Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_02_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_03_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_11_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_11_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_06_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_03_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_07_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_12_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_06_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_03_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_09_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_09_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_12_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_04_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_07_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_06_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_03_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_06_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_05_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_05_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_03_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_04_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_04_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_12_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_02_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_11_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_10_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_08_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_03_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_02_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_11_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_01_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_12_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_09_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_09_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_01_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_12_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_01_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_04_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_08_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_07_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_01_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_02_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_10_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_08_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_05_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_08_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_05_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_04_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_02_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_10_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_07_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_10_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_01_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_11_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_10_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_12_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_08_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_09_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_01_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_02_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_11_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_08_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_07_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_09_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_10_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_A_07_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2167_B_06_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_B_04_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2168_A_05_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_A_06_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/E2166_B_05_a.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD002665/MaxQuantOutput.zipprimaryOK200005170henrik.daub@evotec.comSebastian WandingerMass SpectrometryShotgun proteomicsNot availablePhosphoproteomicsErbb4Erbb3http://www.ebi.ac.uk/pride/archive/projects/PXD002665B CellCell CulturePrior to stimulation, Ba/F3 cells were washed twice with medium without IL3 and seeded at 1 x 105 cells/mL in fresh medium without IL3. 1 h later, cells were treated with either 100 ng/mL NRG1 in PBS or vehicle control for 30 min. Cells were then put on ice, harvested by centrifugation, washed twice with PBS and lysed in ice-cold lysis buffer (8 M urea, 50 mM Tris-HCl pH 8.2, 75 mM NaCl, 5 mM EDTA, 5 mM EGTA, 10 mM sodium pyrophosphate, 10 mM glycerol phosphate, 10 mM sodium fluoride, 2.5 mM sodium orthovanadate, protease inhibitor cocktail Complete Mini (Roche), phosphatase inhibitor cocktails 2 and 3 (Sigma)). Cell extracts were sonicated three times for 1 minute on ice and cleared by centrifugation. Protein concentrations were determined (Bradford assay, Biorad). For each treatment sample 2 mg of total lysate protein were reduced with 10 mM dithiothreitol for 30 min then alkylated in the presence of 55 mM iodoacetamide for 30 min in the dark. Endoproteinase Lys-C (Wako) was added at an enzyme-to-substrate ratio of 1:200 and incubated for 4 h at room temperature. Samples were thereafter diluted 1:4 with 20 mM Tris-HCl pH 8.2 before adding trypsin (Promega) at an enzyme-to-substrate ratio of 1:200 followed by overnight incubation. The resulting peptide mixtures were acidified by the addition of TFA to a final concentration of 0.5% and subsequently desalted using C18 Sep-Pak columns (50 mg sorbent weight, Waters). Peptides were eluted with 50% acetonitrile (ACN), 0.5% acetic acid, snap-frozen in liquid nitrogen and lyophilized. All samples were then chemically labeled with the respective mTRAQ isotopic variants (ABSciex) according to the manufacturer’s instructions. Equal amounts of differentially mTRAQ-labeled peptides were then combined, frozen in liquid nitrogen, lyophilized and desalted via C18 Sep-Pak columns (500 mg sorbent weight, Waters). Peptide samples peptides were fractionated by high pH reversed phase chromatography as described by Wang et al. Briefly, peptides were reconstituted in 20 mM ammonium formate (pH 10, buffer A), loaded onto an XBridge C18, 250 × 4.6 mm analytical column (Waters) operated with the ÄKTA Purifier system (GE Healthcare), and separated by applying a segmented gradient increasing the ACN concentration from 7% to 30% buffer B (buffer A with 80% ACN) over 15 min followed by a 5 min gradient to 55%. Collected peptide fractions were then combined in a non-linear way as described to generate 12 samples with similar peptide amounts. Peptide samples were frozen in liquid nitrogen, lyophilized, reconstituted in 0.1 % TFA and desalted using C18 Sep-Pak columns. Enrichment of phosphopeptides was performed according to a protocol by Mertins et al. Phosphopeptides were eluted onto the C18 material by washing twice with a 500 mM K2HPO4 solution. The C18-bound phosphopeptides were washed with 0.1% formic acid, eluted with 50 % ACN, 0.1% FA, concentrated in a VacufugeTM (Eppendorf) and reconstituted in 0.1% formic acid before LC-MS analysis. All LC-MS analyses were performed on an LTQ Orbitrap Velos (Thermo Fisher Scientific). The samples were loaded by an Easy nano LC II system (Thermo Fisher Scientific) on a 20 cm fused silica column (New Objective) packed in-house with reversed phase material (Reprosil-Pur C18-AQ, 3 µm, Dr. Maisch GmbH) at a maximum pressure of 275 bar. The bound peptides were eluted by a gradient from 10% to 60% of solvent B (80% acetonitrile, 5% DMSO, 0.5% acetic acid) at a flow rate of 200 nl/min and sprayed directly into the mass spectrometer by applying a spray voltage of 2.2 kV using a nanoelectrospray ion source (ProxeonBiosystems). The mass spectrometer was operated in the data dependent mode to automatically switch between MS and MS/MS acquisition. To improve mass accuracy in the MS mode, the lock-mass option was enabled as described. Full scans were acquired in the orbitrap mass analyzer at a resolution R = 60,000 and a target value of 1,000,000 ions. The fifteen most intense ions detected in the MS scan were selected for collision induced dissociation in the LTQ at a target value of 5000 ion counts. The resulting fragmentation spectra were also recorded in the linear ion trap. To improve complete dissociation of phosphopeptides, the multi-stage activation option was enabled for all MS-analyses of phosphopeptide-enriched samples by applying additional dissociation energy on potential neutral loss fragments (precursor ion minus 98, 49 and 32.7 m/z). Ions that were once selected for data-dependent acquisition were dynamically excluded for 90 sec for further fragmentation. General used mass spectrometric settings were: no sheath and auxiliary gas flow; heated capillary temperature, 240°C; normalized collision energy, 35% and an activation q = 0.25.PrideNot availablephosphorylated residueAll raw files acquired in this study were collectively processed with the MaxQuant software suite (version 1.4.3.2) for peptide and protein identification and quantification using a murine Uniprot database (version 01 2014) including human ErbB3 and ErbB4. Carbamidomethylation of cysteine was set as a fixed modification and oxidation of methionine, N-terminal acetylation and phosphorylation on serine, threonine and tyrosine were allowed as variable modifications. Moreover, mTRAQ ∆0, ∆4 and ∆8 were set as modifications. The minimum required peptide length was seven amino acids and up to two missed cleavages and three labeled amino acids were allowed. A false discovery rate (FDR) of 0.01 was selected for both protein and peptide identifications. The match between runs option for a time window of 0.5 min was enabled for corresponding fractions in replicate experiments. All MS raw data and MaxQuant output files will be made available upon request.ProteomicsHenrik DaubLTQ Orbitrap VelosEvotec (München) GmbHPARTIALMus Musculus (mouse)sebastian.wandinger@evotec.com26745281 Wandinger SK, Lahortiga I, Jacobs K, Klammer M, Jordan N, Elschenbroich S, Parade M, Jacoby E, Linders JT, Brehmer D, Cools J, Daub H. Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling. PLoS One. 2016 Jan 8;11(1):e0146100. eCollection 2016 10.1371/journal.pone.0146100BiologicalBiomedicalEvotec517The four members of the epidermal growth factor receptor (EGFR/ERBB) family form homo- and heterodimers which mediate ligand-specific regulation of many key cellular processes in normal and cancer tissues. While signaling through the EGFR has been extensively studied on the molecular level, signal transduction through ERBB3/ERBB4 heterodimers is less well understood. Here, we generated isogenic mouse Ba/F3 cells that