Table I

Proteins and protein classes isolated by anti-pY affinity chromatography from HN5 HNSCC cells

Accession numbers from Swiss-Prot and GenBank, protein names, the number of distinct peptides identified by LC-MS/MS, and the mean percent confidence and score for peptides comprising the identified protein. Key domains are listed. Proteins detected by immunoblot are indicated by bolded accession numbers. Proteins identified by anti-EGFr affinity chromatography are indicated by italic protein names. Proteins uniquely identified by SONAR are indicated by “s.”

Accession IDProtein class and nameUnique peptidesMean % confidenceMean % scoreSelect domains
Calcium regulation
gi‖7656952 Calcyclin binding protein49918SGS, p23
sp‖Q14257 Reticulocalbin 2 precursor (Calcium-binding protein ERC-55)39930EF-hand, ER_TARGET 1
sp‖P31949 S100 calcium-binding protein A11 (Calgizzarin) 29928CaBP_S100, EF-hand
gi‖4506773 S100 calcium-binding protein A9 (Calgranulin B)29926CaBP_S100, EF-hand
sp‖P16615 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 29925Calcium_ATPase, Hydrolase
Cell cycle
gi‖4758046 Cell cycle progression 2 protein 29914FAST_Lau_rich
sp‖P06493 Cell division control protein 2 homolog (p34 protein) 49929Ser_thr_pkin_AS, Ser_thr_pkinase
Cell proliferation, survival
sp‖P42655 14-3-3 protein ε (Mitochondrial import stimulation)3992614-3-3
sp‖P31947 14-3-3 protein ς (Stratifin) (Epithelial cell marker protein 1)4992214-3-3
sp‖P27348 14-3-3 protein τ4992614-3-3
sp‖P29312 14-3-3 protein ζ (PKC inhibitor protein-1)4992814-3-3
sp‖P35222 Catenin β (88kDa)29219Armadillo
sp‖P00533 Epidermal growth factor receptor precursor 859935Furin-like, Tyr_pkinase
sp‖P09382 Galectin-1 (Beta-galactoside-binding lectin L-14-I)29922Galectin, Gal-bind_lectin 1
sp‖P29354 Growth factor receptor-bound protein 2 (GRB2 adapter protein) 49827Neu_cyt_fact_2, SH2, SH3
sp‖P04792 Heat shock 27 kDa protein (Stress-responsive protein 27) 109939Crystallin_alpha, Hsp20
sp‖P08069 Insulin-like growth factor I receptor precursor29923FN_III, Furin-like 1, Tyr_pkinase
sp‖Q14192 LIM-protein 3 (SLIM 3) (LIM-domain protein DRAL) 39820LIM domain
sp‖Q16539 Mitogen-activated protein kinase 1429929p38_MAPK, Ser_thr_pkinase
sp‖P27361 Mitogen-activated protein kinase 3 (and/or MAPK1; Erk 1,2)29923MAPK, Ser_thr_pkinase
sp‖P29597 Non-receptor tyrosine-protein kinase TYK229924FERM, Tyr_pkinase, SH2
gi‖4885525 NSP1; SH2 domain containing 3A; novel SH2-containing protein 149926SH2, GEF for Ras-like small GTPases
gi‖4502371 NSP2, breast cancer antiestrogen resistance 3 119930SH2, GEF for Ras-like small GTPases
sp‖P19174 PLCγ1; 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase γ39923C2, EF-hand, PH, PI_PLC, SH2, SH3
sp‖O75340 Programmed cell death protein 629938EF-hand
