Supplementary Table S1: In this table protein name, uniprot code, gene name p-value and Fold change (FC) for each comparison are shown, for 299 of the 301 significantly regulated proteins found in both comparisons (p-value<0.01, fold change (FC) >+/-0.37) ALS versus control and FTLD-U versus control. Two uncharacterized proteins have been excluded from this list Protein name Uniprot Gene name p value FC FTLD-U p value FC ALS FTLD-U ALS Cytochrome b-c1 complex P14927 UQCRB 1.534E-03 -1.591E+00 6.005E-04 -1.639E+00 subunit 7 NADH dehydrogenase O95182 NDUFA7 4.127E-04 -9.471E-01 3.467E-05 -1.643E+00 [ubiquinone] 1 alpha subcomplex subunit 7 NADH dehydrogenase O43678 NDUFA2 3.230E-04 -9.145E-01 2.113E-04 -1.450E+00 [ubiquinone] 1 alpha subcomplex subunit 2 NADH dehydrogenase O43920 NDUFS5 1.769E-04 -8.829E-01 3.235E-05 -1.007E+00 [ubiquinone] iron-sulfur protein 5 ARF GTPase-activating A0A0C4DGN6 GIT1 1.306E-03 -8.810E-01 1.115E-03 -7.228E-01 protein GIT1 Methylglutaconyl-CoA Q13825 AUH 6.097E-04 -7.666E-01 5.619E-06 -1.178E+00 hydratase, mitochondrial ADP/ATP translocase 1 P12235 SLC25A4 6.068E-03 -6.095E-01 3.595E-04 -1.011E+00 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 Protein kinase C and casein Q9BY11 PACSIN1 3.837E-03 -5.863E-01 3.680E-06 -1.824E+00 kinase substrate in neurons protein 1 Tubulin polymerization- O94811 TPPP 6.466E-03 -5.755E-01 6.943E-06 -1.169E+00 promoting protein MIC C9JRZ6 CHCHD3 2.912E-02 -6.187E-01 2.195E-03 -9.781E-01 Mitochondrial 2- Q02978 SLC25A11 5.385E-03 -5.642E-01 2.067E-04 -6.783E-01 oxoglutarate/malate carrier protein NADH dehydrogenase O75380 NDUFS6 6.385E-04 -5.636E-01 2.521E-04 -1.344E+00 [ubiquinone] iron-sulfur protein 6, mitochondrial ATP-dependent RNA helicase Q08211 DHX9 6.206E-03 -5.489E-01 5.978E-04 -7.282E-01 A Cytochrome b-c1 complex P07919 UQCRH 2.555E-03 -5.462E-01 3.774E-05 -1.112E+00 subunit 6, mitochondrial ATP synthase subunit e, P56385 ATP5I 3.812E-03 -4.960E-01 5.590E-03 -7.127E-01 mitochondrial D-tyrosyl-tRNA(Tyr) Q8TEA8 DTD1 4.453E-03 -4.480E-01 5.201E-04 -6.216E-01 deacylase 1 1 Isoform 2 of NADH Q16718-2 NDUFA5 8.172E-04 -4.311E-01 3.914E-04 -7.745E-01 dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Isoform 2 of Fructose- P04075-2 ALDOA 2.564E-03 -4.256E-01 7.392E-03 -6.171E-01 bisphosphate aldolase A Peptidyl-prolyl cis-trans Q13526 PIN1 1.130E-03 -3.917E-01 9.565E-06 -9.878E-01 isomerase NIMA-interacting 1 Mitochondrial import inner Q9Y5L4 TIMM13 1.759E-04 -3.875E-01 2.658E-03 -4.346E-01 membrane translocase subunit Tim13 14-3-3 protein eta Q04917 YWHAH 4.999E-01 -2.994E-01 5.756E-03 -1.635E+00 26S protease regulatory A0A087X2I1 PSMC6 5.644E-01 1.464E-01 2.276E-03 -8.141E-01 subunit 10B 3-hydroxyacyl-CoA Q99714 HSD17B10 5.735E-01 -7.288E-02 1.485E-04 -6.069E-01 dehydrogenase type-2 3-ketoacyl-CoA thiolase, A0A0B4J2A4 ACAA2 1.972E-01 -1.698E-01 4.707E-04 -5.742E-01 mitochondrial A-kinase anchor protein 12 Q02952 AKAP12 3.603E-01 -9.134E-02 1.614E-03 -4.658E-01 ATP synthase F(0) complex P24539 ATP5F1 2.646E-02 -5.400E-01 2.014E-04 -1.195E+00 subunit B1, mitochondrial ATP synthase subunit O, P48047 ATP5O 2.770E-02 -3.439E-01 1.684E-05 -9.332E-01 