express full-length and functional membrane-integrated ERBB3 and ERBB4 or ERBB4 alone, to serve as a defined cellular model for biological and phosphoproteomics analysis of ERBB3/ERBB4 signaling. ERBB3 co-expression significantly enhanced Ba/F3 cell proliferation upon neuregulin-1 (NRG1) treatment. For comprehensive signaling studies we performed quantitative mass spectrometry (MS) experiments to compare the basal ERBB3/ERBB4 cell phosphoproteome to NRG1 treatment of ERBB3/ERBB4 and ERBB4 cells. We employed a workflow comprising differential isotope labeling with mTRAQ reagents followed by chromatographic peptide separation and final phosphopeptide enrichment prior to MS analysis. Overall, we identified 9686 phosphorylation sites which could be confidently localized to specific residues. Statistical analysis of three replicate experiments revealed 492 phosphorylation sites which were significantly changed in NRG1-treated ERBB3/ERBB4 cells. Bioinformatics data analysis recapitulated regulation of mitogen-activated protein kinase and Akt pathways, but also indicated signaling links to cytoskeletal functions and nuclear biology. Comparative assessment of NRG1-stimulated ERBB4 Ba/F3 cells revealed that ERBB3 did not trigger defined signaling pathways but more broadly enhanced phosphoproteome regulation in cells expressing both receptors. In conclusion, our data provide the first global picture of ERBB3/ERBB4 signaling and provide numerous potential starting points for further mechanistic studies.Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling.Wandinger Sebastian K SK, Lahortiga Idoya I, Jacobs Kris K, Klammer Martin M, Jordan Nicole N, Elschenbroich Sarah S, Parade Marc M, Jacoby Edgar E, Linders Joannes T M JT, Brehmer Dirk D, Cools Jan J, Daub Henrik Hsignalling., Erbb-3, C76256, c-erbB-4, biological signaling, c-erbB-3, ALS19, determination, c-erbB3, number, presence, p85-sErbB3, Erbb3r, ErbB-3, p180-ErbB3, count in organism, LCCS2, signalling process, signaling process, erbB3-S, MDA-BF-1, chemical analysis, nuc-ErbB3, p45-sErbB3, assay, quantitative, p180erbB4, Her3, Her4, HER4, single organism signaling, presence or absence in organism, HER3Erbb-3, Bru, IPP2A2, para Tyrosine, ALS19, Raw, Aminosaeure, Amino acid, L-Threonine, protein, phosphorylation, Long Term, 2-Amino-3-hydroxypropionic acid, ErbB-3, 5730420M11Rik, peptide, Polypeptides, protein polypeptide chains, L-Isomer Methionine, Methionine, ClvPrd, peptido, MDA-BF-1, Min, Software Engineering, protein aggregate, Effect, Computer Program, Threonin, DmelCG42273, Svc, SET, F, amino acids, peptides, TAF-I, M, Open, phosphatase 2A inhibitor I2PP2A, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, Computer Programs and Programming, min, mAPC, proteins, Y, DmelCG4299, AI047805, set, IGAAD, 2-amino-3-hydroxypropanoic acid, DmelCG10574, data., Tyr, erbB3-S, Half Cystine, Racemethionine, Long-Term Effects, ratio, phapii, Zinc Cysteinate, Aminokarbonsaeure, acetylation, 2-Amino-4-(methylthio)butyric acid, 2-Amino-3-(p-hydroxyphenyl)propionic acid, Longterm Effect, Dmel_CG7826, StF-IT-1, para-Tyrosine, not genetically inherited, p85-sErbB3, Source Softwares, alpha-amino carboxylic acids, Software Tools, Programs, Tyrosine, Program, Computer Applications, LCCS2, 3-Hydroxyalanine, Dm1, Computer Applications Software, Computer Applications Softwares, Methionin, methionine, Softwares, Hmet, tyrosine, Dmel_CG7835, Mnb, MNB, Amino Acid, Acid, Software Applications, Serine, HLA-DR-associated protein II, Amino acids, DI-2, Source Software, I-2Dm, L-isomer, proportionality, rate, L-Cysteine, CG4299, inhibitor of granzyme A-activated DNase, AW124434, human, L