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Phosphosignature™ ...From Cell Signaling Technology UNPARALLELED PRODUCT QUALITY, VALIDATION AND TECHNICAL SUPPORT PhosphoSignature™ ...from Cell Signaling Technology PhosphoScan® Profiling Table: SILAC Analysis of H3255 Cells Treated with Iressa www.cellsignal.com Study Background a high-resolution, high mass accuracy mass Select Column Descriptions: spectrometer. From this one sample, one LC- In many forms of non-small-cell lung cancer, Protein Accession Number: Unique protein MS analysis gave 930 phospho-tyrosine-peptide the receptor tyrosine kinase EGFR (epidermal identifier for parent protein from which the cor- assignments, corresponding to 234 phospho- growth factor receptor) is overexpressed. Iressa responding phospho-peptide is derived. Detailed tyrosine sites. This included 63 phospho- protein information for each identifier can be found (Gefitinib) is an EGFR inhibitor approved by tyrosine-peptide assignments to EGFR and 20 in PhosphoSitePlus® (www.phosphosite.org). the FDA for treatment of patients with advanced to the receptor tyrosine kinase Met. The effect of Phospho-Site (Tyr): The phosphorylated (tyro- disease, and the majority of patients who respond Iressa on the level of each phospho-tyrosine site sine) residue number in the protein sequence; the to Iressa treatment have tumors with mutant symbol § denotes a published site; all other sites was reflected in the ratio of normal- and heavy- EGFR genes (Lynch et al., 2004). The molecular are novel and were discovered in PhosphoScan® isotope labeled phosphopeptide ions. Iressa mechanisms underlying Iressa-responsiveness are studies performed by scientists at Cell Signaling treatment lowered the levels of 110 phospho- still largely unknown. Technology. tyrosine sites at least 2.5-fold, and several Phospho-peptide: Sequence assigned based on Study Description phospho-tyrosine sites in EGFR were at least 30- mass spectrometry analysis; y indicates the site(s) of tyrosine phosphorylation. For PhosphoScan® analysis (Guo et al., fold less abundant after Iressa treatment. Other 2007), quantification of Iressa-regulated phospho-tyrosine sites responding strongly to Count in Study: The number of times the phos- ® Iressa were found in the adaptor proteins DLG3 phopeptide was identified in this PhosphoScan phosphorylation was performed with SILAC, study. (Ong and Mann, 2006). Briefly the non-small- and Gab1 and the phospholipase PLCG1. Count at CST: The number of times the phospho- cell lung cancer cell line H3255 was grown in References peptide has been identified in all PhosphoScan® normal culture media, serum starved overnight, studies conducted at Cell Signaling Technology. Guo A, Villén J, Kornhauser J, Lee KA, Stokes and treated with 1 µM Iressa for 3 hours. To Heavy-to-Light Ratio: The ratio of heavy- and M, Rikova K, Possemato A, Nardone J, Innocenti produce an isotope-coded untreated control normal-isotope labeled phosphopeptide ions, re- G, Wetzel R, Wang Y, MacNeill J, Mitchell J, sample, H3255 was grown in media formulated sulting from SILAC labeling of Iressa-treated cells Gygi SP, Rush J, Polakiewicz RD, Comb MJ. to contain heavy isotope-labeled forms of with light-isotope-labeled forms of arginine and Signaling Networks Assembled by Oncogenic lysine. The ratios correspond to the fold-change arginine and lysine. The cells were harvested and in phosphopeptide levels due to Iressa treatment. 