sp‖P07947 Proto-oncogene tyrosine-protein kinase YES (p61-YES) 79933Prot_kinase, SH2, SH3, Tyr_pkinase
sp‖P04626 Receptor protein-tyrosine kinase erbB-2 precursor 79932Furin-like, Tyr_pkinase, YLP_motif
sp‖P29353 SHC transforming protein 69929PID_domain, PTB_PID, SH2
sp‖P40763 Signal transducer and activator of transcription 3 (STAT3) 89825P53-like, SH2, STAT
sp‖P12931 Src proto-oncogene tyrosine-protein kinase69928SH2, SH3, Tyr_pkinase, Tyr_pkinase_AS
Cell adhesion, cytoskeleton
gi‖8922075 ACK1, activated p21cdc42Hs kinase 49723SH3, Tyr_pkinase, UBA_domain
sp‖P02570 Actin, cytoplasmic 1 (and/or α, γ)69937Actin, Actin_like
sp‖O43707 α-actinin 4 (F-actin cross linking; also α-actinin-1)49918Actbind_actnin, Calponin-like, Spectrin, EF-hand
sp‖P04083 Annexin I (lipocortin I; chromobindin 9) (P35)29925Annexin
sp‖P07355 Annexin II (lipocortin II; chromobindin 8)29936Annexin
sp‖P08758 Annexin V (lipocortin V; endonexin II; calphobindin I)39924Annexin
sp‖Q14161 ARF GTPase-activating protein GIT129918ANK, GIT, hRIP_like
trm‖Q99018 BPAG2, 180-kDa bullous pemphigoid antigen-229815Collagen
sp‖P35221 Catenin α-1 (Cadherin-associated protein) (α E-catenin) 109928Alpha_catenin, Vinculin
sp‖O60716 Catenin Δ-1 (p120 catenin; cadherin-associated src) 99932Armadillo
sp‖Q03135 Caveolin-1 29944Caveolin
sp‖P56945 CRK-associated substrate (p130Cas) 169937SH3
gi‖30410805 CUB domain-containing protein 1 isoform 1 (SIMA 135/CDCP1)79721CUB domain
gi‖17975768 Ephrin receptor EphB3 precursor; EPH-like tyrosine kinase-239729Tyrosine kinase, TNFR domain, FN_III
sp‖P29317 Ephrin type-A receptor 2 precursor 79927FN_III, SAM, Tyr_pkinase
sp‖P54760 Ephrin type-B receptor 4 precursor 29929FN_III-like, Gal_bind_like, SAM, Tyr_pkinase
sp‖P98172 Ephrin-B1 precursor (EPH-related receptor tyrosine kinase ligand 2) 29925Cupredoxin, Ephrin
sp‖Q05397 Focal adhesion kinase 1 (FADK 1) (pp125FAK, PTK2) 199931Band_4, Focal_AT, Tyr_pkinase
sp‖Q12931 Heat shock protein 75 kDa (HSP75; TRAP-1)29928ATPbind_ATPase, Hsp90
sp‖P16144 Integrin β-4 precursor (GP150) (CD104 antigen)39926Calx_beta, FN_III, Integrin_B, Plexin-like, VWF_A
sp‖P23229 Integrin α-6 precursor (VLA-6) (CD49f)39828Integrin_alpha
sp‖P14923 Junction plakoglobin (Desmoplakin III; gamma catenin)29924Armadillo
sp‖P13645 Keratin, type I cytoskeletal 1049929IF, Keratin_I
sp‖P02533 Keratin, type I cytoskeletal 14 69939IF, Keratin_I
sp‖Q04695 Keratin, type I cytoskeletal 17 39935IF, Keratin_I
sp‖P04264 Keratin, type II cytoskeletal 1 39925IF, keratin_II
sp‖P13647 Keratin, type II cytoskeletal 5 69926IF, Keratin_II
sp‖P02538 Keratin, type II cytoskeletal 6A 59932IF, Keratin_II
sp‖P49023 Paxillin 119933Paxillin, LIM_DOMAIN_1, LIM_DOMAIN_2
sp‖Q99959 Plakophilin 2 29924Armadillo
