Table 3

Tyrosine phosphorylated peptides that changed their phosphorylation status while ALK was inhibited by shRNA or a pharmacologic inhibitor

Gene symbolPeptidePTyr siteProtein*Average H:LNCBI access no.shALKALK inhibitor
Peptides that decrease when ALK is reduced        
    Kinases        
        ALK R.TSTIMTDYNPNY*CFAGK 1096 Anaplastic lymphoma kinase 1:6.20 NP_004295 
        ALK R.NKPTSLWNPTY*GSWFTEKPTK 1507 Anaplastic lymphoma kinase 1:3.72 NP_004295 
        CDC2 K.IEKIGEGTY*GVVYK 15 Cell division cycle 2 protein 1:2.7 NP_203698 
        CDK2 K.VEKIGEGTY*GVVYK 15 Cyclin dependent kinase 2 >1:6 NP_001789 
        ERK1/MAPK3 R.IADPEHDHTGFLTEY*VATR 187 Mitogen-activated protein kinase 3 1:2.07 NP_002737 Not found 
        p38/MAPK14 R.HTDDEMTGY*VATR 182 Mitogen-activated protein kinase 14 1:3.22 NP_620581 
    Adaptors        
        HGS R.VCEPCY*EQLNR 216 HGF regulated tyrosine kinase substrate >1:4 NP_004703 Not found 
        PAG K.SGQSLTVPESTY*TSIQGDPQR 341 Phosphoprotein associated with glycosphingo 1.47:1 NP_060910 Not found 
        PARD3 R.DVTIGGSAPIY*VK 489 par-3 partitioning defective 3 homolog >1:4 NP_062565 Not found 
    Cytoskeletal proteins        
        ACTB R.KDLY*ANTVLSGGTTMYPGIADR.M 294 Actin, β 1:5.71 NP_001092 Not found 
        ACTB K.EKLCY*VALDFEQEMATAASSSSLEK.S 218 Actin, β >1:3 NP_001092 
        CORO1C R.YFEITDESPY*VHYLNTFSSK.E 301 Coronin, actin binding protein, 1C 1:2.47 NP_055140 
        VASP R.VQIY*HNPTANSFR.V 39 Vasodilator-stimulated phosphoprotein >1:9 NP_003361 
        VIM R.FANY*IDKVR.F 117 Vimentin >1:6 NP_003371 
    Chaperones        
        HSP90AB1 K.SIY*YITGESK.E 484 Heat shock protein 90kDa α 1:2.74 NP_031381 
        HSPA2 R.TTPSY*VAFTDTER.L 43 Heat shock 70kDa protein 2 >1:2 NP_068814 Not found 
        HSPA4 K.LKKEDIY*AVEIVGGATR.I 336 Heat shock 70kDa protein 4 1:2.66 NP_002145 
        TRAP1 R.NIY*YLCAPNR.H 498 TNF receptor-associated protein 1 1:2.9 NP_057376 
    Cytokines        
        PBEF K.YLLETSGNLDGLEY*KLHDFGYR.G 188 Pre-B-cell colony enhancing factor 1 1:2.04 NP_005737 
    Energy metabolism        
        RASA1 K.HFTNPY*CNIYLNSVQVAK.T 615 RAS p21 protein activator 1 1:3.25 NP_072179  
    Metabolic enzymes        
        ACLY R.TTDGVY*EGVAIGGDRYPGSTFMDHVLR.Y 682 ATP cytrate lyase 1:4.27 NP_001087 
        ACP1 K.QLIIEDPYYGNDSDFETVY*QQCVR.C 143 Acidic phosphatase 1 1:5.2 NP_004291 
        ATIC VVACNLyPFVK 104 AICAR formyltransferase/IMP Chase 1:3.70 NP_004035 
        ELP3 R.NLHDALSGHTSNNIY*EAVK.Y 202 Elongation protein 3 1:5.57 NP_060561 
        ENO1 K.SFIKDY*PVVSIEDPFDQDDWGAWQK.F 287 Enolase 1 1:2.91 NP_001419 
        GBE1 R.EGDNVNY*DWIHWDPEHSYEFK.H 173 Glucan (1,4-α-), branching enzyme 1 1:1.86 NP_000149 
