Table 1.
Depletome proteins identified using PAD.
| Identified proteins | Accession number | Molecular weight | Number of unique peptides in thalamus of untreated mouse | Number of unique peptides in depletome | UniProtKB | Gene Symbol |
|---|---|---|---|---|---|---|
| Gamma-enolase | IPI00331704 | 47 kDa | 4 | 12 | P17183 | Eno2 |
| Serum albumin | IPI00131695 | 69 kDa | 2 | 9 | P07724 | Alb |
| Creatine kinase B-type | IPI00136703 | 43 kDa | 4 | 8 | Q04447 | Ckb |
| Malate dehydrogenase, mitochondrial | IPI00323592 | 36 kDa | 1 | 7 | P08249 | Mdh2 |
| Heat shock cognate 71 kDa protein | IPI00323357 | 71 kDa | 0 | 6 | P63017 | Hspa8 |
| Dihydropyrimidinase-related protein 2 | IPI00114375 | 62 kDa | 2 | 6 | O08553 | Dpysl2 |
| Isoform Ib of Synapsin-1 | IPI00136372 (+1) | 70 kDa | 3 | 6 | O88935 | Syn1 |
| 14-3-3 protein gamma | IPI00230707 | 28 kDa | 2 | 5 | P61982 | Ywhag |
| Isoform M2 of Pyruvate kinase isozymes M1/M2 | IPI00407130 (+1) | 58 kDa | 0 | 5 | P52480 | Pkm |
| Aspartate aminotransferase, cytoplasmic | IPI00230204 | 46 kDa | 0 | 5 | P05201 | Got1 |
| Actin, cytoplasmic 1 | IPI00110850 (+4) | 42 kDa | 2 | 4 | P60710 | Actb |
| Superoxide dismutase [Cu–Zn] | IPI00130589 | 16 kDa | 2 | 4 | P08228 | Sod1 |
| Alpha-enolase | IPI00462072 (+2) | 47 kDa | 0 | 4 | P17182 | Eno1 |
| Tubulin beta-4 chain | IPI00109073 (+1) | 50 kDa | 0 | 4 | Q9D6F9 | Tubb4a |
| Isoform 1 of Alpha-synuclein | IPI00115157 (+1) | 14 kDa | 0 | 4 | O55042 | Snca |
| Tubulin alpha-1A chain | IPI00110753 (+3) | 50 kDa | 0 | 3 | P68369 | Tuba1a |
| Stathmin | IPI00551236 | 17 kDa | 0 | 3 | P54227 | Stmn1 |
| Malate dehydrogenase, cytoplasmic | IPI00336324 | 37 kDa | 0 | 3 | P14152 | Mdh1 |
| Isoform 1 of Microtubule-associated protein 1A | IPI00408909 (+1) | 300 kDa | 1 | 2 | Q9QYR6 | Map1a |
| Triosephosphate isomerase | IPI00467833 (+1) | 32 kDa | 1 | 2 | P17751 | Tpi1 |
| SH3 domain-binding glutamic acid-rich-like protein 3 | IPI00127358 | 10 kDa | 1 | 2 | Q91VW3 | Sh3bgrl3 |
| Isoform HuC-L of ELAV-like protein 3 | IPI00122451 | 40 kDa | 0 | 2 | Q60900 | Elavl3 |
| Fructose-bisphosphate aldolase C | IPI00119458 | 39 kDa | 0 | 2 | P05063 | Aldoc |
| 2-iminobutanoate/2-iminopropanoate deaminase | IPI00130640 | 14 kDa | 0 | 2 | P52760 | Rida |
| Peroxiredoxin-2 | IPI00117910 (+1) | 22 kDa | 0 | 2 | Q61171 | Prdx2 |
| Isoform 1 of Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | IPI00121545 (+2) | 59 kDa | 0 | 2 | P63328 | Ppp3ca |
| Annexin A5 | IPI00317309 | 36 kDa | 0 | 2 | P48036 | Anxa5 |
| Heat shock protein HSP 90-alpha | IPI00330804 | 85 kDa | 0 | 2 | P07901 | Hsp90aa1 |
| Elongation factor 1-alpha 2 | IPI00119667 | 50 kDa | 0 | 2 | P62631 | Eef1a2 |
| Isoform Mitochondrial of Peroxiredoxin-5, mitochondrial | IPI00129517 (+3) | 22 kDa | 0 | 2 | P99029 | Prdx5 |
| L-lactate dehydrogenase B chain | IPI00229510 | 37 kDa | 0 | 2 | P16125 | Ldhb |
| Ras-related protein Rab-3A | IPI00122965 | 25 kDa | 0 | 2 | P63011 | Rab3a |
| Ubiquitin carboxyl-terminal hydrolase isozyme L1 | IPI00313962 (+1) | 25 kDa | 0 | 2 | Q9R0P9 | Uchl1 |
| Fructose-bisphosphate aldolase A | IPI00221402 | 39 kDa | 0 | 2 | P05064 | ALDOA |
| Alpha globin 1 | IPI00845802 | 15 kDa | 1 | 2 | Q91VB8 | Hba-a1 |
| Cytochrome P450, family 2, subfamily c, polypeptide 68 | IPI00405136 (+1) | 56 kDa | 0 | 1 | Q8VCP4 | Cyp2c68 |
| Translationally-controlled tumor protein | IPI00129685 | 19 kDa | 0 | 1 | P63028 | Tpt1 |
