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Table II.

Sepharose bead proteome: other proteins of additional classes

Gene Name
Description
NP
 % Exp.
CP
 % Exp.
WC
 % Exp.
ADAR Double-stranded RNA-specific adenosine deaminase 54.5 0.0 11.1 
AHNAK AHNAK nucleoprotein isoform 1 54.5 28.6 55.6 
ALB Albumin 100.0 45.5 57.1 
ANXA1, 2 Annexin 1, A2 100.0 100.0 77.8 
ASCC3L1 Activating signal co-integrator 1 complex subunit 3-like 1 63.6 0.0 22.2 
ASS1 Argininosuccinate synthase 0.0 57.1 55.6 
ATAD ATPase family, AAA domain containing protein 27.3 0.0 22.2 
ATP5A, 5B ATP synthase, H+ transporting, mitochondrial F1 complex 81.8 14.3 77.8 
BAG2 BCL2-associated athanogene 2 27.3 0.0 11.1 
BOLA2B BolA-like protein 2B 22.2 36.4 28.6 
CAD Carbamoylphosphate synthetase 2 0.0 85.7 33.3 
CAND1 Cullin-associated NEDD8-dissociated protein 1 9.1 28.6 33.3 
CAPRIN1 Cytoplasmic activation- and proliferation-associated protein 1 33.3 45.5 
CCT Chaperonin containing TCP1 45.5 28.6 55.6 
CD180 Elongation factor 1-alpha 45.5 57.1 33.3 
CFL1 Cofilin 63.6 85.7 66.7 
CHD3, D4 Chromodomain-helicase-DNA-binding protein 3, 4 18.2 0.0 11.1 
CLEC2D C-type lectin domain family 2, member D 36.4 0.0 0.0 
CLTC Cathrin heavy chain 1 36.4 85.7 77.8 
COPA, B1 Coatomer protein complex, subunits A, B1 18.2 28.6 44.4 
CORO1C Coronin, actin binding protein 1C 66.7 27.3 14.3 
CPS1 Carbamoyl-phosphate synthetase 1 54.5 71.4 44.4 
CRKL Crk-like protein 22.2 9.1 28.6 
CSDA Cold shock domain-containing protein A 55.6 36.4 71.4 
CSRP2 Cysteine and glycine-rich protein 2 54.5 28.6 11.1 
DBN1 Drebrin 1 (developmentally regulated brain protein) 66.7 36.4 28.6 
DHRS2 Dehydrogenase/reductase (SDR family) member 2 36.4 14.3 22.2 
DUT dUTP pyrophosphatase 22.2 18.2 14.3 
DYNLL1 Dynein light chain 1 27.3 28.6 11.1 
EDARRAD EDAR-associated death domain 9.1 0.0 66.7 
ELAVL1 ELAV-like 1 63.6 0.0 22.2 
EMD Emerin 36.4 28.6 0.0 
ENO Enolase 1 9.1 14.3 77.8 
EWSR1 Ewing sarcoma breakpoint region 1 27.3 14.3 33.3 
FARSA,B,FASN Phenylalanyl-tRNA synthetase; Fatty acid synthase 36.4 85.7 88.9 
FBL Fibrillarin 63.6 14.3 22.2 
FKSG30 FKSG30 36.4 57.1 66.7 
FUS Fus-like protein 36.4 14.3 33.3 
G3BP1,2 GTPase activating protein (SH3 domain) binding protein 1, 2 44.4 18.2 14.3 
G6PD Glucose-6-phosphate 1-dehydrogenase 9.1 28.6 22.2 
GAPDH Glyceraldehyde-3-phosphate dehydrogenase 18.2 42.9 55.6 
GFAP Glial fibrillary acidic protein 36.4 42.9 55.6 
GNAS Guanine nucleotide-binding protein G 22.2 9.1 14.3 
GNB2L1 Guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1 36.4 28.6 44.4 
GNL2,3 Guanine nucleotide-binding protein-like 2 (nucleolar) 100 
GSR Glutathione reductase 36.4 42.9 33.3 
GSTM3 Glutathione S-transferase M3 18.2 28.6 22.2 
ILF 2, 3 Interleukin enhancer binding factor 2, 3 54.5 42.9 55.6 