        LDHA K.QVVESAY*EVIK.L 239 Lactate dehydrogenase A 1:3.03 NP_005557 
        LDHB K.MVVESAY*EVIK.L 240 Lactate dehydrogenase B 1:4.00 NP_002291 
        NIT2 K.TLSPGDSFSTFDTPY*CR.V 145 Nitrilase family, member 2 1:4.14 NP_064587 
        NUDT5 R.TLHY*ECIVLVK.Q 74 Nudix-type motif 5 1:10.3 NP_054861 
        PFKFB3 R.ISCY*EASYQPLDPDKCDR.D 194 6-Phosphofructo-2-kinase >1:8 NP_004557 Not found 
        PKM2 R.TATESFASDPILY*RPVAVALDTKGPEIR.T 105 Pyruvate kinase 3 1:4.56 NP_002645 
        SUCLA2 K.SPDEAY*AIAK.K 84 succinate-CoA ligase, ADP-forming, β sub >1:2.64 NP_003841 Not found 
    Metabolism of nucleic acids        
        HIST1H4I R.ISGLIY*EETR.G 52 H4 histone family 1:2.45 NP_068803 
        HNRPF K.ATENDIY*NFFSPLNPVR.V 306 Heterogeneous nuclear ribonucleoprotein F >1:3 NP_004957 Not found 
        MKI67IP R.TGNSKGY*AFVEFESEDVAK.I 88 FHA domain interacting nucleolar phosphopro 1:2.8 NP_115766 Not found 
        PABP 1 R.SLGY*AYVNFQQPADAER.A 56 Poly A binding protein, cytoplasmic 4 >1:8 NP_003810 
        POLR2A R.LTHVY*DLCK.G 145 DNA directed RNA pol. II polyp. A 1:3.58 NP_000928 
        RNPS1 K.GY*AYVEFENPDEAEK.A 205 RNA binding prot S1, serine-rich domain >1:4 NP_542161 
        SFPQ R.FAQHGTFEY*EYSQR.W 488 Splicing factor proline/glutamine rich (polypyri 1:3.63 NP_005057 
        SYNCRIP K.LKDY*AFIHFDERDGAVK.A 373 Synaptotagmin binding, cytoplasmic RNA inte 1:3.88 NP_006363 Not found 
    Regulation of translation        
        PHF19 K.LTEGQY*VLCR.W 45 PHD finger protein 19 1:3.5 NP_082992 Not found 
        PHB2 R.IPWFQY*PIIYDIR.A 77 Prohibitin 2 1:3.43 NP_009204 Not found 
        PHB2 R.LGLDY*EER.V 128 Prohibitin 2 1:1.93 NP_009204 Not found 
        EEF1A1 K.STTTGHLIY*K.C 29 Eukaryotic elongation factor 1 α 1 >1:3 NP_001393 Not found 
        EIF3S2 K.SYSSGGEDGY*VR.I 308 Eukaryotic translation initiation factor 3 >1:13 NP_003748 
        EIF3S9 K.NGDY*LCVK.V 525 Eukaryotic translation initiation factor 3, subun 1:3.75 NP_003742 
        EIF3S7 R.NLAMEATY*INHNFSQQCLR.M 318 Eukaryotic translation initiation factor 3,subun 1:2.68 NP_003744 
        KNTC2 R.AQVY*VPLKELLNETEEEINK.A 458 Kinetochore associated 2 >1:5 NP_006092 Not found 
    Ribosomal proteins        
        RPL18A K.SSGEIVY*CGQVFEK.S 63 Ribosomal protein L18a 1:3.16 NP_000971 
        RPL31 R.NEDEDSPNKLY*TLVTYVPVTTFK.N 103 Ribosomal protein L31 1:2.87 NP_000984 
        RPL7 R.IVEPY*IAWGYPNLK.S 139 Ribosomal protein L7 1:2.10 NP_000962 
        RPL8 R.ASGNY*ATVISHNPETK.K 133 Ribosomal protein L8 1:3.15 NP_000964 
        RPLP0 K.IIQLLDDY*PK.C 24 Ribosomal protein P0 1:5.23 NP_000993 
        RPS10 R.IAIY*ELLFK.E 12 Ribosomal protein S10 1:2.52 NP_001005 Not found 
