Table 1. Common contaminants in immunoprecipitation from HeLa nuclear extract.
Proteins identified by mass spectrometry in the immunoprecipitate from HeLa nuclear extract by rabbit polyclonal antibodies against a variety unrelated proteins. Some of these (highlighted by bold characters) are also identified in the immunoprecipitate by Flag antibody from nuclear extract of HeLa cells that do not express any tagged proteins. We believe that these are common contaminants that interact non-specifically with antibodies.
| Official Symbol | GeneID | Official Full Name | Official Symbol | GeneID | Official Full Name |
|---|---|---|---|---|---|
| ACTA1 | 58 | actin, alpha 1, skeletal muscle | PRKDC | 5591 | protein kinase, DNA-activated, catalytic polypeptide |
| ACTA2 | 59 | actin, alpha 2, smooth muscle, aorta | PRMT5 | 10419 | protein arginine methyltransferase 5 |
| ACTBL2 | 345651 | actin, beta-like 2 | PRPF31 | 26121 | PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae) |
| ACTBL3 | 440915 | actin, beta-like 3 | RBM10 | 8241 | RNA binding motif protein 10 |
| ACTG1 | 71 | actin, gamma 1 | RBM39 | 9584 | RNA binding motif protein 39 |
| AHNAK | 79026 | AHNAK nucleoprotein | RBMX | 27316 | RNA binding motif protein, X-linked |
| ANXA2 | 302 | annexin A2 | RIF1 | 55183 | RAP1 interacting factor homolog (yeast) |
| BAT2D1 | 23215 | BAT2 domain containing 1 | RPL13 | 6137 | ribosomal protein L13 |
| BCLAF1 | 9774 | BCL2-associated transcription factor 1 | RPL29 | 6159 | ribosomal protein L29 |
| C11orf84 | 144097 | chromosome 11 open reading frame 84 | RPL38 | 6169 | ribosomal protein L38 |
| C1QBP | 708 | complement component 1, q subcomponent binding protein | RPLP2 | 6181 | ribosomal protein, large, P2 |
| CAPZA1 | 829 | capping protein (actin filament) muscle Z-line, alpha 1 | RPS4Y1 | 6192 | ribosomal protein S4, Y-linked 1 |
| CCAR1 | 55749 | cell division cycle and apoptosis regulator 1 | RPS8 | 6202 | ribosomal protein S8 |
| CLK3 | 1198 | CDC-like kinase 3 | SF3B1 | 23451 | splicing factor 3b, subunit 1, 155kDa |
| CLNS1A | 1207 | chloride channel, nucleotide-sensitive, 1A | SF3B2 | 10992 | splicing factor 3b, subunit 2, 145kDa |
| CMBL | 134147 | carboxymethylenebutenolidase homolog (Pseudomonas) | SF3B3 | 23450 | splicing factor 3b, subunit 3, 130kDa |
| CORO1C | 23603 | coronin, actin binding protein, 1C | SF3B4 | 10262 | splicing factor 3b, subunit 4, 49kDa |
| DDX17 | 10521 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 17 | SFPQ | 6421 | splicing factor proline/glutamine-rich (polypyrimidine tract binding protein associated) |
| DDX20 | 11218 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 20 | SFRS1 | 6426 | splicing factor, arginine/serine-rich 1 |
| DDX3X | 1654 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked | SFRS10 | 6434 | splicing factor, arginine/serine-rich 10 |
| DDX5 | 1655 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 | SFRS3 | 6428 | splicing factor, arginine/serine-rich 3 |
| DHX15 | 1665 | DEAH (Asp-Glu-Ala-His) box polypeptide 15 | SFRS4 | 6429 | splicing factor, arginine/serine-rich 4 |
| DHX9 | 1660 | DEAH (Asp-Glu-Ala-His) box polypeptide 9 | SFRS5 | 6430 | splicing factor, arginine/serine-rich 5 |
| DNAJA1 | 3301 | DnaJ (Hsp40) homolog, subfamily A, member 1 | SFRS6 | 6431 | splicing factor, arginine/serine-rich 6 |
| EEF1A2 | 1917 | eukaryotic translation elongation factor 1 alpha 2 | SFRS7 | 6432 | splicing factor, arginine/serine-rich 7, 35kDa |
