05 0.17 0.18 Count 3.00 2.00 3.00 ACPM_HUMAN (O14561) Acyl carrier protein, mitochondrial precursor (ACP) (NADH- Mean 1.64 1.50 1.35 ubiquinone oxidoreductase 9.6 kDa subunit) (CI-SDAP) [MASS=17417] SEM 0.41 0.11 0.10 Count 2.00 2.00 3.00 ADT1_HUMAN (P12235) ADP/ATP translocase 1 (Adenine nucleotide translocator 1) (ANT 1) (ADP,ATP carrier protein 1) (Solute carrier family 25 member 4) (ADP,ATP carrier Mean 1.22 1.79 1.35 protein, heart/skeletal muscle isoform T1) [MASS=32933] SEM 0.10 0.05 0.13 Count 3.00 3.00 3.00 ALBU_HUMAN (P02768) Serum albumin precursor [MASS=69366] Mean 0.65 0.70 1.01 SEM 0.02 0.03 0.02 Count 3.00 2.00 2.00 ALDH2_HUMAN (P05091) Aldehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.3) Mean 2.11 1.54 1.17 (ALDH class 2) (ALDHI) (ALDH-E2) [MASS=56381] SEM 0.36 0.15 0.06 Count 3.00 3.00 3.00 ALDOA_HUMAN (P04075) Fructose-bisphosphate aldolase A (EC 4.1.2.13) (Muscle-type Mean 0.56 0.74 1.09 aldolase) (Lung cancer antigen NY-LU-1) [MASS=39289] SEM 0.05 0.06 0.10 Count 2.00 2.00 3.00 ANXA2_HUMAN (P07355) Annexin A2 (Annexin II) (Lipocortin II) (Calpactin I heavy chain) (Chromobindin-8) (p36) (Protein I) (Placental anticoagulant protein IV) (PAP-IV) Mean 1.40 1.64 1.28 [MASS=38473] SEM 0.14 0.01 0.27 Count 3.00 2.00 2.00 AT1A1_HUMAN (P05023) Sodium/potassium-transporting ATPase alpha-1 chain Mean 0.44 0.67 0.96 precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ ATPase 1) [MASS=112895] SEM 0.02 0.13 0.05 Count 3.00 2.00 3.00 AT1A3_HUMAN (P13637) Sodium/potassium-transporting ATPase alpha-3 chain (EC Mean 0.49 0.55 0.99 3.6.3.9) (Sodium pump 3) (Na+/K+ ATPase 3) (Alpha(III)) [MASS=111734] SEM 0.02 0.02 0.04 Count 3.00 3.00 3.00 AT1B1_HUMAN (P05026) Sodium/potassium-transporting ATPase subunit beta-1 Mean 0.46 0.53 1.04 (Sodium/potassium-dependent ATPase beta-1 subunit) [MASS=35061] SEM 0.01 0.00 0.11 Count 3.00 3.00 3.00 AT2A2_HUMAN (P16615) Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA2) (SR Ca(2+)-ATPase 2) (Calcium-transporting Mean 0.97 0.98 0.99 ATPase sarcoplasmic reticulum type, slow twitch skeletal muscle isoform) (Endoplasmic reticulum cla SEM 0.04 0.07 0.02 Count 3.00 2.00 2.00 ATP8_HUMAN (P03928) ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L) Mean 1.23 1.88 1.26 [MASS=7992] SEM 0.15 0.06 0.08 Count 3.00 2.00 3.00 ATPG_HUMAN (P36542) ATP synthase gamma chain, mitochondrial precursor (EC Mean 1.33 1.95 1.25 3.6.3.14) [MASS=32996] SEM 0.07 0.07 0.13 Count 3.00 3.00 3.00 C1QBP_HUMAN (Q07021) Complement component 1 Q subcomponent-binding protein, Mean 2.20 1.56 1.59 mitochondrial precursor (Glycoprotein gC1qBP) (C1qBP) (GC1q-R protein) (Hyaluronan- binding