        RPS13 K.LTSDDVKEQIY*K.L 38 Ribosomal protein S13 1:1.8 NP_001008 Not found 
    Transcription factors        
        DCP1A R.SASPY*HGFTIVNR.L 64 DCP1 decapping enzyme homolog A 1:2.24 NP_060873 Not found 
        STAT3 iso1 K.YCRPESQEHPEADPGSAAPY*LK.T 705 Signal transducer and activator of transcriptio 1:13.23 NP_644805 
        STAT3 iso2 K.YCRPESQEHPEADPGAAPY*LK.T 704 Signal transducer and activator of transcriptio 1:13.57 NP_003141 
    Ubiquitin-proteasome system        
        PSMA2 K.LVQIEY*ALAAVAGGAPSVGIK.A 98 Proteasome subunit α type 2 1:4.37 NP_002778 
        PSMA2 R.KLAQQYY*LVYQEPIPTAQLVQR.V 24 Proteasome subunit α type 2 1:3.18 NP_002778 
    Others        
        ANXA2 K.SLY*YYIQQDTK.G 316 Annexin A2 1:1.91 NP_004030 
        GSDMDC1 R.SRGDNVY*VVTEVLQTQK.E 71 Gasdermin domain containing 1 1:3.27 NP_079012 Not found 
        FAM62B R.NLIAFSEDGSDPY*VR.M 796 Family with sequence similarity 62 member B >1:3 NP_065779 
        WDR1 K.AHDGGIY*AISWSPDSTHLLSASGDK.T 98 WD repeat-containing protein 1 1:3.58 NP_005103 
Peptides with no significant change        
    Kinases        
        DYRK1A R.KVYNDGYDDDNY*DYIVK.N 145 Dual-specificity tyr. phosphorylation regulated 1:1.15 NP_001387 
        DYRK1A R.IYQY*IQSR.F 321 Dual-specificity tyr. phosphorylation regulated 1:1.36 NP_001387 
        GSK3 R.GEPNVSY*ICSR.Y 216 Glycogen synthase kinase 3 α 1:1.15 NP_063937 
        HIPK1 K.AVCSTY*LQSR.Y 352 Homeodomain interacting protein kinase 1 1:1.15 NP_689909 
        HIPK3 K.TVCSTY*LQSR.Y 359 Homeodomain interacting protein kinase 3 1:0.99 NP_005725 
        PRPF4B K.LCDFGSASHVADNDITPY*LVSR.F 849 Serine/threonine-protein kinase PRP4K 1:1.02 NP_003904 
        SRC R.LIEDNEY*TAR.Q 419 (416) v-src sarcoma viral Oncogene homolog 1:1.10 NP_005408 Not found Not found 
    Adaptors        
        SHC R.ELFDDPSY*VNVQNLDK.A 318 SHC 1 1:1.44 NP_003020 
    Chaperones        
        HSPD1 R.GYISPY*FINTSK.G 227 Heat shock 60 kDa protein 1 (chaperonin) 1:1.35 NP_955472 Not found 
        HSP90AA1 K.HIY*YITGETK.D 492 Heat shock 90 kDa protein 1:1.18 NP_005339 Not found 
    Cytokines        
        PBEF K.VY*SYFECR.E 34 Pre-B-cell colony enhancing factor 1 1:1.02 NP_005737 
    Energy metabolism        
        GDI2 R.TDDYLDQPCY*ETINR.I 203 GDP dissociation inhibitor 2 1:1.46 NP_001485 
        RAN K.SNY*NFEKPFLWLAR.K 155 ras-related nuclear protein 1:1.12 NP_006316 Not found 
        WRNIP1 R.MLEGGEDPLY*VAR.R 534 Werner helicase interacting protein 1 1:1.20 NP_064520 
Gene symbolPeptidePTyr siteProtein*Average H:LNCBI access no.shALKALK inhibitor
Peptides that decrease when ALK is reduced        
    Kinases        
