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Table 1 Protein identification by LC/MS/MS of spots in 2DE gels of 3 day mice hypothalamus which were significantly different in averaged normalised volume in HFD compared to LFD mice (n = 6). Proteins are arranged into 4 broad categories associated with specific functions: Proteins Associated with Cytoskeleton and/or Neuronal Plasticity, Proteins Associated with Cellular Stress, Proteins Associated with Energy Metabolism, all remaining proteins are grouped under Proteins Associated with Other Functions. Proteins belonging in more than one category are marked with an asterix (*) next to their UniProtKB identifier References for Table 1 can be found in Additional file 3

From: A high-fat diet induces rapid changes in the mouse hypothalamic proteome

Spot # Anova (p) Fold Change Protein Name pI MW Average Normalised Volumes Other Functional Categories MASCOT Data UniProtKB
Low Fat High Fat
Proteins Associated with Cytoskeleton and/or Neuronal Plasticity
 24 8.14E-04 1.2 Dihydropyrimidinase-related protein 2 6.48 71,179 785,600 644,200 Alzheimer’s disease/Neuronal degeneration (s1-s7) Score: 56 Matches: 5(3) Sequences: 5(3) O08553
 33a 1.00E-03 1.3 6.46 67,358 431,700 342,400 Score: 56 Matches: 5(3) Sequences: 5(3)
 33b 8.00E-03 1.6 6.38 64,410 41,860 25,450 Score: 56 Matches: 5(3) Sequences: 5(3)
 22 2.00E-03 1.2 6.07 75,305 345,200 426,100 Score: 54 Matches: 5(2) Sequences: 5(2)
 34 4.00E-03 1.4 6.58 66,703 130,200 92,110 Score: 96 Matches: 6(2) Sequences: 6(2)
 27 7.00E-03 1.2 6.72 69,760 1,976,000 1,616,000 Score: 555 Matches: 68(37) Sequences: 17(13)
 90 9.00E-03 1.2 6.58 70,524 660,200 534,100 Score: 446 Matches: 50(25) Sequences: 16(14)
 25 1.90E-02 1.5 6.59 74,017 115,700 75,120 Score: 66 Matches: 5(2) Sequences: 5(2)
 23 3.70E-02 1.4 6.35 72,817 26,820 36,860 Score: 159 Matches: 17(10) Sequences:12(9)
 92 1.50E-02 1.2 Dihydropyrimidinase-related protein 1 7.27 67,795 342,400 274,800 Score: 104 Matches: 14(5) Sequences: 12(5) P97427
 35 3.50E-02 1.4 Dihydropyrimidinase-related protein 5 8.18 71,943 553,000 752,200 (s8) Score: 44 Matches: 4(1) Sequences: 4(1) emPAI: 0.06 Q9EQF6
 37 1.00E-03 1.5 Fascin 6.65 54,476 202,200 137,500 Astrocyte specific
Alzheimer’s disease/Neuronal degeneration (s9-s11)
Score: 51 Matches: 2(1) Sequences: 2(1) Q61553
 125 4.00E-03 1.5 6.64 56,114 66,550 44,030 Score: 51 Matches: 2(1) Sequences: 2(1)
 86 1.00E-03 1.4 Thrombospondin type-1 domain-containing protein 1 6.44 89,787 21,030 14,960 Cellular stress
Astrocyte specific
Alzheimer’s disease/Neuronal degeneration (s13)
Score: 36 Matches: 3(1) Sequences: 1(1) Q9JM61*
 17 2.00E-03 1.4 Contactin-2 6.16 77,287 157,100 214,400 Alzheimer’s disease/Neuronal degeneration (s14) Score: 35 Matches: 1(1) Sequences: 1(1) Q61330
