Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100311_Velos3_TaGe_SA_COLLAB_Marjo_EGF8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100311_Velos3_TaGe_SA_COLLAB_Marjo_EGF2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100902_Velos3_TaGe_SA_COLLAB_Marjo_EGF_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100311_Velos3_TaGe_SA_COLLAB_Marjo_EGF5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100902_Velos3_TaGe_SA_COLLAB_Marjo_EGF_7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100902_Velos3_TaGe_SA_COLLAB_Marjo_EGF_9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100311_Velos3_TaGe_SA_COLLAB_Marjo_EGF7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100311_Velos3_TaGe_SA_COLLAB_Marjo_EGF10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100902_Velos3_TaGe_SA_COLLAB_Marjo_EGF_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100902_Velos3_TaGe_SA_COLLAB_Marjo_EGF_6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100311_Velos3_TaGe_SA_COLLAB_Marjo_EGF9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100311_Velos3_TaGe_SA_COLLAB_Marjo_EGF3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100311_Velos3_TaGe_SA_COLLAB_Marjo_EGF1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100902_Velos3_TaGe_SA_COLLAB_Marjo_EGF_5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100311_Velos3_TaGe_SA_COLLAB_Marjo_EGF4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100902_Velos3_TaGe_SA_COLLAB_Marjo_EGF_8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100902_Velos3_TaGe_SA_COLLAB_Marjo_EGF_4_100903144943.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100902_Velos3_TaGe_SA_COLLAB_Marjo_EGF_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100311_Velos3_TaGe_SA_COLLAB_Marjo_EGF6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/20100902_Velos3_TaGe_SA_COLLAB_Marjo_EGF_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD005032/combined.zipprimaryOK200003870geiger@tauex.tau.ac.ilTamar GeigerMass SpectrometryShotgun proteomicsBreast CancerNot availablePhosphoproteomicsEgfBreast cancerhttp://www.ebi.ac.uk/pride/archive/projects/PXD005032Epithelial CellCell CultureThe in-house EGF data was generated by stimulating MCF7 cells for 10 min with EGF. MCF7 cells were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA), where they were authenticated. Cell were routinely verified as having no mycoplasma contamination. For SILAC labeling cells were cultured in RPMI devoid of lysine and arginine and supplemented with light or heavy versions of these amino acids. After EGF stimulation cells were lysed with SDS-based buffer (4% SDS, 100 mM DTT in Tris-HCl pH 7.5). Proteins were digested using the FASP protocol. Phosphopeptide enrichment was performed with titanium dioxide. Phosphopeptides were analyzed on the LTQ-Orbitrap Velos mass spectrometer, with higher energy collisional dissociation fragmentation.PrideSILACphosphorylated residueRaw MS data were analyzed by MaxQuant, and included phospho(STY) sites as variable modifications. All protein identifiers were mapped to Entrez Gene IDs with duplications removed. Experiments were performed using two biological replicates. Replicate measurements were averaged and transformed into a z-scored log2 fold-change. In the cases that the phosphorylation site was identified only in a single replicate the site was excluded from the analysis.ProteomicsTamar GeigerLTQ Orbitrap VelosTel Aviv UniversityPARTIALHomo Sapiens (human)geiger@tauex.tau.ac.ilNot availableTechnicalBiologicalWeizmann Institute of ScienceIsraelDER/faint little ball, Lysine Hydrochloride, L-arginine, DL-Arginine Acetate, brookite, Aminosaeure, Elp-B1, der, RCB1904, classic hairy cell leukaemia, Elp-1, TGF-alpha receptor binding, A4, Amino acid, Monohydrate, Visible Light, SDH, Hydrogenchlorid, dmTAF[[II]]230, SDS, nano-TiO2, Background, Lysine Acetate, hydrogen chloride, Cultural, hnu, HCL-C, 2, Min, titanium white, Arg, d-egf-r, Pleuropneumonia Like Organisms, foton, DmelCG42273, L Lysine, ethnicity, (S)-2-amino-5-guanidinopentanoic acid, amino acids, TFIID TAF250, cel, K, Titania, (S)-2-Amino-5-guanidinovaleric