Table 4.
Summary of proteomics data from the reduction and differential Cys-labelling of 2B4 cells with PDI. The modified Cys residues are indicated by residue number (@ followed by residue number in peptide) and whether the modification detected was MPB itself or a hydrolysis derivative (indicated by +H2O). Protein probability scores from iProphet meta-searches are shown and where applicable weighted spectral index counts (WSC) are shown for the reduced and control samples, respectively. The percentage sequence coverage indicates the percentage of the protein sequence observed. Cys denotes the modified Cysteine number in the protein sequence inclusive of the signal peptides.
| IPI accession | gene | protein description | protein identification probability | % sequence coverage | WSC control | WSC PDI reduced | maleimide-modified peptide | modification | Cys |
|---|---|---|---|---|---|---|---|---|---|
| IPI00131881 | Adam10 | ADAM10 | 1 | 6.1 | PDI only | ||||
| IPI00123329 | Adam15 | ADAM15 | 1 | 6.9 | PDI only | ||||
| IPI00762180 | Adam17 | ADAM17 | 1 | 16 | PDI only | ||||
| IPI00113869 | Bsg | CD147, Basigin | 1 | 43.6 | 6 | 38 | TQLTCSLNSSGVDIVGHR | MPB+H2O@5 | 157 |
| IPI00108001 | Cd2 | CD2 | 1 | 15.1 | PDI only | CEAINPVSK | MPB+H2O@1 | 180 | |
| IPI00119703 | Cd244 | CD244, 2B4 | 1 | 35 | PDI only | ||||
| IPI00114509 | Cd3d | CD3 delta | 1 | 13.3 | PDI only | ||||
| IPI00223769 | Cd44 | CD44 | 1 | 11.5 | 2 | 10 | |||
| IPI00124830 | Cd47 | CD47 | 1 | 25.9 | 1 | 15 | TAFNTDQGSACSYEEEK | MPB+H2O@11 | 142 |
| IPI00380293 | Cd96 | CD96 | 1 | 7.1 | PDI only | YECIFTLYPEGIK | MPB+H2O@3 | 118 | |
| IPI00138061 | Cr1l | complement regulatory protein Crry | 1 | 9.7 | PDI only | ||||
| IPI00923031 | EG665 955 | envelope glycoprotein 52 | 1 | 33.5 | 1.50 | 35 | |||
| IPI00420148 | Env | GP160 | 1 | 44.7 | 12.98 | 188.41 | EECCFYADHTGVVR | MPB+H2O@3 | 533 |
| EGGLCAALKEECCFYADHTGVVR | MPB+H2O@13 | 534 | |||||||
| THQALCNTTQK | MPB@6 | 368 | |||||||
| LTLSEVTGQGLCVGAVPK | MPB+H2O@12 | 356 | |||||||
| IPI00108870 | Ephb2 | ephrin type-B receptor 2 | 1 | 40.6 | 1 | 67.73 | CGDNVQYAPR | MPB@1 | 383 |
| DSGGREDLVYNIICK | MPB+H2O@14 | 370 | |||||||
| NILVNSNLVCK | MPB+H2O@10 | 768 | |||||||
| IEQVIGAGEFGEVCSGHLK | MPB+H2O@14 | 644 | |||||||
| IPI00126300 | H2-D1 | H-2 class I histocompatibility antigen, D-K alpha chain | 1 | 24.6 | PDI only | ||||
| IPI00114492 | H2-K1 | H-2 class I histocompatibility antigen, K-B alpha chain | 1 | 35 | PDI only | ||||
| IPI00129526 | Hsp90b1 | endoplasmin | 1 | 60.5 | 28.94 | 215.59 | |||
| IPI00323357 | Hspa8 | heat shock cognate 71 kDa protein | 1 | 47.1 | 2.99 | 45.74 | |||
| IPI00880839 | Hspa9 | stress-70 protein | 1 | 70 | 5 | 277 | GAVVGIDLGTTNSCVAVMEGK | MPB+H2O@14 | 66 |
| AKCELSSSVQTDINLPYLTMDASGPK | MPB+H2O@3 | 317 | |||||||
| MEEFKDQLPADECNK | MPB@13 | 608 | |||||||
| MEEFKDQLPADECNK | MPB+H2O@13 | 608 | |||||||
| DQLPADECNK | MPB@8 | 608 | |||||||
| IPI00321348 | Igsf8 | CD316, immunoglobulin superfamily member 8 | 1 | 6.2 | PDI only | ||||
| IPI00119612 | Il2rg | CD132, cytokine receptor common subunit gamma | 1 | 30.9 | PDI only | CLQYLVQYR | MPB@1 | 183 | |