| Proteasomal ubiquitin receptor ADRM1 | IPI00331155 | 42 kDa | 0 | 1 | Q9JKV1 | Adrm1 |
| Isoform 1 of Serine/threonine-protein kinase SMG1 | IPI00403352 | 410 kDa | 0 | 1 | Q8BKX6 | Smg1 |
| Isoform 2 of Neurogenic locus notch homolog protein 2 | IPI00621767 | 243 kDa | 0 | 1 | O35516 | Notch2 |
| Isoform 4 of Myocyte-specific enhancer factor 2C | IPI00318314 (+1) | 47 kDa | 0 | 1 | Q8CFN5 | Mef2c |
| Parvalbumin alpha | IPI00230766 | 12 kDa | 0 | 1 | P32848 | Pvalb |
| Neurogranin | IPI00380227 | 7 kDa | 0 | 1 | P60761 | Nrgn |
| Polyadenylate-binding protein 1 | IPI00124287 (+2) | 71 kDa | 0 | 1 | P29341 | Pabpc1 |
| Histidine triad nucleotide-binding protein 1 | IPI00108189 (+1) | 14 kDa | 0 | 1 | P70349 | Hint1 |
| Isoform 1 of 60 kDa heat shock protein, mitochondrial | IPI00308885 (+1) | 61 kDa | 0 | 1 | P63038 | Hspd1 |
| Isoform 1 of Microtubule-associated protein 6 | IPI00115833 | 96 kDa | 0 | 1 | Q7TSJ2 | Map6 |
| Tubulin alpha-4A chain | IPI00117350 | 50 kDa | 0 | 1 | P68368 | Tuba4a |
| Ras-related protein Rab-1A | IPI00114560 (+3) | 23 kDa | 0 | 1 | P62821 | Rab1a |
| V-type proton ATPase subunit B, brain isoform | IPI00119113 | 57 kDa | 0 | 1 | P62814 | Atp6v1b2 |
| Protein kinase C and casein kinase substrate in neurons protein 1 | IPI00123613 | 51 kDa | 0 | 1 | Q61644 | Pacsin1 |
| Isoform IIb of Synapsin-2 | IPI00134492 (+2) | 52 kDa | 0 | 1 | Q64332 | Syn2 |
| Isoform 1 of Alpha-adducin | IPI00136000 (+4) | 81 kDa | 0 | 1 | Q9QYC0 | Add1 |
| Profilin-1 | IPI00224740 (+1) | 15 kDa | 0 | 1 | P62962 | Pfn1 |
| Phosphoglycerate mutase 2 | IPI00230706 (+1) | 29 kDa | 0 | 1 | O70250 | Pgam2 |
| Rho GDP-dissociation inhibitor 1 | IPI00322312 | 23 kDa | 0 | 1 | Q99PT1 | Arhgdia |
| Rab GDP dissociation inhibitor alpha | IPI00323179 | 51 kDa | 0 | 1 | P50396 | Gdi1 |
| Isoform 1 of Structural maintenance of chromosomes protein 5 | IPI00380203 (+1) | 129 kDa | 0 | 1 | Q8CG46 | Smc5 |
| Amphiphysin | IPI00400180 | 75 kDa | 0 | 1 | Q7TQF7 | Amph |
| ATP synthase subunit beta, mitochondrial | IPI00468481 | 56 kDa | 0 | 1 | P56480 | Atp5f1b |
| Choline transporter-like protein 3 | IPI00122287 | 73 kDa | 0 | 1 | Q921V7 | Slc44a3 |
| Ras-related protein Rab-11B | IPI00135869 (+5) | 24 kDa | 0 | 1 | P46638 | Rab11b |
| Ubiquitin-60S ribosomal protein L40 | IPI00138892 (+11) | 15 kDa | 0 | 1 | P62984 | Uba52 |
| Isoform 3 of NSFL1 cofactor p47 | IPI00387232 (+2) | 41 kDa | 0 | 1 | Q9CZ44 | Nsfl1c |
| Mitogen-activated protein kinase 1 | IPI00119663 (+1) | 41 kDa | 0 | 1 | P63085 | Mapk1 |
| Neurocan core protein | IPI00135563 (+1) | 137 kDa | 0 | 1 | P55066 | Ncan |
| Tyrosine-protein phosphatase non-receptor type substrate 1 | IPI00756790 (+3) | 17 kDa | 0 | 1 | P97797 | Sirpa |
| Vomeronasal 2, receptor 112 | IPI00660717 | 98 kDa | 0 | 1 | L7N221 | Vmn2r112 |
| Adaptin ear-binding coat-associated protein 1 | IPI00225533 | 30 kDa | 0 | 1 | Q9CR95 | Necap1 |
| Transcriptional activator protein Pur-beta | IPI00128867 | 34 kDa | 0 | 1 | O35295 | Purb |
| Isoform 1 of D-aminoacyl-tRNA deacylase 1 | IPI00133713 | 23 kDa | 0 | 1 | Q9DD18 | Dtd1 |
| Endophilin-A1 | IPI00331110 (+3) | 40 kDa | 0 | 1 | Q62420 | Sh3gl2 |
| Macrophage migration inhibitory factor | IPI00230427 | 13 kDa | 0 | 1 | P34884 | Mif |
| 14-3-3 protein epsilon | IPI00118384 (+1) | 29 kDa | 0 | 1 | P62259 | Ywhae |
| Phosphorylase b kinase regulatory subunit beta | IPI00380735 | 124 kDa | 0 | 1 | Q7TSH2 | Phkb |