Table 2.
Ubiquitinated proteins identified in nonfunctional pituitary adenomas relative to controls.
| Accession No. | Gene name | Protein name | Modified peptides | Peptide length | Modified positions | Modified probabilities | Modified level (N) | Modified level (T) | Ratio (T/N) | t-test p-value |
|---|---|---|---|---|---|---|---|---|---|---|
| A0A0A6YY96 | IREB2 | Iron-responsive element-binding protein 2 | GFQIAAEK*QK* | 10 | 483;485 | 1; 1 | 3.59E+07 | 1.62E+08 | 4.52 | 4.55E-06 |
| P16104 | H2AFX | Histone H2AX | K*TSATVGPK | 9 | 120 | 1 | 3.50E+07 | 1.43E+09 | 40.96 | 1.39E-05 |
| P48200 | IREB2 | Iron-responsive element-binding protein 2 | GFQIAAEK*QK* | 10 | 483;485 | 1; 1 | 3.46E+07 | 1.63E+08 | 4.71 | 3.31E-05 |
| B2RDW1 | RPS30A | Epididymis luminal protein 112 | TLTGK*TITLEVEPSDTIENVK | 21 | 11 | 1 | 1.70E+08 | 1.26E+09 | 7.40 | 3.64E-05 |
| TLSDYNIQK*ESTLHLVLR | 18 | 63 | 1 | 3.71E+07 | 1.64E+08 | 4.43 | 6.07E-03 | |||
| LIFAGK*QLEDGR | 12 | 48 | 1 | 2.91E+09 | 7.32E+09 | 2.52 | 6.88E-03 | |||
| IQDK*EGIPPDQQR | 13 | 33 | 1 | 2.68E+06 | 3.68E+07 | 13.74 | 9.55E-03 | |||
| TITLEVEPSDTIENVK*AK | 18 | 27 | 0.956 | 1.95E+07 | ||||||
| MQIFVK*TLTGK | 11 | 6 | 0.923 | |||||||
| TITLEVEPSDTIENVKAK* | 18 | 29 | 0.594 | |||||||
| VDENGK*ISR | 9 | 113 | 1 | |||||||
| P62979 | RPS27A | Ubiquitin-40S ribosomal protein S27a | TLTGK*TITLEVEPSDTIENVK | 21 | 11 | 1 | 1.72E+08 | 1.27E+09 | 7.37 | 3.78E-05 |
| TLSDYNIQK*ESTLHLVLR | 18 | 63 | 1 | 3.71E+07 | 1.96E+08 | 5.27 | 6.89E-04 | |||
| P68871 | HBB | Hemoglobin subunit beta | FFESFGDLSTPDAVMGNPK*VK* | 21 | 60;62 | 0.5; 0.5 | 1.69E+06 | 2.01E+07 | 11.87 | 3.71E-04 |
| GTFATLSELHCDK*LHVDPENFR | 22 | 96 | 1 | 1.89E+07 | 9.13E+07 | 4.83 | 1.23E-02 | |||
| K*VLGAFSDGLAHLDNLK | 17 | 67 | 1 | 2.07E+06 | 1.02E+07 | 4.92 | 1.22E-01 | |||
| L7N2F9 | Uncharacterized protein | VNVDK*VLER | 9 | 52 | 1 | 1.04E+07 | 1.23E+08 | 11.86 | 8.99E-04 | |
| ADALQAGASQFETSAAK*LK | 19 | 83 | 0.876 | 2.01E+07 | ||||||
| ADALQAGASQFETSAAKLK* | 19 | 85 | 0.539 | 4.61E+07 | ||||||
| DQK*LSELDDR | 10 | 59 | 1 | 6.10E+06 | 5.24E+07 | 8.60 | 2.47E-03 | |||
| D9YZU5 | HBB | Beta-globin | FFESFGDLSTPDAVMGNPK*VK* | 21 | 60;62 | 0.5; 0.5 | 2.48E+06 | 2.02E+07 | 8.14 | 1.14E-03 |
| K*VLGAFSDGLAHLDNLK | 17 | 67 | 1 | 1.79E+06 | 1.02E+07 | 5.69 | 4.65E-02 | |||
| P62979 | RPS27A | Ubiquitin-40S ribosomal protein S27a | IQDK*EGIPPDQQR | 13 | 33 | 1 | 3.34E+06 | 5.10E+07 | 15.27 | 1.16E-03 |
