Table I. Quantified protein copy number per HeLa cell for immuno-SILAC and PrEST-SILAC. Copy numbers are shown for each replicate, along with the median copy number, relative standard deviation (RSD), and number of peptides used for quantification.
| Gene name | Copy number replicate 1 | Copy number replicate 2 | Copy number replicate 3 | Median copy number | RSD (%) | Number of peptides |
|---|---|---|---|---|---|---|
| Immuno-SILAC | ||||||
| ACOT7 | 1283838 | 998876 | 498230 | 998876 | 42.9 | 2 |
| ANXA1 | 6664952 | 9833375 | 6362332 | 6664952 | 25.2 | 4 |
| ANXA3 | 2219240 | 2298319 | 4650459 | 2298319 | 45.2 | 1 |
| BLVRB | 2148052 | - | 3002937 | 2575495 | 23.5 | 1 |
| CANT1 | - | 70703 | 42667 | 56685 | 35.0 | 1 |
| CAPG | 3078134 | 2579694 | - | 2828914 | 12.5 | 1 |
| CLPP | 1208794 | 1087915 | 777082 | 1087915 | 21.7 | 1 |
| DAP3 | 1498865 | 1016070 | 900236 | 1016070 | 27.9 | 6 |
| DECR1 | - | - | 588225 | 588225 | - | 1 |
| DIMT1 | - | - | 235127 | 235127 | - | 1 |
| ERLIN1 | 529872 | 923508 | 1013719 | 923508 | 31.3 | 2 |
| P4HA1 | 277258 | 307834 | 431686 | 307834 | 24.1 | 1 |
| PDIA5 | 94844 | 166129 | 186790 | 166129 | 32.3 | 3 |
| PRPF4 | 306890 | 316067 | 342904 | 316067 | 5.8 | 1 |
| PTPN1 | 763589 | 1035203 | 686727 | 763589 | 22.1 | 2 |
| SERPINB6 | 885677 | 2539203 | 1477373 | 1477373 | 51.3 | 2 |
| SIL1 | - | 117997 | - | 117997 | - | 1 |
| SLC25A24 | 2317150 | 2099723 | 1239592 | 2099723 | 30.2 | 1 |
| STUB1 | 573646 | 474906 | 490305 | 490305 | 10.4 | 1 |
| UGDH | 193277 | 501192 | 605305 | 501192 | 49.5 | 1 |
| PrEST-SILAC | ||||||
| ACOT7 | 771360 | 1170086 | 955768 | 955768 | 20.7 | 4 |
| ANXA1 | 12516639 | 10077946 | 11725516 | 11725516 | 10.9 | 14 |
| ANXA3 | 1899959 | 2428880 | 4058745 | 2428880 | 40.2 | 12 |
| BLVRB | 779755 | 836484 | 624563 | 779755 | 14.7 | 4 |
| CANT1 | - | 67847 | - | 67847 | - | 2 |
| CAPG | 2238047 | 2535800 | 2762024 | 2535800 | 10.5 | 4 |
| CLPP | 1017569 | 705756 | 639815 | 705756 | 25.6 | 3 |
| DAP3 | 329798 | - | 638890 | 484344 | 45.1 | 2 |
| DECR1 | - | - | - | - | - | - |
| DIMT1 | 337769 | 408358 | 342916 | 342916 | 10.8 | 6 |
| ERLIN1 | 559997 | 963844 | 803794 | 803794 | 26.2 | 5 |
| P4HA1 | 1114521 | 627467 | 733443 | 733443 | 31.0 | 11 |
| PDIA5 | 134089 | 253862 | 152319 | 152319 | 25.5 | 4 |
| PRPF4 | 411509 | 274967 | 566398 | 411509 | 34.9 | 6 |
| PTPN1 | 520007 | 542602 | 597039 | 542602 | 7.2 | 5 |
| SERPINB6 | 576320 | 974111 | 1269089 | 974111 | 37.0 | 9 |
| SIL1 | 96363 | 155829 | 111533 | 111533 | 25.5 | 1 |
| SLC25A24 | 1077749 | 1015007 | 925753 | 1015007 | 7.6 | 4 |
| STUB1 | 719533 | 604201 | 692742 | 692742 | 9.0 | 4 |
| UGDH | 1000743 | 888750 | 746425 | 888750 | 14.5 | 5 |
Number of peptides: the total number of different peptides used for the quantification.