        ALK R.TSTIMTDYNPNY*CFAGK 1096 Anaplastic lymphoma kinase 1:6.20 NP_004295 
        ALK R.NKPTSLWNPTY*GSWFTEKPTK 1507 Anaplastic lymphoma kinase 1:3.72 NP_004295 
        CDC2 K.IEKIGEGTY*GVVYK 15 Cell division cycle 2 protein 1:2.7 NP_203698 
        CDK2 K.VEKIGEGTY*GVVYK 15 Cyclin dependent kinase 2 >1:6 NP_001789 
        ERK1/MAPK3 R.IADPEHDHTGFLTEY*VATR 187 Mitogen-activated protein kinase 3 1:2.07 NP_002737 Not found 
        p38/MAPK14 R.HTDDEMTGY*VATR 182 Mitogen-activated protein kinase 14 1:3.22 NP_620581 
    Adaptors        
        HGS R.VCEPCY*EQLNR 216 HGF regulated tyrosine kinase substrate >1:4 NP_004703 Not found 
        PAG K.SGQSLTVPESTY*TSIQGDPQR 341 Phosphoprotein associated with glycosphingo 1.47:1 NP_060910 Not found 
        PARD3 R.DVTIGGSAPIY*VK 489 par-3 partitioning defective 3 homolog >1:4 NP_062565 Not found 
    Cytoskeletal proteins        
        ACTB R.KDLY*ANTVLSGGTTMYPGIADR.M 294 Actin, β 1:5.71 NP_001092 Not found 
        ACTB K.EKLCY*VALDFEQEMATAASSSSLEK.S 218 Actin, β >1:3 NP_001092 
        CORO1C R.YFEITDESPY*VHYLNTFSSK.E 301 Coronin, actin binding protein, 1C 1:2.47 NP_055140 
        VASP R.VQIY*HNPTANSFR.V 39 Vasodilator-stimulated phosphoprotein >1:9 NP_003361 
        VIM R.FANY*IDKVR.F 117 Vimentin >1:6 NP_003371 
    Chaperones        
        HSP90AB1 K.SIY*YITGESK.E 484 Heat shock protein 90kDa α 1:2.74 NP_031381 
        HSPA2 R.TTPSY*VAFTDTER.L 43 Heat shock 70kDa protein 2 >1:2 NP_068814 Not found 
        HSPA4 K.LKKEDIY*AVEIVGGATR.I 336 Heat shock 70kDa protein 4 1:2.66 NP_002145 
        TRAP1 R.NIY*YLCAPNR.H 498 TNF receptor-associated protein 1 1:2.9 NP_057376 
    Cytokines        
        PBEF K.YLLETSGNLDGLEY*KLHDFGYR.G 188 Pre-B-cell colony enhancing factor 1 1:2.04 NP_005737 
    Energy metabolism        
        RASA1 K.HFTNPY*CNIYLNSVQVAK.T 615 RAS p21 protein activator 1 1:3.25 NP_072179  
    Metabolic enzymes        
        ACLY R.TTDGVY*EGVAIGGDRYPGSTFMDHVLR.Y 682 ATP cytrate lyase 1:4.27 NP_001087 
        ACP1 K.QLIIEDPYYGNDSDFETVY*QQCVR.C 143 Acidic phosphatase 1 1:5.2 NP_004291 
        ATIC VVACNLyPFVK 104 AICAR formyltransferase/IMP Chase 1:3.70 NP_004035 
        ELP3 R.NLHDALSGHTSNNIY*EAVK.Y 202 Elongation protein 3 1:5.57 NP_060561 
        ENO1 K.SFIKDY*PVVSIEDPFDQDDWGAWQK.F 287 Enolase 1 1:2.91 NP_001419 
        GBE1 R.EGDNVNY*DWIHWDPEHSYEFK.H 173 Glucan (1,4-α-), branching enzyme 1 1:1.86 NP_000149 
        LDHA K.QVVESAY*EVIK.L 239 Lactate dehydrogenase A 1:3.03 NP_005557 
        LDHB K.MVVESAY*EVIK.L 240 Lactate dehydrogenase B 1:4.00 NP_002291 
        NIT2 K.TLSPGDSFSTFDTPY*CR.V 145 Nitrilase family, member 2 1:4.14 NP_064587 
        NUDT5 R.TLHY*ECIVLVK.Q 74 Nudix-type motif 5 1:10.3 NP_054861 