isomer, I-2PP1, Applications, TAF-IBETA, L Serine, TAF-Ibeta, L-Tyrosine, Acids, Polypeptide, L-Serine, i2pp2a, Liquimeth, time, Computer Software Applications, human being, Cysteine Hydrochloride, 2-amino-4-(methylsulfanyl)butanoic acid, False, Effects, Aminocarbonsaeure, L Isomer, Computer, alpha-amino acid, protein-containing complex, Erbb3r, PHAPII, CG7826, period, polypeptide chain, template-activating factor I, CG7835, L-Methionine, CG42273, Del(8)44H, Half-Cystine, Pedameth, Application, study, Open Source Softwares, proportion, Longterm, Software Application, L Cysteine, ipp2a2, Open Source Software, Acetylations, 2pp2a, L Threonine, Long-Term, man, CG10574, Computer Software Application, 2PP2A, 2-amino-4-(methylthio)butanoic acid, Tools, L Tyrosine, taf-ibeta, dSET, dSet, peptidos, Long-Term Effect, Tyrosin, metionina, p180erbB4, Applications Software, serine, Open Source, DYRK1, Computer Software, DL-Methionine, protein complex, igaad, Phosphorylations, alpha-amino acids, L-Isomer, Peptide, Tool, p180-ErbB3, polypeptide, Serin, Software Tool, native protein, natural protein, I-2PP2A, tirosina, Protein, Dm I-2, Long Term Effects, I2PP2A, nuc-ErbB3, p45-sErbB3, Dyrk1, Software, Data Base, Met, AU020952, C76256, c-erbB-4, Col4a-1, c-erbB-3, c-erbB3, CC1, Engineering, Amino, Longterm Effects, ME-IV, Computer Programs, dSET/TAF-Ibeta, 2610030F17Rik, Applications Softwares, alpha-amino-gamma-methylmercaptobutyric acid, quotient, Peptid, threonine, variable, AA407739, Her3, Her4, HER4, HER3projections, Forms, malignant Growth, Erbb-3, extracellular signal-regulated kinase activity, GrpL, PRKBA, pp44mapk, GRPL, Akt/PKB, Kinship, CRKII, DAKT1/PKB, Elp-B1, der, Elp-1, Errb1, AKT1, p38-alpha, phosphorylation, p38MAPK, p38a, PIG61, ErbB-3, Hog, p38ALPHA, Receptor Mediated Signal Transduction, dmTAF[[II]]230, Pro-NRG1, Polypeptides, LeMPK3, epidermal growth factor-activated receptor activity, p44mpk, hnRNP A2/B1, Dp38, Life Cycle, Analysis, Cell Signaling, Work Flow, SAPK2, Mpk34C, MST131, p38B, p38A, average, Neuregulin 1, mapk14a, Kinship Network, TFIID TAF250, NDF Protein, Analyses, pp42, cel, hrp40, Tissue, Pathways, hnRNP36, Dm p38b, Hrb87Fa, flb, CA, Hrb85CD, RacPK, hrp36, Grf40, dMKK3, 9030024J15Rik, Signal Transduction Pathways, SMDF, HRG, GRBLG, ESTS:186F5S, single organism signaling, DmMPK2, malignancy, Ligand, dTAF[[II]]230, Pathway, anatomical protrusion, Elp, DEgfr, 6.3.2.-, csbp, ERK-2, TAF200, integral to membrane, heregulin, Normalcy, PMK-2, RAC-PK-alpha, PMK-1, p85-sErbB3, Spectrum Analysis, signal transduction by trans-phosphorylation, PMK-3, Hrb87f, CSBP, torpedo/egfr, AKT/PKB, LCCS2, Workflows, Double ring-finger protein, shelf, Cellular, p-Akt, D-MPK2, GRAP-2, egfr, DmelCG5475, HRGalpha, Mek3, MEK3, DMEK3, HD-33, El, Sensory and motor neuron-derived factor, EGFR, DER/EGFR, EGfr, EgfR, Spectrometry, DER flb, Torpedo/Egfr, c-Crk, projection, dAKT/dPKB, PKB/dAKT, ridge, Degfr, CSBP2, CSBP1, signaling pathway, Taf250, MITOGEN-ACTIVATED PROTEIN KINASE, Proliferation, DEGFR, l(2)05351, Csbp2, Mouse, Csbp1, mitogen-activated protein kinase 1, cancer, Work Flows, humans, TAF230, RAC-ALPHA, D-p38 MAPK, DmelCG4006, localised, D-Egf, proto-oncogene c-ErbB-1, lamellae, cell type cancer, number, F14N23.9, ARIA, mENA, EK2-6, Isotope-Coded Affinity, Normalcies, Exip, process of organ, NRG1 Protein, Erbb3r, lamella, PRKM15, Signal Transduction, dMPK2, p38 MAPK, PRKM14, EGFr, Egfr, sapk2a, torpedo/Egfr, TOP, Number Growth, Isotopically-Coded Affinity, neoplasm, EXIP, malignant tumour, ERK, Normalities, PRKM1, p38beta, PRKM2, Hrp36, dTAF[[II]]250, JTV1, Differentiation Factor, p38Ka, cell, ligand, p38Kb, NDF, Signal, top, Signal