KHDRBS1,2,3 KH domain containing, RNA binding, signal transduction associated 45.5 0.0 11.1 
KHSRP Far upstream element-binding protein 2 36.4 0.0 11.1 
KIF2,4 Kinesin family member 2, 4 44.4 36.4 14.3 
LDHA Lactate dehydrogenase A 9.1 42.9 55.6 
LGALS1,3 Beta-galactoside–binding lectin 72.7 57.1 55.6 
LIMA1 LIM domain and actin-binding protein 1 44.4 9.1 14.3 
LMNA, B Lamin A/C, B 90.9 0.0 33.3 
MATR3 Matrin 3 63.6 0.0 44.4 
MCM3,5 Minichromosome maintenance complex component 3, 5 54.5 14.3 44.4 
MIF Macrophage migration inhibitory factor 9.1 28.6 22.2 
MSH2 MutS protein homologue 2 77.8 14.3 
MTCH2 Mitochondrial carrier homologue 2 36.4 0.0 11.1 
NACA Nascent polypeptide-associated complex subunit alpha 11.1 18.2 14.3 
NCL Nucleolin 72.7 42.9 22.2 
NES Nestin 55.6 9.1 14.3 
NME1, 2 Non-metastatic cells protein 1, 2 18.2 28.6 11.1 
NONO Non-POU domain containing, octamer-binding 36.4 0.0 11.1 
NPM1 Nucleophosmin 1 81.8 0.0 44.4 
NUDT16L1 Nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1 77.8 14.3 
NUMA1 Nuclear mitotic apparatus protein 1 66.7 18.2 42.9 
NUP155 Nucleoporin 155 kD 54.5 0.0 11.1 
PABPC1,3,4 Poly(A) binding protein, cytoplasmic 1, 3, 4 18.2 57.1 33.3 
PALLD Palladin, cytoskeletal associated protein 45.5 0.0 11.1 
PARK7 DJ-1 protein 36.4 28.6 44.4 
PARP1 Poly (ADP-ribose) polymerase family, member 1 27.3 0.0 11.1 
PCBP1, 2 Poly(rC)-binding protein 1, 2 63.6 85.7 55.6 
PCMT Protein-l-isoaspartate(d-aspartate) O-methyltransferase 18.2 57.1 33.3 
PDIA6 Protein disulfide-isomerase A6 63.6 14.3 77.8 
PDLIM2,4 PDZ and LIM domain protein 2 55.6 
PFDN2 Prefoldin subunit 2 9.1 14.3 11.1 
PFN2 Profilin 2 36.4 28.6 33.3 
PHB, PHB2 Prohibitin, prohibitin 2 63.6 42.9 77.8 
PHF5A PHD finger protein 5A 45.5 0.0 11.1 
PHGDH Phosphoglycerate dehydrogenase 18.2 71.4 44.4 
PKM2 Pyruvate kinase, muscle 54.5 71.4 66.7 
POTE2 Protein expressed in prostate, ovary, testis, and placenta 2 54.5 42.9 66.7 
PPIA Peptidylprolyl isomerase A (cyclophilin A) 66.7 27.3 71.4 
PRDX1,2,3,4 Peroxiredoxin 1, 2, 3, 4 90.9 71.4 100.0 
PRKDC Protein kinase, DNA-activated 81.8 14.3 44.4 
PTBP1,2 Polypyrimidine tract-binding protein 1, 2 63.6 14.3 11.1 
RALY RNA-binding protein (autoantigenic, hnRNP-associated with lethal, yellow) 100 27.3 28.6 
RCC2 Regulator of chromosome condensation 2 63.6 0.0 11.1 
S100A6,9,10,14 S100 calcium binding protein A 100 36.4 42.9 
SAP18 Sin3-associated polypeptide, 18 kD 44.4 14.3 
SEC61B Protein transport protein Sec61 beta subunit 45.5 0.0 11.1 
SERBP1 SERPINE1 mRNA binding protein 1 45.5 0.0 22.2 
SERPINH1,A11 Serine (or cysteine) proteinase inhibitor 72.7 28.6 66.7 
SF3B Splicing factor 3B 54.5 0.0 22.2 
SLC25A ADP/ATP translocase 2 (solute carrier family 25) 100.0 71.4 100.0 
THOC4 THO complex subunit 4 44.4 9.1 
TKT Transketolase 36.4 42.9 33.3 
TMPO Thymopoietin 22.2 28.6 