8 EGFR and c-Met. Proc Natl Acad Sci U S A. lysed (2 X 10 cells, corresponding to 10 mg Positive numbers indicate phosphopeptides that 2007, in press. cellular protein), and equal amounts of Iressa- are more abundant in untreated cells than in treated (normal isotope coded) and untreated Lynch TJ, Bell DW, Sordella R, Gurubhagavatula Iressa-treated cells. (heavy isotope coded) lysate were combined. S, Okimoto RA, Brannigan BW, Harris PL, The proteins were reduced and alkylated to Haserlat SM, Supko JG, Haluska FG, Louis stabilize cysteine-containing peptides, and DN, Christiani DC, Settleman J, Haber DA. the extract was digested with trypsin. The Activating mutations in the epidermal growth digested cellular protein extract was taken factor receptor underlying responsiveness of non- through the PhosphoScan® procedure using small-cell lung cancer to gefitinib.N Engl J Med. the phospho-tyrosine antibody P-Tyr-100 to 2004 May 20;350(21):2129-39. isolate phospho-tyrosine-containing peptides. Ong SE, Mann M. A practical recipe for stable The isolated peptides were analyzed by liquid isotope labeling by amino acids in cell culture chromatography-mass spectrometry using (SILAC). Nat. Protoc. 2006;1(6):2650-60. Cytoskeletal protein Other 9% 34% Total peptides = 930 (see pie chart) Total non-redundant sites = 251 Total proteins = 183 Adhesion 11% Adaptor/scaffold Protein kinase, Tyr 13% Protein kinase, 19% Ser/Thr 14% 2 PHOspHOSCAN-SILAC ANalysis OF H3255 Cells TreateD WitH Iressa Count Count Heavy-to-Light Ratio Gene Name Description Accession kD Site Peptide in Study at CST Mean Range Actin binding proteins CTNNA1 Catenin alpha-1 (Cadherin-associated protein) P35221 100 177 NAGNEQDLGIQyK 4 282 1.6 1.5-1.8 CTNND1 Catenin delta-1 (Cadherin-associated Src O60716 108 248 YRPSMEGyR 2 44 14.5 7.2-21.9 substrate) (p120(cas)) CTNND1 Catenin delta-1 (Cadherin-associated Src O60716 108 865 SQSSHSyDDSTLPLIDR 1 21 3.9 substrate) (p120(cas)) CTNND1 Catenin delta-1 (Cadherin-associated Src O60716 108 904 SLDNNySTPNERGDHNR 1 224 5.5 substrate) (p120(cas)) CTNND1 Catenin delta-1 (Cadherin-associated Src O60716 108 904 SLDNNySTPNER 4 1198 3.0 2.8-3.1 substrate) (p120(cas)) CTNND1 Catenin delta-1 (Cadherin-associated Src O60716 108 §228 HYEDGYPGGSDNyGsLSR 4 4 1.8 1.8-1.9 substrate) (p120(cas)) CTNND1 Catenin delta-1 (Cadherin-associated Src O60716 108 §228 HYEDGYPGGSDNyGSLSR 6 754 1.8 1.7-1.9 substrate) (p120(cas)) CTNND1 Catenin delta-1 (Cadherin-associated Src O60716 108 §257 QDVyGPQPQVR 1 482 1.1 substrate) (p120(cas)) CTNND1 Catenin delta-1 (Cadherin-associated Src O60716 108 §280 FHPEPyGLEDDQR 3 109 6.1 3.8-10.5 substrate) (p120(cas)) CTNND1 Catenin delta-1 (Cadherin-associated Src O60716 108 §96 LNGPQDHSHLLySTIPR 1 400 3.0 substrate) (p120(cas)) DBNL Drebrin-like protein (SH3 domain-containing Q9UJU6 48 §162 FQDVGPQAPVGSVyQK 2 511 11.1 7.3-14.9 protein 7) (HIP-55) Adaptor/scaffold proteins ANK3 Ankyrin-3 (ANK-3) (Ankyrin-G) Q12955 480 533 ADIVQQLLQQGASPNAATTSGyTPLHLSAR 3 163 0.7 0.6-0.8 NEDD9 Enhancer