mitochondrial ATP synthase subunit alpha, P25705 ATP5A1 3.394E-01 -1.653E-01 3.065E-03 -6.564E-01 mitochondrial ATP synthase subunit P56381 ATP5E 2.914E-02 -3.728E-01 1.281E-03 -8.244E-01 epsilon, mitochondrial Alpha-internexin Q16352 INA 5.864E-01 -1.547E-01 8.300E-03 -9.529E-01 Ankyrin-2 I6L894 ANK2 4.074E-01 -2.006E-01 1.965E-01 3.564E-01 Ankyrin-2 Q01484 ANK2 1.885E-01 -3.857E-01 7.451E-03 -7.517E-01 Aspartate aminotransferase, P17174 GOT1 1.663E-01 -2.206E-01 3.226E-04 -8.068E-01 cytoplasmic Aspartate aminotransferase, P00505 GOT2 9.215E-02 -4.124E-01 3.229E-03 -8.777E-01 mitochondrial Beta-adducin P35612 ADD2 9.875E-01 -2.137E-03 3.014E-03 -4.535E-01 Beta-synuclein Q16143 SNCB 7.097E-01 -7.728E-02 8.855E-04 -9.587E-01 Brain acid soluble protein 1 P80723 BASP1 5.027E-01 -3.308E-01 2.776E-05 -2.879E+00 CAP-Gly domain-containing Q9UDT6 CLIP2 2.721E-01 1.044E-01 3.807E-03 -3.988E-01 linker protein 2 CLIP-associating protein 2 E7EW49 CLASP2 8.832E-02 2.676E-01 1.164E-04 -6.969E-01 Calcium/calmodulin- Q13554 CAMK2B 6.042E-01 -1.136E-01 2.690E-04 -1.095E+00 dependent protein kinase type II subunit beta Calcyclin-binding protein Q9HB71 CACYBP 9.103E-02 -1.277E-01 6.298E-05 -4.090E-01 Clathrin light chain B P09497 CLTB 1.425E-02 -3.531E-01 9.393E-05 -7.432E-01 Collagen alpha-2(IV) chain P08572 COL4A2 3.343E-02 -6.581E-01 5.603E-03 -9.356E-01 2 Creatine kinase U-type, P12532 CKMT1A 5.027E-01 -1.007E-01 1.093E-06 -9.984E-01 mitochondrial Crk-like protein P46109 CRKL 1.811E-01 -1.899E-01 1.996E-04 -6.290E-01 Cyclin-dependent-like kinase Q00535 CDK5 4.768E-01 -9.335E-02 7.319E-03 -5.475E-01 5 Cystatin-C P01034 CST3 1.337E-01 -3.599E-01 6.755E-03 -6.734E-01 Cysteine and histidine-rich Q9UHD1 CHORDC1 2.767E-01 -1.879E-01 3.906E-03 -6.403E-01 domain-containing protein 1 Cytochrome b-c1 complex P31930 UQCRC1 2.439E-02 -2.676E-01 1.033E-03 -5.904E-01 subunit 1, mitochondrial Cytochrome b-c1 complex P22695 UQCRC2 8.842E-01 3.131E-02 2.903E-04 -1.011E+00 subunit 2, mitochondrial Cytochrome c oxidase subunit P20674 COX5A 1.070E-01 -2.671E-01 4.390E-05 -1.232E+00 5A, mitochondrial Cytochrome c oxidase subunit P10606 COX5B 3.017E-02 -5.270E-01 2.304E-04 -1.864E+00 5B, mitochondrial Cytochrome c oxidase subunit P12074 COX6A1 6.820E-01 -1.015E-01 1.479E-04 -1.462E+00 6A1, mitochondrial Cytochrome c oxidase subunit P14854 COX6B1 4.828E-02 -3.545E-01 2.623E-05 -9.959E-01 6B1 Dihydrolipoyl P09622 DLD 2.040E-01 -1.761E-01 1.535E-03 -5.779E-01 dehydrogenase, mitochondrial Dihydrolipoyllysine-residue P10515 DLAT 9.583E-01 1.003E-02 2.903E-03 -5.745E-01 acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial Drebrin Q16643 DBN1 1.708E-01 -3.295E-01 1.635E-03 -8.918E-01 Elongation factor 1-alpha 2 Q05639 EEF1A2 5.839E-02 -7.670E-01 1.248E-03 -1.765E+00 Endophilin-A3 Q99963 SH3GL3 7.411E-01 5.451E-02 5.477E-04 -8.744E-01 Eukaryotic translation I3L504 EIF5A 7.102E-01 -5.812E-02 1.125E-04 -1.150E+00 initiation factor 5A-1 Fatty acid-binding protein, S4R371 FABP3 1.889E-02 -3.356E-01 1.435E-03 -7.746E-01 heart (Fragment) Fructose-bisphosphate P09972 ALDOC 3.917E-01 -1.088E-01 5.564E-05 -7.127E-01 aldolase C Fumarate hydratase, P07954 FH 