        PFKFB3 R.ISCY*EASYQPLDPDKCDR.D 194 6-Phosphofructo-2-kinase >1:8 NP_004557 Not found 
        PKM2 R.TATESFASDPILY*RPVAVALDTKGPEIR.T 105 Pyruvate kinase 3 1:4.56 NP_002645 
        SUCLA2 K.SPDEAY*AIAK.K 84 succinate-CoA ligase, ADP-forming, β sub >1:2.64 NP_003841 Not found 
    Metabolism of nucleic acids        
        HIST1H4I R.ISGLIY*EETR.G 52 H4 histone family 1:2.45 NP_068803 
        HNRPF K.ATENDIY*NFFSPLNPVR.V 306 Heterogeneous nuclear ribonucleoprotein F >1:3 NP_004957 Not found 
        MKI67IP R.TGNSKGY*AFVEFESEDVAK.I 88 FHA domain interacting nucleolar phosphopro 1:2.8 NP_115766 Not found 
        PABP 1 R.SLGY*AYVNFQQPADAER.A 56 Poly A binding protein, cytoplasmic 4 >1:8 NP_003810 
        POLR2A R.LTHVY*DLCK.G 145 DNA directed RNA pol. II polyp. A 1:3.58 NP_000928 
        RNPS1 K.GY*AYVEFENPDEAEK.A 205 RNA binding prot S1, serine-rich domain >1:4 NP_542161 
        SFPQ R.FAQHGTFEY*EYSQR.W 488 Splicing factor proline/glutamine rich (polypyri 1:3.63 NP_005057 
        SYNCRIP K.LKDY*AFIHFDERDGAVK.A 373 Synaptotagmin binding, cytoplasmic RNA inte 1:3.88 NP_006363 Not found 
    Regulation of translation        
        PHF19 K.LTEGQY*VLCR.W 45 PHD finger protein 19 1:3.5 NP_082992 Not found 
        PHB2 R.IPWFQY*PIIYDIR.A 77 Prohibitin 2 1:3.43 NP_009204 Not found 
        PHB2 R.LGLDY*EER.V 128 Prohibitin 2 1:1.93 NP_009204 Not found 
        EEF1A1 K.STTTGHLIY*K.C 29 Eukaryotic elongation factor 1 α 1 >1:3 NP_001393 Not found 
        EIF3S2 K.SYSSGGEDGY*VR.I 308 Eukaryotic translation initiation factor 3 >1:13 NP_003748 
        EIF3S9 K.NGDY*LCVK.V 525 Eukaryotic translation initiation factor 3, subun 1:3.75 NP_003742 
        EIF3S7 R.NLAMEATY*INHNFSQQCLR.M 318 Eukaryotic translation initiation factor 3,subun 1:2.68 NP_003744 
        KNTC2 R.AQVY*VPLKELLNETEEEINK.A 458 Kinetochore associated 2 >1:5 NP_006092 Not found 
    Ribosomal proteins        
        RPL18A K.SSGEIVY*CGQVFEK.S 63 Ribosomal protein L18a 1:3.16 NP_000971 
        RPL31 R.NEDEDSPNKLY*TLVTYVPVTTFK.N 103 Ribosomal protein L31 1:2.87 NP_000984 
        RPL7 R.IVEPY*IAWGYPNLK.S 139 Ribosomal protein L7 1:2.10 NP_000962 
        RPL8 R.ASGNY*ATVISHNPETK.K 133 Ribosomal protein L8 1:3.15 NP_000964 
        RPLP0 K.IIQLLDDY*PK.C 24 Ribosomal protein P0 1:5.23 NP_000993 
        RPS10 R.IAIY*ELLFK.E 12 Ribosomal protein S10 1:2.52 NP_001005 Not found 
        RPS13 K.LTSDDVKEQIY*K.L 38 Ribosomal protein S13 1:1.8 NP_001008 Not found 
    Transcription factors        
        DCP1A R.SASPY*HGFTIVNR.L 64 DCP1 decapping enzyme homolog A 1:2.24 NP_060873 Not found 
        STAT3 iso1 K.YCRPESQEHPEADPGSAAPY*LK.T 705 Signal transducer and activator of transcriptio 1:13.23 NP_644805 