sp‖Q99569 Plakophilin 4 (p0071)29824Armadillo
sp‖Q15149 Plectin 1 (PLTN) (PCN) (Hemidesmosomal protein 1)269933Actbind_actnin, Calponin-like, Plectin, Spectrin
gi‖4758414 Polypeptide N-acetylgalactosaminyltransferase 329929
gi‖16877878 PRO1855 protein (leucine-rich domain; similar to flightless-1) 5sLeucine-rich repeat (LRR) protein
sp‖Q14289 Protein tyrosine kinase 2 β (Focal adhesion kinase 2) 39927Band_4, Focal_AT, Tyr_pkinase
sp‖Q13671 Ras and Rab interactor 1 (RIN1)29939RA_domain, SH2, VPS9
sp‖Q14155 Rho GEF-7 (PAK-interacting exchange protein)39923GDS_CDC24, PH, RhoGEF, SH3
sp‖Q14247 Src substrate cortactin (Amplaxin) (Oncogene EMS1)29923Hs1/Cortactin, Neu_cyt_fact_2, SH3
sp‖P10599 Thioredoxin (ATL-derived factor) 29827Thiored, Thioredox_dom2
sp‖P05209 Tubulin α-1 chain139929Tubulin_FtsZ
sp‖P05218 Tubulin β-5 chain189929Beta_tubulin, Tub_FtsZ_C, Tubulin_FtsZ
sp‖P52735 Vav-2 protein39417DAG_PE-bind, GDS_CDC24, PH, RhoGEF, SH2, SH3
Nuclear transport
sp‖O43592 Exportin T (tRNA exportin) 29929ARM, Exportin-t
sp‖Q14974 Importin β-1 subunit (Karyopherin β-1 subunit) 89930Armadillo, HEAT_repeat, Importinb_N
sp‖O00410 Importin β-3 subunit (Karyopherin β-3 subunit)59923HEAT_repeat, Importinb_N
sp‖P55060 Importin-α re-exporter (Chromosome segregation 1-like) 49929CAS_CSE1, Importinb_N
gi‖5453998 RAN binding protein 7; RAN binding protein 7; importin 729928Importinb_N, ARM repeat
sp‖P55072 Transitional endoplasmic reticulum ATPase (TER ATPase)39923AAA_ATPase, AAA_CDC48
RNA maturation, protein biosynthesis
sp‖P17075 40S ribosomal protein S202989Ribosomal_S10, Ribosomal_S10s/a
sp‖P46782 40S ribosomal protein S529921Ribosomal_S7, Ribosomal_S7s/a
sp‖O00571 DEAD-box protein 3 (Helicase-like protein 2) (HLP2)29824DEAD_box, DEAD_ATP_HELICASE
sp‖P04720 Elongation factor 1-α 1 (EF-1-α-1) 119925EF1_alpha, EF_GTPbind, EFTU_Cterm, EFTU_D2
sp‖P52597 Heterogeneous nuclear ribonucleoprotein F (hnRNP F) 29927RNA_rec_mot
sp‖P31943 Heterogeneous nuclear ribonucleoprotein H (hnRNP H) 29925RNA_rec_mot
sp‖Q07244 Heterogeneous nuclear ribonucleoprotein K (hnRNP K)29931KH_dom, KH_type_1
sp‖Q13144 Translation initiation factor eIF-2B ε subunit (eIF-2B GDP-GTP)39822eIF5C, Hexapep_transf
sp‖Q9NR50 Translation initiation factor eIF-2Bγ subunit (eIF-2B GDP-GTP)29926NTP_transferase
Protein stability, processing, degradation
sp‖P10809 60 kDa heat shock protein, mitochondrial precursor (Hsp60) 49927Chaprnin_Cpn60, GroEL-ATPase
sp‖P11021 78 kDa glucose-regulated protein precursor (GRP 78) 149933ER_target_S, Hsp70
sp‖P27824 Calnexin precursor (chaperone)29930Calret_calnex_P, ConA_like_lac_gl
sp‖P22681 CBL E3 ubiquitin protein ligase 69929Cbl_N, UBA_domain, ZF_RING_1
sp‖Q13191 CBL-B (SH3-binding protein CBL-B) 139926Cbl_N, SH2, UBA_domain, ZF_RING_1