| LIFAGK*QLEDGR | 12 | 48 | 1 | 2.90E+09 | 7.33E+09 | 2.53 | 6.90E-03 | |||
| F5H5D3 | TUBA1C | Tubulin alpha-1C chain1 | VGINYQPPTVVPGGDLAK*VQR | 21 | 370 | 1 | 2.27E+07 | 3.78E+07 | 1.67 | 1.38E-03 |
| DVNAAIATIK*TK* | 12 | 336;338 | 0.679;0.57 | 2.98E+06 | ||||||
| Q9HCC9 | ZFYVE28 | Lateral signaling target protein 2 | DFCVK*FPEEIR | 11 | 87 | 1 | 7.36E+06 | 2.31E+07 | 3.14 | 1.50E-03 |
| A0A024R017 | HIST1H2AC | Histone H2A | NDEELNK*LLGR | 11 | 96 | 1 | 3.45E+06 | |||
| VTIAQGGVLPNIQAVLLPK*K* | 20 | 119;120 | 0.5; 0.5 | 6.31E+07 | 1.13E+08 | 1.80 | 1.52E-03 | |||
| P69905 | HBA1 | Hemoglobin subunit alpha | AAWGK*VGAHAGEYGAEALER | 20 | 17 | 1 | 7.09E+06 | |||
| TYFPHFDLSHGSAQVK* | 16 | 57 | 1 | 1.94E+06 | 2.06E+08 | 106.34 | 5.10E-03 | |||
| P08670 | VIM | Vimentin | K*LLEGEESR | 9 | 402 | 1 | 1.70E+06 | 5.54E+06 | 3.26 | 5.62E-03 |
| EK*LQEEMLQR | 10 | 188 | 1 | 1.40E+07 | 2.02E+07 | 1.44 | 2.44E-01 | |||
| QVDQLTNDK*AR | 11 | 168 | 1 | 1.99E+06 | 2.97E+06 | 1.49 | 2.74E-01 | |||
| K*LLEGEESR | 9 | 393 | 1 | 5.54E+06 | ||||||
| C8C504 | HBB | Beta-globin | GTFATLSELHCDK*LHVDPENFR | 22 | 96 | 1 | 2.04E+07 | 8.43E+07 | 4.14 | 5.79E-03 |
| Q96T46 | HBA2 | Hemoglobin alpha 2 | TYFPHFDLSHGSAQVK* | 16 | 33 | 1 | 1.94E+06 | 2.03E+08 | 104.44 | 6.08E-03 |
| Q9H582 | ZNF644 | Zinc finger protein 644 | RSFLQQDVNK* | 10 | 11 | 1 | 9.99E+06 | 4.56E+07 | 4.56 | 6.13E-03 |
| Q9H3H9 | TCEAL2 | Transcription elongation factor A protein-like 2 | QYK*EAIHDMNFSNEDMIR | 18 | 154 | 1 | 3.49E+06 | 1.77E+07 | 5.07 | 6.49E-03 |
| E9PL57 | NEDD8-MDP1 | Protein NEDD8-MDP1 | TLTGK*EIEIDIEPTDKVER | 19 | 11 | 1 | 3.50E+06 | 1.20E+07 | 3.43 | 6.76E-03 |
| Q59EJ3 | Heat shock 70kDa protein 1A variant | MVQEAEK*YK | 9 | 592 | 0.891 | 9.34E+05 | 9.36E+06 | 10.02 | 1.11E-02 | |
| D6R956 | UCHL1 | Ubiquitin carboxyl-terminal hydrolase | CFEK*NEAIQAAHDAVAQEGQCR | 22 | 135 | 1 | 5.86E+06 | |||
| MQLK*PMEINPEMLNK | 15 | 4 | 1 | 2.77E+06 | 8.80E+06 | 3.17 | 1.61E-02 | |||
| P14735 | IDE | Insulin-degrading enzyme | EVNAVDSEHEK*NVMNDAWR | 19 | 192 | 1 | 2.05E+06 | 7.47E+06 | 3.65 | 1.94E-02 |
| Q6ZUF2 | cDNA FLJ43763 fis, clone TESTI2048603 | FFSPPNMSVTHK*EAHERK | 18 | 19 | 0.977 | 1.39E+08 | 2.50E+08 | 1.80 | 5.15E-02 | |
| P61088 | UBE2N | Ubiquitin-conjugating enzyme E2 N | ICLDILKDK* | 9 | 94 | 0.962 | 1.74E+07 | 2.27E+07 | 1.30 | 7.06E-02 |