acid, R, min, epsilon-diaminocaproic acid, Arginine, mAPC, Monohydrate DL-Arginine Acetate, proteins, flb, rutile, MCF7 cell, AI047805, transforming growth factor alpha receptor binding, Wasserstoffchlorid, LYS, SOLO DANCERS, Lysin, nano-anatase, D-EGFR, Eperythrozoon, MCF 7 cell, gamma, DER1, Asteromyces <mycoplasmas>, L-Arginin, dTAF[[II]]230, Radiation, Elp, l(2)09261, DEgfr, Bovimyces, Aminokarbonsaeure, Arginine Hydrochloride, Dmel_CG7826, TAF200, arginine, AI836084, Light, TAFII-250, classic hairy cell leukemia, TAF250/230, CG10079, alpha-amino carboxylic acids, torpedo/egfr, Cultural Background, TAFII250, LIGHT, Dm1, Cultures, lysine, HCL, Chlorwasserstoff, leukemic reticuloendotheliosis, Urogastrone, Dmel_CG7835, Mnb, MNB, L-Arginine, Visible Radiations, egfr, Amino Acid, Acid, Haemobartonella, Visible Radiation, HD-33, El, HVEML, Amino acids, DER/EGFR, EGFR, EGfr, EgfR, anatase titanium dioxide, dEgfr, HCl, Epidermal growth factor, DER flb, alpha, Torpedo/Egfr, AW124434, CG17603, study protocol, TAF[[II]], Pleuropneumonia, Degfr, MCF7, DMDA, light quantum, Taf250, SR3-5, DEGFR, l(2)57DEFa, l(2)05351, Mycoplasma putrefaciens, dEGFR, Acids, DmHD-33, chlorane, TGFalpha receptor binding, TAF230, F10B6_15, EGF receptor binding, Beliefs, d230, D-Egf, Asterococcus <mycoplasmas>, Pleuropneumonia-Like Organisms, chlorure d'hydrogene, C-erb, Aminocarbonsaeure, mor1, L Isomer, Gene, dTAFII250, high weight, alpha-amino acid, EK2-6, EfW1, Phosphopeptide., TYPE, CG7826, F10B6.15, L-(+)-arginine, Ly113, Buffer, DAGA4, method, (2S)-2-amino-5-(carbamimidamido)pentanoic acid, dmTAF1, AI790464, Taf230, method used in an experiment, anatase, c-erbB, EGFr, heavy, CG7835, Gene Products, CG42273, torpedo/Egfr, TOP, Egf-r, Lysine, light, MAM, SCG3, cloruro de hidrogeno, epidermal growth factor, Backgrounds, TAF250, EGF-R, Taf200, transforming growth factor alpha receptor ligand, dTAF[[II]]250, epidermal growth factor receptor ligand, URG, Hydrogen chloride, cell, Lichtquant, EGFR binding, top, Borrelomyces, 4733401P19Rik, Torpedo/DER, Cultural Relativisms, Taf1p, labeling, food additive E171, Visible, top/flb, dTAF250, hairy cell leukemia, HOMG4, l(2)57EFa, EGF receptor ligand, photon, Customs, L-Arg, l(2)57Ea, TR2, culture, TAF, MCF-7 cell, Elp-B1RB1, data, DYRK1, TAF[[II]]250, dEGFR1, Proteins, l(3)84Ab, titanium oxide, BG:DS00004.13, alpha-amino acids, chloridohydrogen, Cultural Backgrounds, L-Isomer, DL Arginine Acetate, CD258, buffer, Cell, LGMD2C, Belief, dTAF230, [HCl], PPLO, transforming growth factor alpha, DmelCG10079, L-Isomer Arginine, Acetate, p230, Protein, Hydrochloride, TAF[[II]]250/230, TFIID, Dyrk1, L Arginine, DER/top, L-Lysine, Radiations, AU020952, Taf[[II]]250, TAF[[II]]230, DMDA1, top/DER, HVEM-L, CC1, (2S)-2-amino-5-guanidinopentanoic acid, Photoradiation, SWDS, TAF[II]250, Amino, CGI-97, LTg, ME-IV, Protein Gene Products, plan specification, Gene Proteins, EGF, Egf, EFG-R, DmelCG17603, Photoradiations, SCARMD2, Der, DER, Relativisms, Relativism, Cultural Relativism, 6-diaminohexanoic acid, Enisyl, DER/torpedo, hydrochloric acid, TAF1CLK, Bru, data, MPS2, Raw, determination, region or site annotation, protein complex, Ass-1, Phosphorylations, protein, STY, Sty, Ids, protein-containing complex, phosphorylation, CG1921, binding site, CLK/STY, Spry, l(3)rJ812, protein polypeptide chains, l(3)rQ526, native protein, natural protein, polypeptide chain, DmelCG1921, AA408052, Protein, fold, Del(8)44H, protein aggregate, sty, l(3)05959, l(3)j5E11, region, Svc, SIDS, positional, Col4a-1, positional polypeptide feature, gil, INSDC_feature:misc_binding, spry, CLK|STY, Argos, chemical analysis., CG4531, proteins, INSDC_feature:gene, arg, Sry, l(3)05845, dSPRY, DmelCG4531, ASS, Aos, binding_or_interaction_site, DmAos, l(3)rJ472, site, assay, variable, rlt, CS3-3DER/faint little ball, Soluble, Insulin B Chain, EGF receptor binding, biological signaling, D-Egf, single-organism developmental process, Activity, Procedures, determination, region or site annotation, C-erb, Elp-B1, der, RCB1904, Elp-1, mor1, Cue, TGF-alpha receptor binding, Gene, mEET, insuline humaine, protein, Insulin B, EK2-6, protein-containing