sp‖P31689 DnaJ homolog A member 1 (Hsp40 protein 4) 49928DnaJ_CXXCXGXG, Hsp_DnaJ
sp‖O60884 DnaJ homolog A member 2 (cell cycle progression) 29922DnaJ_CXXCXGXG, Hsp_DnaJ
sp‖Q96EY1 DnaJ homolog A member 3 (Tumorous imaginal discs protein) 29925DnaJ_CXXCXGXG, Hsp_DnaJ
sp‖Q9UBS4 DnaJ homolog B member 11 precursor (ER-associated dnaJ)29938DnaJ_CXXCXGXG, Hsp_DnaJ
gi‖15812198 F-box only protein 2; F-box protein 2; F-box gene 129822F-box associated region
sp‖P04792 Heat shock 27 kDa protein (HSP 27) 109939Hsp20
sp‖P08107 Heat shock 70 kDa protein 1 (HSP70.1) 59933Hsp70
sp‖P11142 Heat shock cognate 71 kDa protein 159933Hsp70
sp‖P08238 Heat shock protein HSP 90-β (HSP 84) (HSP 90) 59934ATPbind_ATPase, Hsp90
sp‖P05092 Peptidyl-prolyl cis-trans isomerase A49926CSA_PPlase
sp‖P38646 Stress-70 protein, mitochondrial precursor (75 kDa glucose regulated) 219931Hsp70
sp‖P02248 Ubiquitin 39935Ubiquitin
Small molecule transport, energy utilization
sp‖P05141 Adenine nucleotide translocator 2 (solute carrier family 25) 89927Mit_carrier, Mit_uncoupling, Mitoch_carrier
sp‖P06576 ATP synthase β chain, mitochondrial precursor49937AAA_ATPase
sp‖P56134 ATP synthase f chain, mitochondrial29931
gi‖4503571 Enolase 1; phosphopyruvate hydratase; MYC promoter-binding protein29924Enolase
sp‖P04406 Glyceraldehyde 3-phosphate dehydrogenase49929GAP_dhdrogenase, GAPDH-I
sp‖Q00325 Phosphate carrier protein, mitochondrial precursor (PTP) 49926Mitoch_carrier
sp‖P14786 Pyruvate kinase, M2 isozyme (and/or M1)29915Pyruvate_kinase
gi‖21361344 Solute carrier family 3 (4F2 heavy chain; CD98) 59929Alpha_amyl_cat
sp‖P00938 Triosephosphate isomerase29917Triophos_ismrse
sp‖P07919 Ubiquinol-cytochrome C reductase complex 11 kDa protein29923UCR_hinge
Transcription, chromatin regulation
sp‖P78527 DNA-dependent protein kinase catalytic subunit39925FAT, P13_P14_kinase,
sp‖P10412 Histone H1.4 (Histone H1b) 49930Histone_H1/H5
sp‖P02278 Histone H2B 29935Hist_TAF, Histone_core_D, Histone_H2A
gi‖17402907 Tripartite motif protein TRIM29 isoform β, ataxia group D-associated129833B-Box-type zinc finger
sp‖Q03164 Zinc finger protein HRX (ALL-1) (Trithorax-like protein)29939Bromodomain, Fynch, SET, Znf_CXXC, Znf_PHD
Unknown
sp‖P42704 130kDa Leucine-rich protein (Irp 130) (gp 130)29922Prenyl_trans, TPR-like
gi‖7106299 Like mouse brain protein E46 (possible b-catenin-like) 39926Uncharacterized conserved protein
sp‖P40855 Peroxisomal farnesylated protein (33 kDa housekeeping protein) 39929Pex19
gi‖19920317 Transmembrane protein (63kD), endoplasmic reticulum/Golgi interm39727Myosin class II heavy chain
Vesicle transport
sp‖O75843 Adapter-related protein complex 1 γ 2 subunit29928A/G_adapt_C, Adaptin_N, Gamma_adaptin_C
sp‖Q13438 Protein OS-9 precursor (amplified in osteosarcoma)29934Man_6_P_R_bind