TOMM22 Translocase of outer membrane 22-kD subunit homologue 22.2 28.6 
TRAP1 Tumor necrosis factor type 1 receptor-associated protein (heat shock protein 75) 44.4 27.3 42.9 
TRIM21 52-kD Ro protein 18.2 28.6 33.3 
TRIM25 Tripartite motif-containing protein 25 (Zinc finger protein 147) 18.2 0.0 0.0 
TTBK2 Tau-tubulin kinase 18.2 14.3 44.4 
TUFM Tu translation elongation factor, mitochondrial 63.6 14.3 55.6 
TXN Thioredoxin 27.3 57.1 55.6 
U2AF1 U2 small nuclear RNA auxillary factor 1 27.3 0.0 11.1 
UBA52 Ubiquitin and ribosomal protein L40 precursor 36.4 57.1 55.6 
UBE2D2,3 Ubiquitin-conjugating enzyme E2D 2, E2D 3 18.2 14.3 0.0 
UQCRC1 Ubiquinol-cytochrome c reductase core protein I 63.6 0.0 22.2 
VAPA/B VAMP (vesicle-associated membrane protein)-associated protein A, B 44.4 27.3 28.6 
VCP Valosin-containing protein 44.4 18.2 42.9 
VDAC2,3 Voltage-dependent anion channel 2, 3 63.6 0.0 22.2 
XPO1 Exportin 1 9.1 0.0 22.2 
XRCC5, 6 ATP-dependent DNA helicase II 18.2 14.3 0.0 
YBX1 Y box binding protein 1 36.4 28.6 33.3 
YWHAZ,YWHAB Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein 27.3 28.6 44.4 
Gene Name
Description
NP
 % Exp.
CP
 % Exp.
WC
 % Exp.
ADAR Double-stranded RNA-specific adenosine deaminase 54.5 0.0 11.1 
AHNAK AHNAK nucleoprotein isoform 1 54.5 28.6 55.6 
ALB Albumin 100.0 45.5 57.1 
ANXA1, 2 Annexin 1, A2 100.0 100.0 77.8 
ASCC3L1 Activating signal co-integrator 1 complex subunit 3-like 1 63.6 0.0 22.2 
ASS1 Argininosuccinate synthase 0.0 57.1 55.6 
ATAD ATPase family, AAA domain containing protein 27.3 0.0 22.2 
ATP5A, 5B ATP synthase, H+ transporting, mitochondrial F1 complex 81.8 14.3 77.8 
BAG2 BCL2-associated athanogene 2 27.3 0.0 11.1 
BOLA2B BolA-like protein 2B 22.2 36.4 28.6 
CAD Carbamoylphosphate synthetase 2 0.0 85.7 33.3 
CAND1 Cullin-associated NEDD8-dissociated protein 1 9.1 28.6 33.3 
CAPRIN1 Cytoplasmic activation- and proliferation-associated protein 1 33.3 45.5 
CCT Chaperonin containing TCP1 45.5 28.6 55.6 
CD180 Elongation factor 1-alpha 45.5 57.1 33.3 
CFL1 Cofilin 63.6 85.7 66.7 
CHD3, D4 Chromodomain-helicase-DNA-binding protein 3, 4 18.2 0.0 11.1 
CLEC2D C-type lectin domain family 2, member D 36.4 0.0 0.0 
CLTC Cathrin heavy chain 1 36.4 85.7 77.8 
COPA, B1 Coatomer protein complex, subunits A, B1 18.2 28.6 44.4 
CORO1C Coronin, actin binding protein 1C 66.7 27.3 14.3 
CPS1 Carbamoyl-phosphate synthetase 1 54.5 71.4 44.4 
CRKL Crk-like protein 22.2 9.1 28.6 
CSDA Cold shock domain-containing protein A 55.6 36.4 71.4 
CSRP2 Cysteine and glycine-rich protein 2 54.5 28.6 11.1 
DBN1 Drebrin 1 (developmentally regulated brain protein) 66.7 36.4 28.6 
DHRS2 Dehydrogenase/reductase (SDR family) member 2 36.4 14.3 22.2 
DUT dUTP pyrophosphatase 22.2 18.2 14.3 
DYNLL1 Dynein light chain 1 27.3 28.6 11.1 
