Table 1.
Proteins exhibiting decreased phosphorylation in N2a58/22L cells.
| No. | Uniprot | Protein Names | Ratioa | Peptb | sequence coverage [%] |
PEPc | Biological Process |
|---|---|---|---|---|---|---|---|
| 1 | P43276 | Histone H1.5 | 0.46237 | 1 | 13.9 | 5.61E-16 | nucleosome assembly |
| 2 | P30681 | High mobility group protein B2 | 0.48683 | 2 | 11 | 3.33E-02 | genome maintenance; differentiation |
| 3 | P11440 | Cell division control protein 2 homolog | 0.49428 | 5 | 7.7 | 3.03E-03 | cell cycles; protein phosphorylation |
| 4 | P97310 | DNA replication licensing factor MCM2 | 0.54657 | 1 | 2.4 | 1.65E-05 | cell cycle; nucleosome assembly; transcription |
| 5 | P43275 | Histone H1.1 | 0.56637 | 1 | 19.2 | 8.42E-04 | nucleosome assembly |
| 6 | P43274 | Histone H1.4 | 0.58367 | 4 | 24.2 | 1.04E-14 | nucleosome assembly |
| 7 | Q9Z2X1-1 | Heterogeneous nuclear ribonucleoprotein F | 0.60054 | 2 | 6.5 | 5.45E-22 | RNA processing |
| 8 | P70670 | Nascent polypeptide-associated complex subunit alpha, muscle-specific form | 0.60501 | 2 | 1.2 | 5.07E-11 | protein transport; transcription |
| 9 | P60843 | Eukaryotic initiation factor 4A-I | 0.65781 | 5 | 4.9 | 5.39E-03 | translation |
| 10 | P27659 | 60S ribosomal protein L3 | 0.65906 | 12 | 7.7 | 1.49E-03 | translation |
| 11 | P28656 | Nucleosome assembly protein 1-like 1 | 0.70087 | 1 | 7.2 | 1.16E-05 | nucleosome assembly |
| 12 | Q62167 | ATP-dependent RNA helicase DDX3X | 0.70816 | 3 | 3.3 | 3.12E-19 | putative helicase activity |
| 13 | P68040 | Guanine nucleotide-binding protein subunit beta-2-like1 | 0.71371 | 1 | 7.9 | 5.15E-08 | unknown |
| 14 | P47911 | 60S ribosomal protein L6 | 0.71887 | 7 | 12 | 7.26E-07 | translation |
| 15 | Q61937 | Nucleophosmin | 0.72062 | 7 | 29.8 | 4.38E-07 | cell cycle; nuclear export |
| 16 | P15532 | Nucleoside diphosphate kinase A | 0.72108 | 2 | 17.8 | 7.93E-03 | NTP biosynthesis; nervous system development |
| 17 | O70251 | Elongation factor 1-beta | 0.73137 | 1 | 24 | 2.20E-18 | translation |
| 18 | Q61656 | Probable ATP-dependent RNA helicase DDX5 | 0.73832 | 4 | 3.7 | 1.41E-03 | RNA processing; transcription |
| 19 | Q9ERK4 | Exportin-2 | 0.74333 | 1 | 2.1 | 8.97E-05 | cell proliferation; protein transport |
| 20 | P09411 | Phosphoglycerate kinase 1 | 0.74902 | 2 | 6.7 | 3.40E-03 | glycolysis; phosphorylation |
| 21 | P48962 | ADP/ATP translocase 1 | 0.75149 | 6 | 18.8 | 3.87E-36 | transmembrane transport |
| 22 | Q9D8N0 | Elongation factor 1-gamma | 0.76191 | 3 | 7.8 | 1.45E-10 | translation |
| 23 | P49312-2 | Heterogeneous nuclear ribonucleoprotein A1 | 0.77303 | 5 | 12.1 | 7.20E-05 | alternative splicing; nuclear export/import |
| 24 | Q9CZM2 | 60S ribosomal protein L15 | 0.77591 | 9 | 10.3 | 2.04E-15 | translation |