| IPI00120155 | Il6st | CD130, interleukin-6 receptor subunit beta | 1 | 12.9 | PDI only | ||||
| IPI00266264 | Itgb3 | integrin beta-3 | 1 | 6.7 | PDI only | NACLPMFGYK | MPB+H2O@3 | 209 | |
| IPI00785217 | Ldlr | low-density lipoprotein receptor | 1 | 40 | 7.93 | 85.24 | TTEDELHICR | MPB+H2O@9 | 843 |
| IPI00119809 | Lgals3bp | galectin-3-binding protein | 1 | 32.6 | 3 | 30 | |||
| IPI00761657 | Lgals8 | galectin-8 | 1 | 20.9 | PDI only | ||||
| IPI00114396 | Lgals9 | galectin-9 | 1 | 54 | 7 | 90 | FEEGGYVVCNTK | MPB+H2O@9 | 73 |
| GMPFELCFLVQR | MPB+H2O@7 | 101 | |||||||
| IPI00223987 | Lnpep | leucyl–cystinyl aminopeptidase | 1 | 63.3 | 11 | 361 | SAFPCFDEPAFK | MPB@5 | 305 |
| LPTAIIPLCYELSLHPNLTSMTFR | MPB+H2O@9 | 175 | |||||||
| IPI00121600 | Lrp8 | low-density lipoprotein receptor-related protein 8 | 1 | 17.7 | PDI only | ||||
| IPI00129253 | Ly75 | CD205, CLEC13B | 1 | 6.5 | PDI only | ||||
| IPI00129646 | Ly9 | CD229, LY-9 | 1 | 35.4 | 8 | 40 | DAEIEHIIWNCPPK | MPB+H2O@11 | 82 |
| IPI00108844 | M6pr | CD222, cation-independent mannose-6-phosphate receptor | 1 | 37.4 | PDI only | AVVMISCNR | MPB+H2O@7 | 146 | |
| GGDEYDNHCGK | MPB+H2O@9 | 133 | |||||||
| IPI00125890 | Pdcd1 | CD279, PD-1 | 1 | 24 | 2 | 23 | QAAFCNGLSQPVQDAR | MPB+H2O@5 | 84 |
| QAAFCNGLSQPVQDAR | MPB@5 | 84 | |||||||
| IPI00230108 | Pdia3 | PDI-A3 | 1 | 42.4 | 6 | 36 | |||
| IPI00406901 | Pecam1 | CD31, PECAM-1 | 0.9998 | 5 | PDI only | ||||
| IPI00316976 | Ptprcap | CD45-associated protein | 1 | 20.3 | PDI only | CQAEQTR | MPB@1 | 133 | |
| IPI00406609 | Ptprj | CD148 | 1 | 1.9 | PDI only | ||||
| IPI00177179 | Pvr | CD155, poliovirus receptor | 1 | 6.9 | PDI only | ||||
| IPI00116921 | Scarb1 | CD36L1, SCARB-1 | 1 | 18.3 | PDI only | ESGIQNVSTCR | MPB+H2O@10 | 334 | |
| EHSLFLDIHPVTGIPMNCSVK | MPB+H2O@18 | 385 | |||||||
| CFLFWSGSK | MPB@1 | 470 | |||||||
| IPI00127447 | Scarb2 | CD36L2, SCARB-2 | 1 | 50.4 | PDI only | TSLDWWTTDTCNMINGTDGDSFHPLISK | MPB@11 | 245 | |
| DEVLYLFPSDLCR | MPB@12 | 274 | |||||||
| IPI00464135 | Sema4b | semaphorin-4B | 1 | 7.3 | PDI only | ||||
| IPI00890869 | Sema4c | semaphorin-4C | 1 | 6.5 | PDI only | ||||
| IPI00273801 | Slc39a10 | zinc transporter ZIP10 | 1 | 11.4 | PDI only | ||||
| IPI00469000 | Slc39a6 | zinc transporter ZIP6 | 1 | 7.8 | PDI only | ||||
| IPI00114641 | Slc3a2 | CD98, 4F2 heavy chain | 1 | 82.3 | 38 | 223 | |||
| IPI00331577 | Slc7a5 | 4F2 light chain | 1 | 25 | 0.50 | 19.50 | |||
| IPI00914724 | Tcirg1 | T cell immune regulator 1 | 1 | 5.2 | PDI only | ||||
| IPI00124700 | Tfrc | CD71, transferrin receptor protein | 1 | 68.8 | 30 | 219 | WNIDSSCK | MPB+H2O@7 | 365 |
| IPI00114457 | Tgfb1 | transforming growth factor beta-1 | 1 | 34.6 | PDI only | ||||
| IPI00109727 | Thy1 | CD90, Thy-1 | 1 | 37.7 | PDI only | ||||
| IPI00121341 | Tmx1 | thioredoxin-related transmembrane protein 1 | 1 | 29.8 | 1 | 16 | FIITALPSIYHCK | MPB+H2O@12 | 106 |
| IPI00122738 | Trbv5 | T cell receptor beta chain V region | 1 | 33.9 | PDI only | ||||
| IPI00378224 | Txndc15 | thioredoxin domain-containing protein 15 | 1 | 25.9 | PDI only |