protein 1) (Mitochondrial matrix protein p32) (p33) [MASS=31362] SEM 0.93 0.09 0.05 Count 3.00 2.00 3.00 C560_HUMAN (Q99643) Succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (Integral membrane protein CII-3) (QPs1) (QPs-1) (Succinate Mean 1.02 1.45 1.68 dehydrogenase complex subunit C) (Succinate-ubiquinone oxidoreductase cytochrome B large subunit) (CY SEM 0.06 0.08 0.13 Count 3.00 3.00 3.00 CD59_HUMAN (P13987) CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory protein) (MAC-IP) (Protectin) (MEM43 antigen) Mean 0.49 0.59 0.83 (Membrane inhibitor of reactive lysis) (MIRL) (20 kDa homologous restriction factor) (HRF- 20 SEM 0.06 0.02 0.06 Count 3.00 2.00 3.00 CD9_HUMAN (P21926) CD9 antigen (p24) (Leukocyte antigen MIC3) (Motility-related Mean 0.95 0.94 0.16 protein) (MRP-1) (Tetraspanin-29) (Tspan-29) [MASS=25285] SEM 0.04 0.02 0.01 Count 2.00 2.00 2.00 CH60_HUMAN (P10809) 60 kDa heat shock protein, mitochondrial precursor (Hsp60) (60 Mean 1.29 1.67 1.23 kDa chaperonin) (CPN60) (Heat shock protein 60) (HSP-60) (Mitochondrial matrix protein P1) (P60 lymphocyte protein) (HuCHA60) [MASS=61054] SEM 0.05 0.10 0.02 Count 3.00 3.00 3.00 CHCH3_HUMAN (Q9NX63) Coiled-coil-helix-coiled-coil-helix domain-containing protein 3 Mean 1.27 1.41 1.10 [MASS=26152] SEM 0.10 0.09 0.13 Count 3.00 2.00 3.00 CISY_HUMAN (O75390) Citrate synthase, mitochondrial precursor (EC 2.3.3.1) Mean 1.46 1.69 1.30 [MASS=51712] SEM 0.07 0.19 0.05 Count 3.00 3.00 3.00 CJ070_HUMAN (Q9NZ45) Protein C10orf70 [MASS=12199] Mean 1.16 1.61 1.24 SEM 0.08 0.12 0.04 Count 3.00 3.00 3.00 CLH1_HUMAN (Q00610) Clathrin heavy chain 1 (CLH-17) [MASS=191482] Mean 0.61 0.55 1.25 SEM 0.08 0.02 0.13 Count 3.00 2.00 2.00 CMC1_HUMAN (O75746) Calcium-binding mitochondrial carrier protein Aralar1 (Mitochondrial aspartate glutamate carrier 1) (Solute carrier family 25 member 12) Mean 1.07 1.43 1.05 [MASS=74755] SEM 0.08 0.15 0.07 Count 3.00 3.00 3.00 CN37_HUMAN (P09543) 2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) (CNP) Mean 1.01 0.97 0.96 (CNPase) [MASS=47578] SEM 0.05 0.03 0.05 Count 3.00 3.00 3.00 COX5B_HUMAN (P10606) Cytochrome c oxidase polypeptide Vb, mitochondrial precursor Mean 1.44 1.87 1.35 (EC 1.9.3.1) [MASS=13696] SEM 0.10 0.41 0.03 Count 3.00 2.00 3.00 COX7C_HUMAN (P15954) Cytochrome c oxidase polypeptide VIIc, mitochondrial Mean 1.02 1.49 1.14 precursor (EC 1.9.3.1) [MASS=7245] SEM 0.02 0.23 0.06 Count 3.00 2.00 3.00 CRTC_HUMAN (P27797) Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) Mean 1.86 1.41 1.21 (grp60) [MASS=48141] SEM 0.09 0.21 0.15 Count 3.00 3.00 2.00 CSPG2_HUMAN (P13611) Versican core protein precursor (Large fibroblast proteoglycan) (Chondroitin sulfate proteoglycan core protein 2) (PG-M) (Glial hyaluronate-binding protein) Mean 0.52 0.44 0.78 (GHAP) [MASS=372817] SEM 0.05 0.04 0.06 Count 3.00 2.00 2.00 CY1_HUMAN (P08574) Cytochrome c1, heme protein, mitochondrial precursor Mean 1.18 1.81 1.26 (Cytochrome c-1) [MASS=35390] SEM 0.10 0.18 0.05 Count 3.00 3.00 3.00 DHE3_HUMAN (P00367) Glutamate dehydrogenase 1, mitochondrial precursor (EC Mean 2.40 1.61 1.25 1.4.1.3) (GDH) [MASS=61397] SEM 0.14 0.09 0.04 Count 3.00 3.00 3.00 DHSA_HUMAN (P31040) Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (Fp) (Flavoprotein subunit of complex II) Mean 1.33 1.37 1.26 [MASS=72691] SEM 0.13 0.11 0.14 Count 3.00 3.00 3.00 DHSB_HUMAN (P21912) Succinate dehydrogenase [ubiquinone] iron-sulfur protein, Mean 1.68 1.79 1.28 mitochondrial precursor (EC 1.3.5.1) (Ip) (Iron-sulfur subunit of complex II) [MASS=31630] SEM 0.31 0.07 0.10 Count 3.00 3.00 3.00 DLDH_HUMAN (P09622) Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase) (Glycine cleavage system L protein) Mean 1.36 1.49 1.14 [MASS=54150] SEM 0.07 0.18 0.15 Count 3.00 3.00 3.00 DPYL2_HUMAN (Q16555) Dihydropyrimidinase-related protein 2 (DRP-2) (Collapsin Mean 0.56 0.61 0.98 response mediator protein 2) (CRMP-2) (N2A3) [MASS=62293] SEM 0.04 0.02 0.09 Count 3.00 3.00 3.00 DYN1_HUMAN (Q05193) Dynamin-1 (EC 3.6.5.5) [MASS=97407] Mean 0.70 0.73 1.11 SEM 0.16 0.12 0.15 Count 3.00 2.00 2.00 EAA2_HUMAN (P43004) Excitatory amino acid transporter 2 (Sodium-dependent Mean 0.44 0.50 0.83 glutamate/aspartate transporter 2) [MASS=62104] SEM 0.05 0.05 0.05 Count 3.00 2.00 3.00 ECHA_HUMAN (P40939) Trifunctional enzyme subunit alpha, mitochondrial precursor (TP- Mean 1.37 1.37 1.20 alpha) (78 kDa gastrin-binding protein) [Includes: Long-chain enoyl-CoA hydratase (EC 4.2.1.17); Long chain 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211)] [MASS=82999] SEM 0.07 0.06 0.15 Count 3.00 2.00 3.00 ECHM_HUMAN (P30084) Enoyl-CoA hydratase, mitochondrial precursor (EC 4.2.1.17) Mean 1.31 1.95 1.31 (Short chain enoyl-CoA hydratase) (SCEH) (Enoyl-CoA hydratase 1) [MASS=31387] SEM 0.23 0.14 0.23 Count 2.00 3.00 2.00 EF1A1_HUMAN (P68104) Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor 1 Mean 1.11 1.40 1.08 A-1) (eEF1A-1) (Elongation factor Tu) (EF-Tu) [MASS=50141] SEM 0.27 0.56 0.11 Count 2.00 3.00 2.00 EFTU_HUMAN (P49411) Elongation factor Tu, mitochondrial precursor (EF-Tu) (P43) Mean 1.36 1.57 1.19 [MASS=49541] SEM 0.06 0.22 0.03 Count 3.00 2.00 3.00 ETFD_HUMAN (Q16134) Electron transfer flavoprotein-ubiquinone oxidoreductase, Mean 1.91 1.96 1.22 mitochondrial precursor (EC 1.5.5.1)