| D1MGQ2 | HBA2 | Alpha-2 globin chain | AAWGK*VGAHAGEYGAEALER | 20 | 17 | 1 | 7.09E+06 | |||
| TYFPHFDLSHGSAQVK* | 16 | 57 | 1 | 2.22E+06 | 1.26E+08 | 56.71 | 1.21E-01 | |||
| P02042 | HBD | Hemoglobin subunit delta | GTFSQLSELHCDK*LHVDPENFR | 22 | 96 | 1 | 1.57E+07 | 2.01E+07 | 1.28 | 1.43E-01 |
| D3DQ48 | TMEM59 | Transmembrane protein 59, isoform CRA_e | TEDHEEAGPLPTK*VNLAHSEI | 21 | 316 | 1 | 3.64E+06 | 1.31E+07 | 3.61 | 1.63E-01 |
| K7EPI4 | GFAP | Glial fibrillary acidic protein | GGK*STK*DGENHK* | 12 | 10;13;19 | 1;1;1 | 2.32E+06 | 2.06E+07 | 8.87 | 2.34E-01 |
| A0A024R5H9 | PLEKHB1 | Pleckstrin homology domain containing, family B (Evectins) member 1, isoform CRA_a | LHLCAETK*DDALAWK | 15 | 113 | 0.999 | 6.23E+06 | 0.00E+00 | 0.00 | 1.39E-01 |
| B7WPA5 | PLEKHB2 | Pleckstrin homology domain-containing family B member 2 | QNIEDK*VHMPMDCINIR | 17 | 46 | 1 | 1.30E+07 | 7.08E+06 | 0.54 | 3.41E-01 |
| Q3BBV0 | NBPF1 | Neuroblastoma breakpoint family member 1 | VGWALDMDEIEK* | 12 | 950 | 1 | 8.76E+06 | 5.34E+06 | 0.61 | 4.18E-01 |
| A4UGR9 | XIRP2 | Xin actin-binding repeat-containing protein 2 | WLFETQPMESLYEK* | 14 | 934 | 1 | 1.82E+07 | 2.61E+07 | 1.44 | 5.39E-01 |
| B7ZMF0 | CEP192 | CEP192 protein | IVSPK*NSDLK | 10 | 556 | 0.908 | 1.14E+07 | 1.96E+07 | 1.71 | 6.03E-01 |
| A0N071 | HBD | Delta globin | GTFSQLSELHCDK*LHVDPENFR | 22 | 96 | 1 | 2.08E+07 | 2.20E+07 | 1.05 | 8.73E-01 |
| A0A024QZP6 | H2AFY2 | Core histone macro-H2A | IHPELLAK*K* | 9 | 116;117 | 0.705; 0.585 | ||||
| A0A024R466 | ITM2C | Integral membrane protein 2C, isoform CRA_a | ISFQPAVAGIK*GDK | 14 | 14 | 0.855 | 1.33E+07 | |||
| A0A024R6B3 | TMEM63C | Transmembrane protein 63C, isoform CRA_a | DIEDPELIIK*HFHEAYPGSVVTR | 23 | 239 | 1 | 3.89E+06 | |||
| A0A024R7G8 | RAD23A | RAD23 homolog A (S. cerevisiae), isoform CRA_a | LIYAGK*ILSDDVPIR | 15 | 53 | 1 | 1.24E+07 | |||
| A0A024RDB0 | UBE1L2 | Ubiquitin-activating enzyme E1-like 2, isoform CRA_a | IDAHLNK*VCPTTETIYNDEFYTK | 23 | 544 | 1 | 4.66E+06 | |||
| A0A087WZE4 | SPTA1 | Spectrin alpha chain, erythrocytic 1 | VNILTDK*SYEDPTNIQGK | 18 | 79 | 1 | 6.34E+06 | |||
| A0A0K0KMI2 | POU5F1 | POU class 5 homeobox 1 transcript variant OCT4B4 | K*LGGQLGR | 8 | 1 | 1 | 7.82E+06 | |||
| A0A0U1RRH7 | Histone H2A | NDEELNK*LLGK | 11 | 96 | 0.996 | |||||
| A0A140VJZ1 | Testicular tissue protein Li 218 | LEK*IFQNAPTDPTQDFSTQVAK | 22 | 360 | 1 | |||||