| EEF1AL3 | 158078 | eukaryotic translation elongation factor 1 alpha-like 3 | SFRS9 | 8683 | splicing factor, arginine/serine-rich 9 |
| EIF4B | 1975 | eukaryotic translation initiation factor 4B | SLTM | 79811 | SAFB-like, transcription modulator |
| FLNA | 2316 | filamin A, alpha (actin binding protein 280) | SNRP70 | 6625 | small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) |
| FMR1 | 2332 | fragile X mental retardation 1 | SNRPB | 6628 | small nuclear ribonucleoprotein polypeptides B and B1 |
| FUS | 2521 | fusion (involved in t(12;16) in malignant liposarcoma) | SNRPD1 | 6632 | small nuclear ribonucleoprotein D1 polypeptide 16kDa |
| FUSIP1 | 10772 | FUS interacting protein (serine/arginine-rich) 1 | SNRPD3 | 6634 | small nuclear ribonucleoprotein D3 polypeptide 18kDa |
| FXR1 | 8087 | fragile X mental retardation, autosomal homolog 1 | SPATS2 | 65244 | spermatogenesis associated, serine-rich 2 |
| FXR2 | 9513 | fragile X mental retardation, autosomal homolog 2 | SPIN1 | 10927 | spindlin 1 |
| GAPDH | 2597 | glyceraldehyde-3-phosphate dehydrogenase | SPTAN1 | 6709 | spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) |
| GEMIN4 | 50628 | gem (nuclear organelle) associated protein 4 | SPTB | 6710 | spectrin, beta, erythrocytic |
| HNRNPH1 | 3187 | heterogeneous nuclear ribonucleoprotein H1 (H) | SPTBN1 | 6711 | spectrin, beta, non-erythrocytic 1 |
| HNRNPK | 3190 | heterogeneous nuclear ribonucleoprotein K | SR140 | 23350 | U2-associated SR140 protein |
| HNRNPM | 4670 | heterogeneous nuclear ribonucleoprotein M | STK38 | 11329 | serine/threonine kinase 38 |
| HNRNPR | 10236 | heterogeneous nuclear ribonucleoprotein R | STK38L | 23012 | serine/threonine kinase 38 like |
| HNRNPU | 3192 | heterogeneous nuclear ribonucleoprotein U | SYNCRIP | 10492 | synaptotagmin binding, cytoplasmic RNA interacting protein |
| HSPA1A | 3303 | heat shock 70kDa protein 1A | TAF15 | 8148 | TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa |
| HSPA1L | 3305 | heat shock 70kDa protein 1-like | THRAP3 | 9967 | thyroid hormone receptor associated protein 3 |
| HSPA2 | 3306 | heat shock 70kDa protein 2 | TOP2A | 7153 | topoisomerase (DNA) II alpha 170kDa |
| HSPA5 | 3309 | heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) | TPM1 | 7168 | tropomyosin 1 (alpha) |
| HSPA6 | 3310 | heat shock 70kDa protein 6 (HSP70B’) | TRA2A | 29896 | transformer-2 alpha |
| HSPA8 | 3312 | heat shock 70kDa protein 8 | TUBA1C | 84790 | tubulin, alpha 1c |
| IGKV2-40 | 28916 | immunoglobulin kappa variable 2–40 | TUBA3C | 7278 | tubulin, alpha 3c |
| KHDRBS1 | 10657 | KH domain containing, RNA binding, signal transduction associated 1 | TUBB | 203068 | tubulin, beta |
| KIF11 | 3832 | kinesin family member 11 | TUBB1 | 81027 | tubulin, beta 1 |
| LMO7 | 4008 | LIM domain 7 | TUBB2C | 10383 | tubulin, beta 2C |
| MATR3 | 9782 | matrin 3 | TUBB4Q | 56604 | tubulin, beta polypeptide 4, member Q |
| MYCBP | 26292 | c-myc binding protein | TUBB6 | 84617 | tubulin, beta 6 |
| MYH10 | 4628 | myosin, heavy chain 10, non-muscle | VIM | 7431 | vimentin |
| MYH11 | 4629 | myosin, heavy chain 11, smooth muscle | WDHD1 | 11169 | WD repeat and HMG-box DNA binding protein 1 |
| MYH9 | 4627 | myosin, heavy chain 9, non-muscle | WDR77 | 79084 | WD repeat domain 77 |
| NONO | 4841 | non-POU domain containing, octamer-binding | YBX1 | 4904 | Y box binding protein 1 |
| PABPC4 | 8761 | poly(A) binding protein, cytoplasmic 4 (inducible form) | YLPM1 | 56252 | YLP motif containing 1 |
| PPP1CC | 5501 | protein phosphatase 1, catalytic subunit, gamma isoform |