 88 3.00E-03 1.4 Dynamin-1-like protein 6.65 88,262 44,130 31,300 Cellular stress
Mitochondrial (s15,s16)
Score: 56 Matches: 6(4) Sequences: 6(4) Q8K1M6*
 87 1.90E-02 1.4 6.52 88,872 44,600 32,400 Score: 37 Matches: 2(1) Sequences: 2(1)
 85 1.90E-02 1.3 7.21 91,921 31,110 24,030 Score: 53 Matches: 4(2) Sequences: 4(2)
 52 4.00E-03 1.7 F-actin-capping protein subunit alpha-1 6.06 35,065 33,650 55,680 Alzheimer’s disease/Neuronal degeneration (s17, s18) Score: 82 Matches: 1(1) Sequences: 1(1) e P47753
 58 1.00E-02 1.2 F-actin-capping protein subunit β 6 29,413 633,600 780,600 Score: 80 Matches: 6(2) Sequences: 6(2) P47757
 124 4.00E-03 1.3 Fatty acid-binding protein, brain 5.69 12,708 329,600 413,500 Cellular stress
Astrocyte specific
Alzheimer’s disease/Neuronal degeneration (s19-s21)
Score: 47 Matches: 2(1) Sequences: 2(1) P51880*
 99 4.00E-03 1.3 Dual specificity mitogen-activated protein kinase kinase 1 6.78 45,886 588,200 453,000 Alzheimer’s disease/Neuronal degeneration (s22-s24) Score: 100 Matches: 7(4) Sequences: 6(4) P31938
 82 5.00E-03 2 Profilin-1 9.98 12,625 23,210 47,490 Alzheimer’s disease/Neuronal degeneration (s25-s28) Score: 73 Matches: 5(2) Sequences: 3(2) P62962
 122 7.00E-03 1.5 Profilin-2 5.65 13,875 115,800 171,500 Score: 62 Matches: 2(2) Sequences: 2(2) Q9JJV2
 96 8.00E-03 1.5 Actin-related protein 3 6.18 50,983 31,780 47,350 Alzheimer’s disease/Neuronal degeneration (s29) Score: 47 Matches: 4(1) Sequences: 4(1) Q99JY9
 93 1.20E-02 1.5 Plastin-3 6.09 68,341 25,000 36,730 Alzheimer’s disease/Neuronal degeneration (s30) Score: 65 Matches: 5(3) Sequences: 5(3) Q99K51
 76 1.50E-02 1.4 Nucleoside diRAphosphate kinase A 7.14 15,333 279,200 205,400 Alzheimer’s disease/Neuronal degeneration (s31, s32) Score: 101 Matches: 15(8) Sequences: 6(4) emPAI: 1.23 P15532
 116 1.70E-02 1.3 GTP-binding nuclear protein Ran 7.61 24,820 524,100 398,300 Alzheimer’s disease/Neuronal degeneration (s33, s34) Score: 131 Matches: 11(5) Sequences: 6(4) P62827
 26 2.10E-02 1.3 WD repeat-containing protein 1 6.89 73,690 146,600 116,800 (s35, s36) W Score: 65 Matches: 11(3) Sequences: 8(3) O88342
 55 2.30E-02 1.2 T Tropomyosin alpha-1 chain 4.72 30,497 340,400 407,500 Alzheimer’s disease/Neuronal degeneration (s37, s38) Score: 70 Matches: 3(3) Sequences: 3(3) P58771
 89 2.10E-02 1.2 6.47 87,348 30,950 25,160 Score: 119 Matches: 9(3) Sequences: 9(3)
 69 2.60E-02 1.2 Stathmin 6.07 16,606 642,900 761,200 Alzheimer’s disease/Neuronal degeneration (s39, s40) Score: 36 Matches: 2(1) Sequences: 2(1) P54227
 60 2.60E-02 1.3 Talin-2 6.66 31,968 63,640 47,710 (s41) Score: 34 Matches: 2(1) Sequences: 2(1) Q71LX4
 63 2.70E-02 1.4 Sepiapterin reductase 6.05 26,394 111,900 157,000 Alzheimer’s disease/Neuronal degeneration (s42) Score: 34 Matches: 2(1) Sequences: 2(1) Q64105