complex, phosphorylation, binding site, Techniques, method, protein polypeptide chains, polypeptide chain, AI790464, Method, human insulin, method used in an experiment, Insulin, c-erbB, EGFr, NEDD4 WW domain-binding protein 3, hnu, Gene Products, Studies, torpedo/Egfr, TOP, Egf-r, d-egf-r, protein aggregate, Technique, foton, epidermal growth factor, Chain, EGF-R, positional, insulin, transforming growth factor alpha receptor ligand, epidermal growth factor receptor ligand, URG, Lichtquant, EGFR binding, top, Torpedo/DER, proteins, procedures, LPS-induced TNF-alpha factor homolog, flb, top/flb, MCF7 cell, genetic, LITAF-like protein, Study, transforming growth factor alpha receptor binding, Iletin, insulin human, HOMG4, Methodological Studies, Insulin recombinant, l(2)57EFa, signaling process, EGF receptor ligand, photon, site, D-EGFR, l(2)57Ea, constitutitional genetic, MCF-7 cell, MCF 7 cell, single organism signaling, gamma, DER1, Elp-B1RB1, insulinum humanum, data, Regular, Elp, Data Set, l(2)09261, protein complex, dEGFR1, DEgfr, Arts, Proteins, familial, Phosphorylations, Maps, Light, Procedure, CG10079, Cell, Regular Insulin, development, torpedo/egfr, insulin (recombinant), transforming growth factor alpha, native protein, Sodium Insulin, DmelCG10079, natural protein, chemical analysis, Protein, Insulin A Chain, Sodium, Novolin, techniques, DER/top, Soluble Insulin, Urogastrone, region, egfr, Industrial, Exubera, HD-33, El, Industrial Arts, positional polypeptide feature, top/DER, INSDC_feature:misc_binding, DER/EGFR, EGFR, EGfr, EgfR, INS, dEgfr, insulina humana, Epidermal growth factor, DER flb, Epistemology., Methodological, Torpedo/Egfr, Methodological Study, signalling, Degfr, Protein Gene Products, plan specification, Gene Proteins, MCF7, EGF, Egf, EFG-R, light quantum, signalling process, binding_or_interaction_site, DEGFR, l(2)57DEFa, l(2)05351, Der, DER, dEGFR, inherited genetic, assay, DmHD-33, TGFalpha receptor binding, hereditary, General activity, DER/torpedo, methodology, Estrogen-enhanced transcript proteinDER/faint little ball, Elp-B1RB1, EGF receptor binding, Elp, D-Egf, l(2)09261, C-erb, dEGFR1, DEgfr, Elp-B1, der, RCB1904, Elp-1, mor1, TGF-alpha receptor binding, EK2-6, CG10079, torpedo/egfr, transforming growth factor alpha, DmelCG10079, AI790464, c-erbB, EGFr, torpedo/Egfr, Cell., TOP, Egf-r, DER/top, d-egf-r, Urogastrone, epidermal growth factor, egfr, EGF-R, transforming growth factor alpha receptor ligand, HD-33, El, top/DER, epidermal growth factor receptor ligand, URG, DER/EGFR, EGFR, EGfr, EgfR, dEgfr, EGFR binding, Epidermal growth factor, DER flb, top, Torpedo/DER, Torpedo/Egfr, flb, top/flb, Degfr, MCF7 cell, MCF7, transforming growth factor alpha receptor binding, EGF, Egf, EFG-R, HOMG4, l(2)57EFa, DEGFR, l(2)57DEFa, l(2)05351, EGF receptor ligand, Der, DER, D-EGFR, dEGFR, l(2)57Ea, DmHD-33, TGFalpha receptor binding, DER/torpedo, MCF-7 cell, MCF 7 cell, DER1387truePhosphoproteomics of EGF stimulated MCF7 cellsPhosphoproteomic analysis of EGF stimulated MCF7 cells. This dataset is the basis for the development of modeling of signaling networks. A fundamental challenge in biology is to delineate the signaling pathways that govern cellular responses to genetic and environmental cues. Phosphoproteomics is an emerging technology that provides key data on activity levels of proteins under conditions of interest. However, the interpretation of these data is hampered by the lack of methods that can translate site-specific information into global maps of active proteins and signaling networks. To meet this challenge, we propose PHOTON, a method for integrating phosphorylation data with protein-protein interaction networks to identify active proteins and pathways and pinpoint functional phosphosites. We demonstrate the utility of PHOTON by applying it to interpret existing and novel phosphoproteomic datasets related to EGF and insulin responses. PHOTON substantially outperforms the widely-used cutoff approach, providing highly reproducible predictions that are more in line with current biological 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