EDARRAD EDAR-associated death domain 9.1 0.0 66.7 
ELAVL1 ELAV-like 1 63.6 0.0 22.2 
EMD Emerin 36.4 28.6 0.0 
ENO Enolase 1 9.1 14.3 77.8 
EWSR1 Ewing sarcoma breakpoint region 1 27.3 14.3 33.3 
FARSA,B,FASN Phenylalanyl-tRNA synthetase; Fatty acid synthase 36.4 85.7 88.9 
FBL Fibrillarin 63.6 14.3 22.2 
FKSG30 FKSG30 36.4 57.1 66.7 
FUS Fus-like protein 36.4 14.3 33.3 
G3BP1,2 GTPase activating protein (SH3 domain) binding protein 1, 2 44.4 18.2 14.3 
G6PD Glucose-6-phosphate 1-dehydrogenase 9.1 28.6 22.2 
GAPDH Glyceraldehyde-3-phosphate dehydrogenase 18.2 42.9 55.6 
GFAP Glial fibrillary acidic protein 36.4 42.9 55.6 
GNAS Guanine nucleotide-binding protein G 22.2 9.1 14.3 
GNB2L1 Guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1 36.4 28.6 44.4 
GNL2,3 Guanine nucleotide-binding protein-like 2 (nucleolar) 100 
GSR Glutathione reductase 36.4 42.9 33.3 
GSTM3 Glutathione S-transferase M3 18.2 28.6 22.2 
ILF 2, 3 Interleukin enhancer binding factor 2, 3 54.5 42.9 55.6 
KHDRBS1,2,3 KH domain containing, RNA binding, signal transduction associated 45.5 0.0 11.1 
KHSRP Far upstream element-binding protein 2 36.4 0.0 11.1 
KIF2,4 Kinesin family member 2, 4 44.4 36.4 14.3 
LDHA Lactate dehydrogenase A 9.1 42.9 55.6 
LGALS1,3 Beta-galactoside–binding lectin 72.7 57.1 55.6 
LIMA1 LIM domain and actin-binding protein 1 44.4 9.1 14.3 
LMNA, B Lamin A/C, B 90.9 0.0 33.3 
MATR3 Matrin 3 63.6 0.0 44.4 
MCM3,5 Minichromosome maintenance complex component 3, 5 54.5 14.3 44.4 
MIF Macrophage migration inhibitory factor 9.1 28.6 22.2 
MSH2 MutS protein homologue 2 77.8 14.3 
MTCH2 Mitochondrial carrier homologue 2 36.4 0.0 11.1 
NACA Nascent polypeptide-associated complex subunit alpha 11.1 18.2 14.3 
NCL Nucleolin 72.7 42.9 22.2 
NES Nestin 55.6 9.1 14.3 
NME1, 2 Non-metastatic cells protein 1, 2 18.2 28.6 11.1 
NONO Non-POU domain containing, octamer-binding 36.4 0.0 11.1 
NPM1 Nucleophosmin 1 81.8 0.0 44.4 
NUDT16L1 Nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1 77.8 14.3 
NUMA1 Nuclear mitotic apparatus protein 1 66.7 18.2 42.9 
NUP155 Nucleoporin 155 kD 54.5 0.0 11.1 
PABPC1,3,4 Poly(A) binding protein, cytoplasmic 1, 3, 4 18.2 57.1 33.3 
PALLD Palladin, cytoskeletal associated protein 45.5 0.0 11.1 
PARK7 DJ-1 protein 36.4 28.6 44.4 
PARP1 Poly (ADP-ribose) polymerase family, member 1 27.3 0.0 11.1 
PCBP1, 2 Poly(rC)-binding protein 1, 2 63.6 85.7 55.6 
PCMT Protein-l-isoaspartate(d-aspartate) O-methyltransferase 18.2 57.1 33.3 
PDIA6 Protein disulfide-isomerase A6 63.6 14.3 77.8 
PDLIM2,4 PDZ and LIM domain protein 2 55.6 
PFDN2 Prefoldin subunit 2 9.1 14.3 11.1 
PFN2 Profilin 2 36.4 28.6 33.3 
PHB, PHB2 Prohibitin, prohibitin 2 63.6 42.9 77.8 
PHF5A PHD finger protein 5A 45.5 0.0 11.1 
PHGDH Phosphoglycerate dehydrogenase 18.2 71.4 44.4 
PKM2 Pyruvate kinase, muscle 54.5 71.4 66.7 