 74 3.10E-02 1.2 Spastin 4.91 15,061 311,900 375,100 Alzheimer’s disease/Neuronal degeneration (s43-s45) Score: 34 Matches: 1(1) Sequences: 1(1) Q9QYY8
 71 4.80E-02 1.1 Peptidyl-prolyl cis-trans isomerase A 7.33 16,394 173,900 153,400 Alzheimer’s disease/Neuronal degeneration (s46-s48) Score: 53 Matches: 4(2) Sequences: 4(2) P17742
 67 3.80E-02 1.1 Beta-synuclein 4.13 17,576 1,879,000 2,051,000 Alzheimer’s disease/Neuronal degeneration (s49, s50) Score: 57 Matches: 2(1) Sequences: 1(1) Q91ZZ3
Proteins Associated with Cellular Stress
 20a 1.00E-03 1.6 Heat shock 70 kDa protein 12A 6.68 79,878 61,440 39,140 Alzheimer’s disease/Neuronal degeneration (s51, s52) Score: 69 Matches: 4(2) Sequences: 4(2) Q8K0U4
 20b 3.00E-03 1.5 6.71 83,079 95,300 64,690 Score: 69 Matches: 4(2) Sequences: 4(2)
 20c 1.50E-02 1.3 6.75 80,640 119,400 88,760 Score: 69 Matches: 4(2) Sequences: 4(2)
 79 8.00E-03 1.5 10 kDa heat shock protein, mitochondrial 7.29 10,958 645,800 427,900 Mitochondrial (s53) Score: 47 Matches: 3(1) Sequences: 3(1) Q64433
 31 2.50E-02 1.2 60 kDa heat shock protein, mitochondrial 5.79 63,646 1,008,000 1,245,000 Mitochondrial
Alzheimer’s disease/Neuronal degeneration (s54)
Score: 604 Matches: 70(41) Sequences: 18(15) P63038
 21 2.90E-02 1.2 Heat shock cognate 71 kDa protein 5.73 75,915 4,300,000 5,025,000 Alzheimer’s disease/Neuronal degeneration (s2) Score: 51 Matches: 7(2) Sequences: 7(2) P63017
 42 2.90E-02 1.3 8.07 48,958 1,434,000 1,799,000 Score: 183 Matches: 10(7) Sequences: 8(6)
 19 9.00E-03 1.3 Heat shock protein 105 kDa 6.72 88,567 67,300 50,100 (s55) Score: 35 Matches: 1(1) Sequences: 1(1) Q61699
 114 1.00E-03 1.4 PITH domain-containing protein 1 5.95 25,039 52,050 73,410   Score: 66 Matches: 6(3) Sequences: 6(3) Q8BWR2
 45 2.00E-03 1.5 Elongation factor Tu, mitochondrial 7 46,325 170,000 110,000 Mitochondrial
Alzheimer’s disease/Neuronal degeneration s56)
Score: 66 Matches: 6(4) Sequences: 6(4) Q8BFR5
 165 2.00E-03 1.3 Amyloid beta A4 precursor protein-binding family B member 3 6.16 23,597 101,500 135,700 Alzheimer’s disease/Neuronal degeneration (s57) Score: 44 Matches: 7(1) Sequences: 1(1) Q8R1C9
 15 1.70E-02 1.3 6.05 88,110 31,970 40,700 Score: 51 Matches: 8(3) Sequences: 1(1)
 38 3.80E-02 1.4 7.25 55,131 165,400 114,700 Score: 49 Matches: 10(5) Sequences: 3(1)
 48 8.00E-03 1.3 6.83 41,004 128,000 95,720 Score: 55 Matches: 8(3) Sequences: 1(1)
 2 6.00E-03 1.4 5.91 211,272 47,200 66,770 Score: 48 Matches: 11(3) Sequences: 1(1)
 8 4.00E-03 1.4 Lon protease homolog, mitochondria 6.78 143,046 95,550 66,140 Mitochondrial (s58) Score: 50 Matches: 4(2) Sequences: 4(2) Q8CGK3
 112 5.00E-03 1.3 Biliverdin reductase 7.26 32,355 306,500 241,400 Alzheimer’s disease/Neuronal degeneration (s59) Score: 49 Matches: 5(2) Sequences: 5(2) Q9CY64