        STAT3 iso2 K.YCRPESQEHPEADPGAAPY*LK.T 704 Signal transducer and activator of transcriptio 1:13.57 NP_003141 
    Ubiquitin-proteasome system        
        PSMA2 K.LVQIEY*ALAAVAGGAPSVGIK.A 98 Proteasome subunit α type 2 1:4.37 NP_002778 
        PSMA2 R.KLAQQYY*LVYQEPIPTAQLVQR.V 24 Proteasome subunit α type 2 1:3.18 NP_002778 
    Others        
        ANXA2 K.SLY*YYIQQDTK.G 316 Annexin A2 1:1.91 NP_004030 
        GSDMDC1 R.SRGDNVY*VVTEVLQTQK.E 71 Gasdermin domain containing 1 1:3.27 NP_079012 Not found 
        FAM62B R.NLIAFSEDGSDPY*VR.M 796 Family with sequence similarity 62 member B >1:3 NP_065779 
        WDR1 K.AHDGGIY*AISWSPDSTHLLSASGDK.T 98 WD repeat-containing protein 1 1:3.58 NP_005103 
Peptides with no significant change        
    Kinases        
        DYRK1A R.KVYNDGYDDDNY*DYIVK.N 145 Dual-specificity tyr. phosphorylation regulated 1:1.15 NP_001387 
        DYRK1A R.IYQY*IQSR.F 321 Dual-specificity tyr. phosphorylation regulated 1:1.36 NP_001387 
        GSK3 R.GEPNVSY*ICSR.Y 216 Glycogen synthase kinase 3 α 1:1.15 NP_063937 
        HIPK1 K.AVCSTY*LQSR.Y 352 Homeodomain interacting protein kinase 1 1:1.15 NP_689909 
        HIPK3 K.TVCSTY*LQSR.Y 359 Homeodomain interacting protein kinase 3 1:0.99 NP_005725 
        PRPF4B K.LCDFGSASHVADNDITPY*LVSR.F 849 Serine/threonine-protein kinase PRP4K 1:1.02 NP_003904 
        SRC R.LIEDNEY*TAR.Q 419 (416) v-src sarcoma viral Oncogene homolog 1:1.10 NP_005408 Not found Not found 
    Adaptors        
        SHC R.ELFDDPSY*VNVQNLDK.A 318 SHC 1 1:1.44 NP_003020 
    Chaperones        
        HSPD1 R.GYISPY*FINTSK.G 227 Heat shock 60 kDa protein 1 (chaperonin) 1:1.35 NP_955472 Not found 
        HSP90AA1 K.HIY*YITGETK.D 492 Heat shock 90 kDa protein 1:1.18 NP_005339 Not found 
    Cytokines        
        PBEF K.VY*SYFECR.E 34 Pre-B-cell colony enhancing factor 1 1:1.02 NP_005737 
    Energy metabolism        
        GDI2 R.TDDYLDQPCY*ETINR.I 203 GDP dissociation inhibitor 2 1:1.46 NP_001485 
        RAN K.SNY*NFEKPFLWLAR.K 155 ras-related nuclear protein 1:1.12 NP_006316 Not found 
        WRNIP1 R.MLEGGEDPLY*VAR.R 534 Werner helicase interacting protein 1 1:1.20 NP_064520 

Average H:L indicates SILAC quantification performed on samples treated with ALK shRNA.

1Phosphopeptides that are present both in CEP11988 and CEP14083, in shALK and shALK+.

2Phosphopeptides that are present in CEP11988 and in shALK, but not in CEP14083 and shALK+.

3Phosphopeptides that are present in CEP14083 and shALK+, but not in CEP11988 and in shALK.

4Phosphopeptides detected twice with ambiguous results.

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