of filamentation 1 (CRK-associated Q14511 93 §166 TGHGYVyEYPSR 4 325 1.2 1.1-1.3 substrate-related protein)(CasL) CRK Proto-oncogene C-crk (p38) (Adapter molecule P46108 34 136 QGSGVILRQEEAEyVR 1 2 9.9 crk) CRK Proto-oncogene C-crk (p38) (Adapter molecule P46108 34 136 QEEAEyVR 1 6 >8.4 crk) DLG3 Disks large homolog 3 (Synapse-associated Q92796 90 673 RDNEVDGQDyHFVVSR 7 597 >58.4 >27.9-65.2 protein 102) (SAP102) DLG3 Disks large homolog 3 (Synapse-associated Q92796 90 673 DNEVDGQDyHFVVSR 3 67 25.5 18.1-33.5 protein 102) (SAP102) EPS8 Epidermal growth factor receptor kinase substrate Q12929 92 §485 LSTEHSSVSEyHPADGYAFSSNIYTR 2 43 19.9 17.0-22.9 8 FLOT1 Flotillin-1 O75955 47 203 VSAQyLSEIEMAK 3 116 1.3 1.2-1.3 GAB1 GRB2-associated-binding protein 1 (GRB2- Q13480 77 §406 DASSQDCyDIPR 2 937 13.9 9.2-18.5 associated binder 1) GAB1 GRB2-associated-binding protein 1 (GRB2- Q13480 77 §627 GDKQVEyLDLDLDSGK 4 272 >11.0 >5.9->16.7 associated binder 1) GAB1 GRB2-associated-binding protein 1 (GRB2- Q13480 77 §659 SSGSGSSVADERVDyVVVDQQK 3 807 >22.0 >6.6->51.9 associated binder 1) ITSN2 Intersectin-2 (SH3 domain-containing protein 1B) Q9NZM3 193 §552 LIyLVPEK 2 335 8.7 7.8-9.5 (SH3P18) WASL Neural Wiskott-Aldrich syndrome protein (N- O00401 55 §256 VIyDFIEK 2 593 1.0 1.0-1.1 WASP) PAG1 Phosphoprotein associated with glycosphingolipid- Q9NWQ8 47 §227 AEFAEyASVDR 4 340 1.6 1.5-1.7 enriched microdomains 1 PAG1 Phosphoprotein associated with glycosphingolipid- Q9NWQ8 47 §341 SGQSLTVPESTyTSIQGDPQR 1 413 3.2 enriched microdomains 2 PAG1 Phosphoprotein associated with glycosphingolipid- Q9NWQ8 47 §359 SPSSCNDLyATVK 4 432 2.6 2.0-3.2 enriched microdomains 3 PAG1 Phosphoprotein associated with glycosphingolipid- Q9NWQ8 47 §417 ATLGTNGHHGLVPKENDyESISDLQQGR 4 184 >10.4 >6.0-13.9 enriched microdomains 4 PAG1 Phosphoprotein associated with glycosphingolipid- Q9NWQ8 47 §417 ENDyESISDLQQGR 4 578 3.2 3.0-3.4 enriched microdomains 5 PARD3 Partitioning-defective 3 homolog (Atypical PKC Q8TEW0 151 388 FSPDSQyIDNR 2 228 1.7 1.5-1.8 isotype-specific-interacting prot) 3 LEGEND: § published site * phosphorylation site # oxidized methionine SUMMARY TABLE PHOspHOSCAN-SILAC ANalysis OF H3255 Cells TreateD WitH Iressa Count Count Heavy-to-Light Ratio Gene Name Description Accession kD Site Peptide in Study at CST Mean Range PARD3 Partitioning-defective 3 homolog (Atypical PKC Q8TEW0 151 489 DVTIGGSAPIyVK 4 146 1.3 1.2-1.4 isotype-specific-interacting prot) PARD3 Partitioning-defective 3 homolog (Atypical PKC Q8TEW0 151 719 RISHSLySGIEGLDESPSR 1 67 1.4 isotype-specific-interacting prot) PARD3 Partitioning-defective 3 homolog (Atypical PKC Q8TEW0 151 719 ISHSLySGIEGLDESPSR 5 150 0.9 0.7-1.1 isotype-specific-interacting prot) PARD3 Partitioning-defective 3 homolog (Atypical PKC Q8TEW0 151 719 RIsHSLySGIEGLDESPSR 2 2 0.3 0.3-0.4 isotype-specific-interacting prot) PARD3 Partitioning-defective 3 homolog (Atypical PKC Q8TEW0 151 §1127 EGHMMDALyAQVK 1 63 0.8 isotype-specific-interacting prot) MPZL1 Myelin protein zero-like protein 1 O95297 29 §263 SESVVyADIR 3 449 2.1 2.1-2.2 DLG1 Disks large homolog 1 (Synapse-associated Q12959 100 760 DyHFVTSR 1 15 1.5 protein 97) (SAP-97) (hDlg) DLG1
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