POTE2 Protein expressed in prostate, ovary, testis, and placenta 2 54.5 42.9 66.7 
PPIA Peptidylprolyl isomerase A (cyclophilin A) 66.7 27.3 71.4 
PRDX1,2,3,4 Peroxiredoxin 1, 2, 3, 4 90.9 71.4 100.0 
PRKDC Protein kinase, DNA-activated 81.8 14.3 44.4 
PTBP1,2 Polypyrimidine tract-binding protein 1, 2 63.6 14.3 11.1 
RALY RNA-binding protein (autoantigenic, hnRNP-associated with lethal, yellow) 100 27.3 28.6 
RCC2 Regulator of chromosome condensation 2 63.6 0.0 11.1 
S100A6,9,10,14 S100 calcium binding protein A 100 36.4 42.9 
SAP18 Sin3-associated polypeptide, 18 kD 44.4 14.3 
SEC61B Protein transport protein Sec61 beta subunit 45.5 0.0 11.1 
SERBP1 SERPINE1 mRNA binding protein 1 45.5 0.0 22.2 
SERPINH1,A11 Serine (or cysteine) proteinase inhibitor 72.7 28.6 66.7 
SF3B Splicing factor 3B 54.5 0.0 22.2 
SLC25A ADP/ATP translocase 2 (solute carrier family 25) 100.0 71.4 100.0 
THOC4 THO complex subunit 4 44.4 9.1 
TKT Transketolase 36.4 42.9 33.3 
TMPO Thymopoietin 22.2 28.6 
TOMM22 Translocase of outer membrane 22-kD subunit homologue 22.2 28.6 
TRAP1 Tumor necrosis factor type 1 receptor-associated protein (heat shock protein 75) 44.4 27.3 42.9 
TRIM21 52-kD Ro protein 18.2 28.6 33.3 
TRIM25 Tripartite motif-containing protein 25 (Zinc finger protein 147) 18.2 0.0 0.0 
TTBK2 Tau-tubulin kinase 18.2 14.3 44.4 
TUFM Tu translation elongation factor, mitochondrial 63.6 14.3 55.6 
TXN Thioredoxin 27.3 57.1 55.6 
U2AF1 U2 small nuclear RNA auxillary factor 1 27.3 0.0 11.1 
UBA52 Ubiquitin and ribosomal protein L40 precursor 36.4 57.1 55.6 
UBE2D2,3 Ubiquitin-conjugating enzyme E2D 2, E2D 3 18.2 14.3 0.0 
UQCRC1 Ubiquinol-cytochrome c reductase core protein I 63.6 0.0 22.2 
VAPA/B VAMP (vesicle-associated membrane protein)-associated protein A, B 44.4 27.3 28.6 
VCP Valosin-containing protein 44.4 18.2 42.9 
VDAC2,3 Voltage-dependent anion channel 2, 3 63.6 0.0 22.2 
XPO1 Exportin 1 9.1 0.0 22.2 
XRCC5, 6 ATP-dependent DNA helicase II 18.2 14.3 0.0 
YBX1 Y box binding protein 1 36.4 28.6 33.3 
YWHAZ,YWHAB Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein 27.3 28.6 44.4 

In addition to the common classes of proteins listed in Table I, there are over 100 proteins, shown here, that do not fall into these specific classes yet still bind Sepharose nonspecifically. This list was screened against datasets from 27 independent SILAC immunoprecipitation experiments using either nucleoplasmic (NP; 11 experiments), cytoplasmic (CP; 7 experiments), or whole cell (WC; 9 experiments) extracts to determine the frequency of detection and distribution of these nonspecific binding proteins among these distinct cellular extracts. The frequency is listed as the percentage of experiments in which the protein was detected.

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