| A0AVT1 | UBA6 | Ubiquitin-like modifier-activating enzyme 6 | IDAHLNK*VCPTTETIYNDEFYTK | 23 | 544 | 1 | 4.54E+06 | |||
| A4D2P6 | GRID2IP | Delphilin | GK*MGTVSK*SR | 10 | 570;576 | 1; 1 | ||||
| A6NNT2 | C16orf96 | Uncharacterized protein C16orf96 | SALAGK*ASR | 9 | 819 | 1 | ||||
| A6ZKI3 | FAM127A | Protein FAM127A | K*ESPLLNDYR | 10 | 86 | 1 | 1.64E+07 | |||
| A8K6M4 | cDNA FLJ75725, highly similar to Homo sapiens vesicle transport through interaction with t-SNAREs homolog 1B (yeast) (VTI1B), mRNA | ASSAASSEHFEK*LHEIFR | 18 | 13 | 1 | 9.09E+06 | ||||
| B1A4G6 | GH1 | Growth hormone 1 isoform 1 | EETQQK*SNLELLR | 13 | 96 | 1 | 5.87E+06 | |||
| B4DPP6 | cDNA FLJ54371, highly similar to Serum albumin | K*LVAASQAALGL | 12 | 607 | 1 | |||||
| K*QTALVELVK | 10 | 558 | 1 | |||||||
| B4DR52 | Histone H2B | HAVSEGTK*AVTK | 12 | 117 | 1 | 4.70E+07 | ||||
| B4E1J8 | cDNA FLJ56285, highly similar to ADP-ribosylation factor-like protein 8B | DLPNALDEK*QLIEK | 14 | 193 | 1 | |||||
| B9EGU6 | RC3H1 | Ring finger and CCCH-type zinc finger domains 1 | KEIMAQLEERK* | 11 | 769 | 0.999 | 7.15E+06 | |||
| C9JLQ8 | AEBP1 | Adipocyte enhancer-binding protein 1 | MPPEKTK*DK* | 9 | 7;9 | 0.985;1 | ||||
| E7EX29 | YWHAZ | 14-3-3 protein zeta/delta | MDKNELVQKAK* | 11 | 11 | 0.537 | 2.35E+06 | |||
| K7EPF9 | APOC1 | Apolipoprotein C-I | EFGNTLEDK*AR | 11 | 47 | 1 | 7.55E+06 | |||
| M1VKI3 | SDC4-ROS1_S4;R32 | Tyrosine-protein kinase receptor | AGSGSQVPTEPKK* | 13 | 105 | 0.554 | 1.53E+07 | |||
| P01241 | GH1 | Somatotropin | EETQQK*SNLELLR | 13 | 96 | 1 | 4.23E+06 | |||
| P02671 | FGA | Fibrinogen alpha chain | EK*VTSGSTTTTR | 12 | 448 | 1 | 4.06E+06 | |||
| TVIGPDGHK*EVTK | 13 | 476 | 0.86 | |||||||
| P02768 | ALB | Serum albumin | K*LVAASQAALGL | 12 | 598 | 1 | ||||
| K*QTALVELVK | 10 | 549 | 1 | |||||||
| P04908 | HIST1H2AB | Histone H2A type 1-B/E | NDEELNK*LLGR | 11 | 96 | 1 | 3.45E+06 | |||
| P09960 | LTA4H | Leukotriene A-4 hydrolase | FSYK*SITTDDWK | 12 | 418 | 1 | 4.10E+06 | |||
| P19021 | PAM | Peptidyl-glycine alpha-amidating monooxygenase | AFGDSEHK*LETSSGR | 15 | 901 | 1 | ||||
| P23396 | RPS3 | 40S ribosomal protein S3 | KPLPDHVSIVEPK*DEILPTTPISEQK | 26 | 214 | 1 | 2.84E+07 | |||
| P31946 | YWHAB | 14-3-3 protein beta/alpha | SELVQKAK* | 8 | 13 | 0.672 | ||||
| P35212 | GJA4 | Gap junction alpha-4 protein | ALPAK*DPQVER | 11 | 119 | 1 | 2.26E+06 | |||