Pathways, AI848995, BC023857, Signal Transduction Pathway, D230005F13Rik, GRB2L, dTAF250, CG12749, AKT, Akt, peptidos, HRP36, STK26, p38-2, laminae, Signal Pathway, p180erbB4, myelin basic protein kinase activity, Elp-B1RB1, Dp38b, signalling., Dp38a, RING finger protein 19A, Individual Health, SAPK2A, Family Research, nrg1-A, akt, TGF-alpha receptor activity, ERBB, dEGFR1, anatomical process, Breast cancer cell differentiation factor p45, Phosphorylations, Receptor-Mediated Signal Transductions, Glial Growth Factor, MAP-2 kinase activity, DAkt1, BG:DS00004.13, DAKT1, Cell, neu, dTAF230, Family Members, polypeptide, DmMKK3, PKB, MT, CWS6, Stable Isotope, p38MAPKK, GGF2, chemical analysis, PKB-ALPHA, TAF[[II]]250/230, p45-sErbB3, CG4006, DER/top, signalling cascade, p38 beta, Mass Spectrum Analyses, organ process, Dakt1, Taf[[II]]250, C76256, primary cancer, c-erbB3, P42MAPK, Crk1, Crk3, wa-2, Isotope Labeling, CSPB1, malignant tumor, Isotopically-Coded, signalling, processes, 38 kDa DNA polymerase delta interaction protein, dAkt/PKB, signalling process, D-MKK3, CRK1, Families, Erbb, regulation, quantitative, Relatives, Data Analyses, thymoma viral proto-oncogene, DER/faint little ball, Networks, Signal Transductions, ALS19, determination, sapk2, Mpk2, Mpk3, Crko, p42mapk, D-p38, Cell Growth in Number, Crk-II, p38 alpha, peptide, ClvPrd, peptido, AI552599, MDA-BF-1, kinase-related transforming protein, Cell Number Growth, mitogen-activated protein kinase activity, Q14, Q16, d-egf-r, RK, mpk2, Isotopically-Coded Affinity Tagging, Family Life Cycle, signal transduction by protein phosphorylation, Mass Spectrum Analysis, Growth, DMKK3, peptides, MEK3/MKK3, neoplasm (disease), membrane region, PKB|Akt, MP kinase activity, Dmp38a, AHA1, malignant neoplasm, Dmp38b, papilla, signaling process, erbB3-S, MBP kinase II activity, DmelCG12749, P11, RCB0805, D-EGFR, Transductions, 6030402G23Rik, house mouse, Family Life Cycles, CG5475, Tagging, Stable Isotope Labeling, NISBD2, DER1, PKB alpha, MAP kinase 2 activity, dakt, Wa5, l(2)09261, lamina, mouse, signal transduction by conformational transition, flanges, ERK1, ERK2, Erk2, A230093K24Rik, Hrb2, TAFII-250, membranous organ component, l(3)89Bq, TAF250/230, CG10079, D-P38a, GrbX, AKT1 kinase, Spectroscopy, D-p38b, D-p38a, signaling cascade, PKB/Akt, PKB/AKT, TAFII250, protein kinase B alpha, p41mapk, dAkt, dAKT, wa2, Syn, MAPK, organ system cancer, Acetylcholine receptor-inducing activity, P38, Individual, Filiation, C14orf3, DAkt, Transduction, CG12244, HRB87F/hrp36, l(3)04226, DPKB, membrane of organ, GADS, pAkt, JTV-1, mice, shelves, System, dEgfr, HRB87F, Neuregulin-1, Mona, p38alpha, p38, Prkm15, proto-oncogene c-Akt, CG17603, TAF[[II]], Prkm14, protein kinase B, Proto-oncogene c-Crk, Life Cycles, Health, Dakt, spine, SR3-5, p41, p40, dPKB, l(2)57DEFa, Cell Number, dEGFR, DmelCG12304, Polypeptide, DmHD-33, 186F5S, receptor tyrosine-protein kinase erbB-1, F14N23_9, DRAC-PK85, Signal Transduction Systems, biological signaling, d230, l(1)G0252, Family Member, Heregulin, CG7393, C-erb, GGFII, Receptor-Mediated, mor1, Signal Transduction System, dTAFII250, Network, Spectrum Analyses, EfW1, presence, protrusion, CrkIII, p38Hog, Dpkb, dp38a, dp38b, Gads, dmTAF1, Taf230, integral component of membrane, Hgl, HGL, c-erbB, Mass, EGF receptor activity, Egf-r, p42-MAPK, Mass Spectroscopy, TAF250, Mkk3, MKK3, EGF-R, Taf200, HRGA, Research, DmelCG12244, neu Differentiation Factor, Torpedo/DER, Taf1p, ridges, p42 mitogen-activated protein kinase activity, Crk-III, ATP:protein phosphotransferase (MAPKK-activated) activity, top/flb, signalling pathway, cell proliferation, GGF, GRID, Glial