3.974E-01 -1.306E-01 8.325E-04 -5.567E-01 mitochondrial Gamma-enolase P09104 ENO2 7.987E-02 -1.478E-01 5.903E-04 -5.851E-01 Gamma-soluble NSF Q99747 NAPG 7.597E-02 -1.588E-01 2.599E-04 -5.203E-01 attachment protein Gamma-synuclein O76070 SNCG 2.869E-01 -1.793E-01 8.657E-05 -7.801E-01 Glucose-6-phosphate A0A0A0MTS2 GPI 3.983E-01 -1.014E-01 2.509E-03 -4.165E-01 isomerase (Fragment) Glutathione S-transferase Q9Y2Q3 GSTK1 9.588E-01 1.509E-02 5.204E-03 -1.161E+00 kappa 1 3 HIG1 domain family member C9JNU6 HIGD1A 3.272E-01 -2.261E-01 4.101E-04 -1.001E+00 1A, mitochondrial Heterogeneous nuclear P52272 HNRNPM 7.168E-01 -1.616E-02 1.937E-04 -4.287E-01 ribonucleoprotein M Hyaluronan and proteoglycan Q9GZV7 HAPLN2 9.009E-02 -5.195E-01 4.286E-05 -1.562E+00 link protein 2 Hypoxanthine-guanine P00492 HPRT1 6.308E-01 -7.132E-02 3.900E-03 -5.122E-01 phosphoribosyltransferase Immunoglobulin superfamily Q969P0 IGSF8 6.157E-02 -2.599E-01 3.015E-04 -7.467E-01 member 8 Interferon-inducible double- O75569 PRKRA 4.241E-02 -4.771E-01 4.848E-04 -1.147E+00 stranded RNA-dependent protein kinase activator A Isoaspartyl peptidase/L- Q7L266 ASRGL1 8.671E-01 -2.464E-02 7.620E-03 -5.145E-01 asparaginase Isoform 2 of Cytoplasmic O14576-2 DYNC1I1 2.327E-02 -8.297E-01 5.765E-04 -1.651E+00 dynein 1 intermediate chain 1 Isoform 2 of MIC Q16891-2 IMMT 2.545E-01 -1.080E-01 3.325E-05 -4.886E-01 Isoform 2 of NADH O95168-2 NDUFB4 1.728E-02 -4.495E-01 1.082E-06 -2.206E+00 dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Isoform 2 of Serine/arginine- Q01130-2 SRSF2 4.255E-01 -1.399E-01 2.264E-03 -6.406E-01 rich splicing factor 2 Isoform 3 of Neurochondrin Q9UBB6-3 NCDN 8.974E-01 -3.598E-02 1.296E-03 -1.165E+00 Isoform 4 of Clathrin coat O60641-4 SNAP91 5.556E-02 -3.402E-01 8.500E-03 -5.470E-01 assembly protein AP180 Isoform 5 of Actin-binding Q6H8Q1-5 ABLIM2 2.073E-01 -3.341E-01 4.047E-03 -1.110E+00 LIM protein 2 Isoform 7 of Cytosolic acyl O00154-7 ACOT7 8.427E-01 -3.136E-02 1.739E-06 -1.556E+00 coenzyme A thioester hydrolase Isoform 9 of Calpastatin P20810-9 CAST 4.090E-01 -1.721E-01 3.625E-03 -1.020E+00 Leucine-rich repeat- Q8N1G4 LRRC47 3.200E-02 -3.239E-01 1.376E-04 -7.923E-01 containing protein 47 MAP6 domain-containing Q9H9H5 MAP6D1 3.703E-01 -2.553E-01 1.834E-04 -1.477E+00 protein 1 ATP synthase subunit d, O75947 ATP5H 3.103E-03 -3.821E-01 4.434E-04 -5.497E-01 mitochondrial MIC C9JRZ6 CHCHD3 2.912E-02 -6.187E-01 2.195E-03 -9.781E-01 Macrophage migration P14174 MIF 6.514E-02 -5.958E-01 7.627E-03 -8.703E-01 inhibitory factor Malate dehydrogenase, P40925 MDH1 7.469E-01 -3.783E-02 6.571E-05 -6.417E-01 cytoplasmic Malate dehydrogenase, P40926 MDH2 2.991E-02 -3.994E-01 1.317E-04 -7.848E-01 mitochondrial 4 Microtubule-associated F8W9U4 MAP4 2.742E-01 -2.519E-01 4.201E-03 -9.554E-01 protein Microtubule-associated E7EVA0 MAP4 3.660E-01 2.141E-01 9.383E-01 -1.732E-02 protein Microtubule-associated P11137 MAP2 1.979E-01 -4.528E-01 3.386E-03 -1.073E+00 protein 2 Microtubule-associated Q96JE9 MAP6 4.823E-02 -3.578E-01 2.345E-05 -1.030E+00 protein 6 Microtubule-associated Q9UPY8 MAPRE3 3.929E-01 3.012E-01 6.312E-03 -9.822E-01 protein RP/EB family member 3 NADH