 106 6.00E-03 1.3 Pyridoxal kinase 6.12 37,439 541,300 681,500 Alzheimer’s disease/Neuronal degeneration (s60, s61) Score: 142 Matches: 11(8) Sequences: 8(7) Q8K183
 47 9.00E-03 1.2 Serine/threonine-protein phosphatase 2A activator 6.5 40,401 325,700 261,300 Alzheimer’s disease/Neuronal degeneration (s62) Score: 55 Matches: 4(1) Sequences: 4(1) P58389
 113 1.00E-02 1.5 Purine nucleoside phosphorylase 6.15 29,645 60,300 89,000 Alzheimer’s disease/Neuronal degeneration (s63, s64) Score: 56 Matches: 6(2) Sequences: 6(2) e P23492
 77 1.30E-02 2 Peroxiredoxin-5 8.69 15,091 208,000 409,900 Mitochondrial
Alzheimer’s disease/Neuronal degeneration (s65, s66)
Mass: 22226 Score: 181 Matches: 14(9) Sequences: 8(6) P99029
 78 3.20E-02 1.9 9.13 15,121 155,800 83,470 Score: 84 Matches: 9(4) Sequences: 6(4) emPAI: 0.88
 94 1.70E-02 1.4 Alpha-aminoadipic semialdehyde dehydrogenase 6.57 59,170 56,390 41,730 (67) Score: 110 Matches: 6(4) Sequences: 6(4) Q9DBF1
 49 4.00E-02 1.7 Fructose-bisphosphate aldolase C 8 40,291 67,960 114,800 Glucose metabolism
Mitochondrial
Alzheimer’s disease/Neuronal degeneration (s68-s70)
Score: 143 Matches: 8(5) Sequences: 8(5) P05063*
 95 4.20E-02 1.3 Aldehyde dehydrogenase, mitochondrial 6.79 54,367 713,100 564,900 Mitochondrial
Alzheimer’s disease/Neuronal degeneration (s71, s72)
Score: 160 Matches: 14(10) Sequences: 11(9) P47738
 101 4.40E-02 1.4 DNA fragmentation factor subunit alpha 6.93 43,473 200,500 147,500 Alzheimer’s disease/Neuronal degeneration(s73, 7 s4) Score: 42 Matches: 1(1) Sequences: 1(1) O54786
Proteins Associated with Energy Metabolism
 13 5.09E-04 1.2 Aconitate hydratase, mitochondrial 7.99 93,902 617,800 528,900 Cellular stress
Mitochondrial
Alzheimer’s disease/Neuronal degeneration(s9, s75)
Score: 159 Matches: 16(6) Sequences: 13(6) Q99KI0*
 53 9.00E-03 1.5 Malate dehydrogenase, cytoplasmic 6.07 34,445 68,430 104,200 Alzheimer’s disease/Neuronal degeneration (s9) Score: 65 Matches: 4(1) Sequences: 4(1) emPAI: 0.11 P14152
 108 1.50E-02 1.2 6.46 37,603 129,700 104,000 Score: 62 Matches: 2(1) Sequences: 2(1)
 109 7.00E-03 1.2 6.53 34,252 3,506,000 2,996,000 Score: 435 Matches: 39(24) Sequences: 10(7)
 104 7.00E-03 1.3 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial 6.06 41,608 130,800 164,600 Mitochondrial
Alzheimer’s disease/Neuronal degeneration (s76, s77)
Score: 73 Matches: 6(3) Sequences: 6(3) Q9D6R2
 105 7.00E-03 1.2 6.04 40,456 647,600 774,800 Score: 205 Matches: 21(12) Sequences: 13(8)
 117 9.00E-03 1.9 Triosephosphate isomerase 8.56 26,200 94,250 178,000 Alzheimer’s disease/Neuronal degeneration (s78, s79) Score: 128 Matches: 13(7) Sequences: 6(5) P17751
 41 1.00E-02 1.2 Alpha-enolase 6.89 48,793 3,024,000 2,527,000 Alzheimer’s disease/Neuronal degeneration (s75, s80) Score: 310 Matches: 55(26) Sequences: 15(12) P17182