| 25 | P97855 | Ras GTPase-activating protein-binding protein 1 | 0.78021 | 2 | 7.3 | 1.11E-15 | protein transport |
| 26 | Q9EQU5-1 | Protein SET | 0.79357 | 7 | 7.9 | 5.77E-12 | nucleosome assembly |
| 27 | Q7TPV4 | Myb-binding protein 1A | 0.79496 | 2 | 1.5 | 2.39E-11 | cytoplasmic transport; transcription |
| 28 | P80318 | T-complex protein 1 subunit gamma | 0.79504 | 1 | 6.6 | 2.89E-05 | protein folding |
| 29 | P25444 | 40S ribosomal protein S2 | 0.79516 | 20 | 12.3 | 2.99E-04 | translation |
| 30 | P10126 | Elongation factor 1-alpha 1 | 0.80203 | 5 | 18.6 | 1.06E-33 | translational elongation |
| 31 | P61979-2 | Heterogeneous nuclear ribonucleoprotein K | 0.80502 | 6 | 11.9 | 1.17E-15 | RNA processing |
| 32 | P07901 | Heat shock protein HSP 90-alpha | 0.80637 | 2 | 32.7 | 1.38E-94 | CD8 T-cell differentiation; chaperone activity |
| 33 | Q61598-1 | Rab GDP dissociation inhibitor beta | 0.81242 | 3 | 5.6 | 1.93E-05 | protein transport; regulation of GTPase activity |
| 34 | P54775 | 26S protease regulatory subunit 6B | 0.81795 | 2 | 7.2 | 1.59E-09 | blastocyst development; protein catabolism |
| 35 | Q20BD0 | Heterogeneous nuclear ribonucleoprotein A/B | 0.82349 | 3 | 19.3 | 3.26E-11 | nucleotide binding |
| 36 | P14206 | 40S ribosomal protein SA;Laminin receptor 1 | 0.8261 | 7 | 20.7 | 2.57E-17 | translation |
| 37 | P68134 | Actin, alpha skeletal muscle | 0.83457 | 10 | 27.3 | 4.38E-26 | cytoskeleton |
| 38 | P80314 | T-complex protein 1 subunit beta | 0.83579 | 2 | 11.6 | 1.05E-21 | protein folding |
| 39 | P50580 | Proliferation-associated protein 2G4 | 0.84048 | 2 | 8.1 | 1.53E-03 | rRNA processing; transcription; translation |
| 40 | P11983-1 | T-complex protein 1 subunit alpha B | 0.84687 | 4 | 8.8 | 5.73E-23 | protein folding |
| 41 | P35564 | Calnexin | 0.85134 | 1 | 6.3 | 2.08E-06 | protein folding |
| 42 | Q8BUP7 | Putative uncharacterized protein;26S protease regulatory subunit 6A | 0.85207 | 3 | 7.3 | 9.72E-03 | blastocyst development; protein catabolism |
| 43 | P63017 | Heat shock cognate 71 kDa protein | 0.85947 | 9 | 32.2 | 2.16E-96 | response to stress |
| 44 | Q01768 | Nucleoside diphosphate kinase B | 0.86107 | 4 | 17.8 | 1.35E-04 | NTP biosynthesis |
| 45 | P62082 | 40S ribosomal protein S7 | 0.86306 | 3 | 10.3 | 8.39E-03 | translation |
| 46 | P80315 | T-complex protein 1 subunit delta | 0.86423 | 1 | 6.9 | 3.81E-12 | protein folding |
| 47 | Q71LX8 | Heat shock protein 84b | 0.8654 | 4 | 32 | 6.13E-136 | protein folding; stress response |
| 48 | P58252 | Elongation factor 2 | 0.86672 | 2 | 7.9 | 3.57E-25 | translation |
| 49 | P08249 | Malate dehydrogenase, mitochondrial | 0.86743 | 1 | 9.2 | 2.49E-35 | glycolysis |
| 50 | P70168 | Importin subunit beta-1 | 0.87257 | 2 | 2.7 | 3.47E-13 | nuclear import |