| P35251 | RFC1 | Replication factor C | KLVSETVK* | 8 | 22 | 1 | ||||
| P45974 | USP5 | Ubiquitin carboxyl-terminal hydrolase 5 | LEK*IFQNAPTDPTQDFSTQVAK | 22 | 360 | 1 | 9.83E+06 | |||
| P54725 | RAD23A | UV excision repair protein RAD23 homolog A | LIYAGK*ILSDDVPIR | 15 | 53 | 1 | 1.39E+07 | |||
| LIYAGK*ILNDDTALK | 15 | 51 | 0.993 | |||||||
| P54727 | RAD23B | UV excision repair protein RAD23 homolog B | LIYAGK*ILNDDTALK | 15 | 51 | 0.993 | ||||
| P55072 | VCP | Transitional endoplasmic reticulum ATPase | ASGADSK*GDDLSTAILK | 17 | 8 | 1 | 7.91E+06 | |||
| P60709 | ACTB | Actin, cytoplasmic 1 | DSYVGDEAQSK*R | 12 | 61 | 1 | 2.05E+06 | |||
| P60866 | RPS20 | 40S ribosomal protein S20 | DTGK*TPVEPEVAIHR | 15 | 8 | 1 | 9.48E+06 | |||
| P61981 | YWHAG | 14-3-3 protein gamma | EQLVQK*AR | 8 | 10 | 1 | ||||
| P62979 | RPS27A | Ubiquitin-40S ribosomal protein S27a | TITLEVEPSDTIENVK*AK | 18 | 27 | 0.956 | 1.72E+07 | |||
| MQIFVK*TLTGK | 11 | 6 | 0.923 | |||||||
| TITLEVEPSDTIENVKAK* | 18 | 29 | 0.594 | |||||||
| VDENGK*ISR | 9 | 113 | 1 | |||||||
| P83916 | CBX1 | Chromobox protein homolog 1 | KEESEK*PR | 8 | 109 | 1 | ||||
| Q0VDD8 | DNAH14 | Dynein heavy chain 14, axonemal | SLLSNVSQWDTFK* | 13 | 2919 | 1 | ||||
| Q13753 | LAMC2 | Laminin subunit gamma-2 | ITSTFHQDVDGWK* | 13 | 219 | 1 | 1.99E+07 | |||
| Q15149 | PLEC | Plectin | SELELTLGK*LEQVR | 14 | 1210 | 1 | 2.72E+06 | |||
| Q4LE39 | ARID4B | AT-rich interactive domain-containing protein 4B | K*ENIK*PSLGSK* | 11 | 462;466;472 | 1;1;1 | 2.05E+07 | |||
| Q59EQ3 | Nudix-type motif 6 isoform a variant | LDAAAFQK*GLQGK* | 13 | 84;89 | 1;1 | 5.22E+06 | ||||
| Q5I0G2 | PRL | Growth hormone A1 | AVEIEEQTK*R | 10 | 153 | 1 | 5.21E+06 | |||
| Q5JWF2 | GNAS | Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas | IDVIK*QADYVPSDQDLLR | 18 | 829 | 1 | ||||
| Q5VXU3 | CHIC1 | Cysteine-rich hydrophobic domain-containing protein 1 | SIQK*LIEWENNR | 12 | 176 | 1 | ||||
| Q92625 | ANKS1A | Ankyrin repeat and SAM domain-containing protein 1A | GK*EQELLEAAR | 11 | 3 | 1 | 8.07E+06 | |||
| Q93045 | STMN2 | Stathmin-2 | DLSLEEIQKK* | 10 | 87 | 0.569 | 2.05E+06 | |||
| DLSLEEIQK*K | 10 | 86 | 0.5 | |||||||
| Q93100 | PHKB | Phosphorylase b kinase regulatory subunit beta | AYLQLGINEK* | 10 | 546 | 1 | 2.91E+07 | |||
| Q96AP7 | ESAM | Endothelial cell-selective adhesion molecule | ALEEPANDIK*EDAIAPR | 17 | 286 | 1 | ||||