 40 1.70E-02 1.3 6.66 49,013 1,724,000 1,284,000 Score: 125 Matches: 17(9) Sequences: 11(7)
 97 1.20E-02 2.5 Pyruvate kinase 8.82 48,848 47,750 117,800 Alzheimer’s disease/Neuronal degeneration (s81) Score: 121 Matches: 14(8) Sequences: 10(7) P52480
 49 2.60E-02 1.2 Phosphoglucomutase-1 7.02 67,904 384,900 309,800 Alzheimer’s disease/Neuronal degeneration (s82, s83) Score: 349 Matches: 28(18) Sequences: 20(17) Q9D0F9
 110 2.70E-02 1.4 Glycerol-3-phosphate dehydrogenase 1-like protein 7 39,084 138,600 99,230 Alzheimer’s disease/Neuronal degeneration (s84) Score: 160 Matches: 12(7) Sequences: 11(7) Q3ULJ0
 49 4.00E-02 1.7 Fructose-bisphosphate aldolase C 8 40,291 67,960 114,800 Cellular stress
Mitochondrial
Alzheimer’s disease/Neuronal degeneration (s68-s71)
Score: 143 Matches: 8(5) Sequences: 8(5) P05063*
 64 4.30E-02 1.2 Phosphoglycerate mutase 1 7.32 27,981 999,700 830,600 Alzheimer’s disease/Neuronal degeneration(s85) Score: 127 Matches: 12(5) Sequences: 6(4) Q9DBJ1
Protein Associated with Other Functions
 107 5.94E-04 1.4 Glycine--tRNA ligase 6.47 81,250 112,900 79,050 Protein synthesis
Alzheimer’s disease/Neuronal degeneration (s86)
Score: 82 Matches: 10(4) Sequences: 9(4) Q9CZD3
 98 8.10E-04 1.5 RNA polymerase II-associated factor 1 homolog 6.49 44,734 131,600 88,860 Regulation of transcription, Wnt signaling pathway
Alzheimer’s disease/Neuronal degeneration (s87)
Score: 39 Matches: 2(1) Sequences: 2(1) Q8K2T8
 16 8.11E-04 1.4 Ski oncogene 6.15 88,567 83,770 115,100 Signalling, Inhibits TGF beta signalling Score: 37 Matches: 3(1) Sequences: 1(1) Q60698
 9 1.70E-02 1.6 6.82 119,868 157,100 99,730 Score: 34 Matches: 1(1) Sequences: 1(1)
 36 4.00E-03 1.6 Histidine--tRNA ligase, cytoplasmic 6.16 55,349 88,260 144,700 Protein synthesis
Alzheimer’s disease/Neuronal degeneration (s88)
Score: 136 Matches: 10(6) Sequences: 9(6) Q61035
 7a 4.00E-03 1.4 Putative helicase Mov10l1 6.14 123,179 29,440 42,400 Negative regulation of cell cycle Score: 43 Matches: 1(1) Sequences: 1(1) Q99MV5
 7b 6.00E-03 1.5 6.19 121,854 32,970 49,230 Score: 43 Matches: 1(1) Sequences: 1(1)
 44 5.00E-03 1.3 Rab GDP dissociation inhibitor beta 6.65 47,312 412,900 311,300 Signalling, Positive regulation of GTPase activity
Alzheimer’s disease/Neuronal degeneration (s89)
Score: 104 Matches: 9(4) Sequences: 8(4) Q61598
 84 6.00E-03 1.6 Transcription termination factor 1 6.12 99,390 8292.349 13,440 Regulation of transcription Score: 36 Matches: 2(1) Sequences: 2(1) Q62187
 32 7.00E-03 1.5 HMG box-containing protein 6.12 64,083 137,800 200,000 Regulation of transcription, Wnt signaling Score: 40 Matches: 1(1) Sequences: 1(1) Q8R316
 118 8.00E-03 1.4 UMP-CMP kinase 6.16 22,194 133,000 187,600 Pyrimidine biosynthesis Score: 91 Matches: 6(4) Sequences: 6(4) Q9DBP5