| 51 | P51859 | Hepatoma-derived growth factor | 0.87395 | 2 | 12.7 | 2.95E-07 | transcription |
| 52 | P14152 | Malate dehydrogenase, cytoplasmic | 0.87522 | 1 | 7.8 | 1.09E-03 | glycolysis |
| 53 | P80313 | T-complex protein 1 subunit eta | 0.89251 | 1 | 8.6 | 1.22E-39 | protein folding |
| 54 | P62827 | GTP-binding nuclear protein Ran | 0.89794 | 3 | 22.7 | 2.27E-09 | cell cycle; nuclear import; signal transduction |
| 55 | P20029 | 78 kDa glucose-regulated protein | 0.89996 | 1 | 7 | 4.16E-04 | cerebellar Purkinje cell development/organization |
| 56 | P56480 | ATP synthase subunit beta, mitochondrial | 0.90399 | 1 | 18.5 | 1.85E-42 | proton transport; lipid metabolism |
| 57 | P17742 | Peptidyl-prolyl cis-trans isomerase A | 0.90719 | 10 | 20.4 | 4.97E-20 | neuron differentiation; protein folding |
| 58 | P20152 | Vimentin | 0.90814 | 10 | 26.2 | 2.22E-34 | cytoskeleton |
| 59 | P09103 | Protein disulfide-isomerase | 0.91019 | 2 | 4.7 | 8.84E-02 | redox homeostasis |
| 60 | P80317 | T-complex protein 1 subunit zeta | 0.91579 | 1 | 10.2 | 1.49E-02 | protein folding |
| 61 | Q569Z6 | Thyroid hormone receptor-associated protein 3 | 0.93507 | 3 | 3.7 | 4.27E-04 | transcription |
| 62 | P09405 | Nucleolin | 0.93545 | 1 | 12.7 | 8.06E-34 | nucleotide binding |
| 63 | Q9D6F9 | Tubulin beta-4 chain | 0.93722 | 4 | 23.2 | 9.43E-32 | cytoskeleton |
| 64 | Q8C2Q7 | Heterogeneous nuclear ribonucleoprotein H1 | 0.93795 | 3 | 5.7 | 2.30E-06 | nucleotide binding |
| 65 | Q8K019-1 | Bcl-2-associated transcription factor 1 | 0.94132 | 4 | 5.3 | 2.22E-05 | transcription |
| 66 | P62908 | 40S ribosomal protein S3 | 0.94247 | 2 | 9.1 | 1.74E-06 | translation |
| 67 | P99024 | Tubulin beta-5 chain | 0.9446 | 3 | 36.3 | 1.15E-54 | cytoskeleton |
| 68 | P15331-2 | Peripherin | 0.95087 | 3 | 17.2 | 3.41E-40 | cytoskeleton |
| 69 | P63038-1 | 60 kDa heat shock protein, mitochondrial | 0.96089 | 6 | 13.8 | 9.17E-37 | T cell activation; interferon production |
| 70 | P27773 | Protein disulfide-isomerase A3 | 0.96765 | 1 | 7.9 | 1.26E-03 | redox homeostasis; apoptosis |
| 71 | P16858 | Glyceraldehyde-3-phosphate dehydrogenase | 0.96943 | 58 | 23.4 | 5.69E-66 | glycolysis |
| 72 | Q3TED3 | Putative uncharacterized protein; ATP-citrate synthase | 0.97174 | 2 | 4.3 | 4.63E-03 | acetyl-CoA biosynthesis |
| 73 | Q03265 | ATP synthase subunit alpha, mitochondrial | 0.98925 | 2 | 13.6 | 1.81E-22 | proton transport; lipid metabolism |
| 74 | Q9ERD7 | Tubulin beta-3 chain | 0.99071 | 2 | 27.3 | 5.05E-33 | cytoskeleton |
| 75 | P17751 | Triosephosphate isomerase | 0.9967 | 1 | 11.2 | 1.52E-04 | gluconeogenesis; glycolysis |
a. Ratio of N2a58/22L vs. N2a58# cells
b. Number of identified peptides
c. posterior error probability (PEP) estimates the probability of wrong assignment of a spectrum to a peptide sequence