| Q96EI5 | TCEAL4 | Transcription elongation factor A protein-like 4 | EYK*EAIHDMNFSNEDMIR | 18 | 142 | 1 | 8.59E+06 | |||
| Q96N64 | PWWP2A | PWWP domain-containing protein 2A | TGLEK*MRSGK* | 10 | 496;501 | 1; 1 | 1.06E+07 | |||
| Q9BT67 | NDFIP1 | NEDD4 family-interacting protein 1 | TK*AEATIPLVPGR | 13 | 83 | 1 | ||||
| Q9BUL8 | PDCD10 | Programmed cell death protein 10 | QILSK*IPDEINDR | 13 | 116 | 1 | 2.54E+07 | |||
| Q9BWQ8 | FAIM2 | Protein lifeguard 2 | APGTEGQQQVHGEK*K | 15 | 25 | 0.822 | 2.50E+06 | |||
| Q9H3Z4 | DNAJC5 | DnaJ homolog subfamily C member 5 | FK*EINNAHAILTDATK | 16 | 58 | 1 | 4.81E+06 | |||
| Q9H598 | SLC32A1 | Vesicular inhibitory amino acid transporter | DQVGGGGEFGGHDK*PK | 16 | 113 | 0.832 | 9.03E+06 | |||
| Q9NQX7 | ITM2C | Integral membrane protein 2C | ISFQPAVAGIK*GDK | 14 | 14 | 0.855 | 1.33E+07 | |||
| Q9NV96 | TMEM30A | Cell cycle control protein 50A | DEVDGGPPCAPGGTAK*TR | 18 | 24 | 1 | 3.72E+06 | |||
| Q9NX12 | cDNA FLJ20496 fis, clone KAT08729 | SGEEALIIPPDAVAVDCK*DPDDVVPVGQR | 29 | 39 | 1 | 6.69E+06 | ||||
| VTFNSALAQK*EAK | 13 | 13 | 0.733 | |||||||
| Q9P0M6 | H2AFY2 | Core histone macro-H2A.2 | IHPELLAK*K* | 9 | 116;117 | 0.705; 0.585 | ||||
| Q9P1W3 | TMEM63C | Calcium permeable stress-gated cation channel 1 | DIEDPELIIK*HFHEAYPGSVVTR | 23 | 239 | 1 | 5.57E+06 | |||
| Q9UBB4 | ATXN10 | Ataxin-10 | ITSDEPLTK*DDIPVFLR | 17 | 262 | 1 | 1.14E+07 | |||
| Q9UEU0 | VTI1B | Vesicle transport through interaction with t-SNAREs homolog 1B | ASSAASSEHFEK*LHEIFR | 18 | 13 | 1 | 9.35E+06 | |||
| Q9UF11 | PLEKHB1 | Pleckstrin homology domain-containing family B member 1 | LHLCAETK*DDALAWK | 15 | 113 | 0.999 | 6.23E+06 | |||
| Q9UKJ5 | CHIC2 | Cysteine-rich hydrophobic domain-containing protein 2 | SIEK*LLEWENNR | 12 | 117 | 1 | 4.92E+06 | |||
| Q9UQB3 | CTNND2 | Catenin delta-2 | SPSIDSIQK*DPR | 12 | 540 | 1 | 3.06E+06 | |||
| Q9Y287 | ITM2B | Integral membrane protein 2B | SGEEALIIPPDAVAVDCK*DPDDVVPVGQR | 29 | 39 | 1 | 6.69E+06 | |||
| VTFNSALAQK*EAK | 13 | 13 | 0.733 | |||||||
| S4R435 | RPS10-NUDT3 | Protein RPS10-NUDT3 | SAVPPGADKK* | 10 | 139 | 0.574 | 5.99E+07 | |||
| SAVPPGADK*K | 10 | 138 | 0.846 | 6.91E+07 | ||||||
| U6FSN9 | Mprip-Ntrk1 fusion gene | Tyrosine-protein kinase receptor | GWLTK*QYEDGQWK | 13 | 396 | 1 |
Ratio (T/N), Ration of tumors (B) to controls(A). K*, Ubiquitinated lysine residue.