 100 9.00E-03 1.4 Paraspeckle component 1 6.86 46,160 178,800 126,900 Control of transcription
Circadian rhythms
Score: 37 Matches: 3(0) Sequences: 3(0) Q8R326
 43 1.07E-02 1.3 Ornithine aminotransferase, mitochondrial 6.42 46,949 495,800 385,200 Amino acid metabolism
Mitochondrial
Score: 90 Matches: 7(5) Sequences: 7(5) P29758
 61 1.10E-02 1.2 Omega-amidase NIT2 6.88 30,652 104,200 87,480 Amino acid metabolism Score: 45 Matches: 3(1) Sequences: 3(1) Q9JHW2
 121 1.30E-02 1.5 Cytidine deaminase 5.63 15,212 32,230 47,840 Pyrimidine metabolism, Negative regulation of cell growth Score: 34 Matches: 1(1) Sequences: 1(1) P56389
 59 1.70E-02 1.3 Haloacid dehalogenase-like hydrolase domain-containing protein 2 6.16 30,652 216,800 280,000 Metabolism, Dephosphorylation Score: 50 Matches: 5(2) Sequences: 2(1) Q3UGR5
 120 1.80E-02 1.4 Sec1 family domain-containing protein 1 4.66 13,958 79,910 109,000 Cell morphogenesis, protein transport Score: 48 Matches: 3(1) Sequences: 1(1) Q8BRF7
 103 1.80E-02 1.3 Ras-like protein family member 10B 6.07 43,143 78,700 105,900 Signaling Score: 39 Matches: 1(1) Sequences: 1(1) Q5SSG5
 5 1.90E-02 1.5 Neutral alpha-glucosidase AB 6.13 146,358 32,530 47,230 Glycoprotein syntheses, Glycan metabolism Score: 40 Matches: 3(1) Sequences: 3(1) Q8BHN3
 119 2.00E-02 1.4 Acylamino-acid-releasing enzyme 6.99 19,848 113,700 83,510 Beta amyloid processes, Proteolysis Alzheimer’s disease/Neuronal degeneration (s90) Score: 39 Matches: 5(1) Sequences: 2(1) Q8R146
 111 2.10E-02 1.2 Phosphatidylinositol transfer protein alpha isoform 6.68 33,206 394,200 338,000 Transport of PtdIns and phosphatidylcholine, Axonogenesis Score: 51 Matches: 11(1) Sequences: 7(1) P53810
 83 2.20E-02 1.3 Solute carrier family 12 member 1 4.62 98,323 38,480 51,740 Regulation of ionic balance and cell volume Score: 39 Matches: 3(1) Sequences: 3(1) P55014
 14 2.30E-02 1.2 RalBP1-associated Eps domain-containing protein 2 5.21 83,232 525,500 609,200 Growth factor signaling, Cell migration Score: 36 Matches: 1(1) Sequences: 1(1) Q80XA6
 115 2.40E-02 1.3 Isopentenyl-diphosphate delta-isomerase 2 6.13 25,465 19,710 26,100 Cholesterol metabolism Score: 39 Matches: 1(1) Sequences: 1(1) Q8BFZ6
 102 2.50E-02 1.2 Glutamine synthetase 7.25 45,228 1,248,000 1,016,000 Positive regulation of synaptic transmission, Cellular response to starvation
Alzheimer’s disease/Neuronal degeneration (s91)
Score: 160 Matches: 32(9) Sequences: 10(7) P15105
 70 2.70E-02 1.2 Glycolipid transfer protein 7.25 20,036 113,000 92,910 Glycolipid transport, Glucoceramide transport Score: 36 Matches: 2(1) Sequences: 2(1) Q9JL62
 123 3.20E-02 1.2 Cystatin-B 7.14 12,833 63,610 52,090 Protease inhibitor, Negative regulation of proteolysis
Alzheimer’s disease/Neuronal degeneration (s92)
Mass: 11153 Score: 45 Matches: 1(1) Sequences: 1(1) Q62426