growth factor, Stable, l(2)57EFa, Isotope-Coded Affinity Tagging, region of membrane, DRAC-PK, signal transduction by cis-phosphorylation, ATMPK1, l(2)57Ea, HRG1, Kinship Networks, TAF, Family, statistical analysis, Multiplication, membrane, data, TAF[[II]]250, Cellular Proliferation, DMPK2, malignant, anon-sts23, Ba/F3, l(3)84Ab, P11/Hrb87F, NRG-1, Labeling, Peptide, Crk-I, DMKK3/lic, DmelCG7393, p180-ErbB3, p38delta, Isotope, count in organism, epidermal growth factor receptor activity, Neu differentiation factor, DmelCG10079, Mus, Receptor-Mediated Signal Transduction, p230, group 2, malignant neoplasm (disease), Systems, nuc-ErbB3, whole membrane, MBP kinase I activity, TFIID, D-Akt, focal, flange, Isotope Coded Affinity Tagging, BA/F3, serine-threonine kinase Akt, Mass Spectrum, c-erbB-4, transmembrane, c-erbB-3, TAF[[II]]230, top/DER, akt1, Normality, MSTP131, dAkt1, mitogen activated kinase activity, DRAC-PK66, Mxi2, Sapk2A, ERBB1, TAF[II]250, MAPK2, Affinity Tagging, GGF Protein, dp38, Dorfin, process, NRG1-IT2, Egf, dakt1, EFG-R, DmelCG17603, mxi2, Errp, malignant neoplastic disease, Data, ERT1, PKBalpha, Cell Multiplication, Der, DER, Isotope-Coded, processus, Peptid, BG:DS00797.3, dAKT1, transforming growth factor-alpha receptor activity, assay, Rac, RAC, DER/torpedo, Her3, HER1, Her4, HER4, MAP kinase 1 activity, HER3, TAF1, presence or absence in organismsignalling., Erbb-3, C76256, c-erbB-4, biological signaling, c-erbB-3, ALS19, determination, c-erbB3, number, presence, p85-sErbB3, Erbb3r, ErbB-3, p180-ErbB3, count in organism, LCCS2, signalling process, signaling process, erbB3-S, MDA-BF-1, chemical analysis, nuc-ErbB3, p45-sErbB3, assay, quantitative, p180erbB4, Her3, Her4, HER4, single organism signaling, presence or absence in organism, HER3sodium salt, ammonium formate, bar-h1, dalpha-SNAP, 13C-labeled, ion, CASP-1, magnesium formate, Apaf-1, zinc salt, Solvent, (ethylenedinitrilo)tetraacetic acid, dmTAF[[II]]230, M(3L)i, E260, T22F8_160, ATGPR7, azanium, B1, SEC, HCL-C, Extracts, 1, HRR-1, 2, NEPII, germacrene A synthase activity, Sodium Ion, SEH, dJ1068F16.2, WMS, SEP, (R*, C79325, hac-1, cel, M, N, dimethyl sulphoxide, Fluoride, Acetic Acid Glacial, sEP, salt, decreased, scientific observation, D1, Acn, MeCO2H, n, D9, HRG, Ammonium(1+), nickel salt, SGS, dTAF[[II]]230, chronic obstructive lung disease [Ambiguous], Caspase-1 subunit p10, HRR1, cobalt (+2) salt, anon-53Fa, 2'', breast sarcoma, not genetically inherited, DmelCG7788, ACMICD, CHRONIC OBSTRUCTIVE AIRWAY DIS, (CH3)2SO, common salt, Glacial, sodium (4:1:1) salt, magnesium salt, BH1, hrr1, activation, dark/hac-1/dapaf-1, rpS17, Chronic obstructive lung disease, HRGalpha, FU, formate, lysed material, study protocol, Ossin, nitrogen, Taf250, OBSTRUCTIVE PULMONARY DISEASE (COPD), RIC4, Fu, bacteriolytic toxin activity, ammonium (4:1) salt, HH, Extract, DrICE, developmental stage, number, 2-trans, ARIA, CHRONIC OBSTRUCTIVE PULM DIS, precursor, Chronic obstructive pulmonary disease NOS, R*)-, body system, CG7826, Hh, mass-to-charge ratio, Chronic obstructive pulmonary disease finding, Ion Level, ammonium cation, PULMONARY DISEASE (COPD), M(3)i, CG7835, system, sulfinylbis(methane), anatomical systems, dTAF[[II]]250, 2'''-(ethane-1, Acinus, Hydrogen chloride, thallium (+1) salt, cell, PCE-2, rubidium salt, pk18, ions, study assay, MBR, acinusL, dTAF250, Fluoristats, hairy cell leukemia, Caspase-1 subunit p20, ATGRP7, acinusS, xfor, ATGRP8, PTBR, Chronic, peptidos, Kb, PTHB1, Ki, inhibitors, measuring, dark/dapaf-1/hac-1, AcOH, DmelCG6625, nrg1-A, 1-(14)C-labeled, chronic obstructive airways disease NOS, Mell1, NH4+, copper (+2) salt, COLD - Chronic obstructive lung disease, buffer, (+)-(10R)-germacrene A synthase activity, mKIAA0670, dTAF230, APAF1, Temperatures, native protein, DmelCG5529, carbonyldiamide, Hac-1, C18, GGF2, cupric formate, chemical analysis, barH1, BPA, BcDNA:RE44119, MFS1, Sodium, chronic airway obstruction, NaCl, chronic obstructive, aluminum formate, Cleland's, Taf[[II]]250, AU020952, FXR, holin, Separations, M(3)q, GR-RBP7, GR-RBP8, Na, dimethyl sulfoxide, Natrium, ethanenitrile, azote, Interleukin-1 beta-converting enzyme, anon-EST:Posey48, plan specification, ACETIC ACID, chronic obstructive lung disease (disorder), M(3L)i[55], quotient, quantitative, Sodium 23, ADRB2R, NEP2, Ethanoic acid, reversed, Rps17, T22F8.160, NCMe, Il-3, Chronic Airflow Obstructions, DmelCG6829, classic hairy cell leukaemia, Nl1, zinc formate, CG7788, crice, lead salt, protein, bA416N4.2, Csfmu, Bar H1, peptide, BETA2AR, ammonium tetraformate, anon-WO0134654.19, ClvPrd, peptido, DmelCG4637, IL-3, Apaf1, Chronic Obstructive Pulmonary Disease (COPD), protein aggregate, COLD (chronic obstructive lung disease), peptides, NEC in ICD9CM_2006, E927b, 2610036I19Rik, hypoplasia, arc, mAPC, IBP, ark, T1, Chronic airflow limitation, lithium salt, Sputolysin, ICE, GLYCINE RICH PROTEIN 7, AI316800, C16orf53, RCB0805, ethoic acid, blood capillary, (ethane-1, Bladder pain syndrome, GPHYSD2, ammonium (2:1) salt, activation., CHRONIC, (+)-germacrene A synthase activity, ethylenediaminetetraacetate, obstructive lung disease, iCE, D-Apaf-1, drice, rip14, Dmel_CG7826, Th, TAFII-250, TAF250/230, Airflow Obstructions, Sodium-23, NH4(+), TAFII250, Cleland, weight, MMEL2, drIce, CHRONIC OBSTRUCTIVE, bacteriocin activity, GAS, nickel (+2) salt, Dmel_CG7835, Acetic acid, MNB, CHRONIC OBSTRUCTIVE LUNG DIS, ammonium salt, (methanesulfinyl)methane, Painful Bladder Syndrome, mast cell growth factor, P45, cobaltous formate, alphaSnap, 3-Butanediol, AW124434, CG17603, merged with, TAF[[II]], apaf-1, lysin activity, COPD - Chronic obstructive pulmonary disease, copper salt, p45, 1728, Bladder Pain Syndrome, Ammonium, dalphaSNAP, Dapaf-1/HAC-1, cesium salt, CH3-COOH, dTAFII250, PLEXIN-B1, ethylenediaminetetraacetic acid, Cold, Methanecarboxylic acid, Hac1, M(3)S33, Bar-H1, Sodium Fluorides, polypeptide chain, dmTAF1, subnumerary, ECTOL1, Hgl, 14C-labeled, l(3)77ABa, l(3)77ABc, tiny, RIC-4, Pro-Mega, TAF250, Cold Temperatures, CG2916, ammonium ion, Selb, dapaf-1, Minute, dapaf, calcium formate, 2-diyldinitrilo)tetraacetic acid, GGF, inhibidor, DmelCG3922, Zymafluors, IL3, TAF, 2-iodo-, Controlled, small, Controlling, DYRK1, COAD - Chronic obstructive airways disease, TAF[[II]]250, dSNAP, protein complex, 6-trans-farnesyl-diphosphate diphosphate-lyase [(+)-germacrene-A-forming] activity, Ba/F3, l(3)84Ab, NRG-1, dsnap, strontium salt, acido edetico, [HCl], Axin, count in organism, secret agent, HOAc, p230, Dyrk1, CES2A1, Dark, connected anatomical system, Dimethyl sulfoxide, tetrasodium pyrophosphate, ACETONITRILE, Temperature, 10^[-9], Ossins, TAF[[II]]230, ammonium, MSTP131, CC1, Tripcellim, phosphoric monoester hydrolase activity, acide acetique, dApaf-1/DARK/HAC-1, sample population, chromic formate, Interleukin-1 beta convertase, DmelCG17603, Pressures, concentration, SSKS, 3.4.22.36, calcium salt, Bar, cold (chronic obstructive lung disease), INS No. 260, edetic acid, Chronic Obstructive Lung Disease, 1700112N14Rik, dAPAF-1, TAF1, sodium chloride, presence or absence in organism, DIMETHYL SULFOXIDE, IL1BC, MeCN, cadmium salt, PLXN5, Vinegar, Ethylenediaminetetraacetic acid, bar, chronic obstructive pulmonary disease (COPD), Basodexan, SeP, Polypeptides, protein polypeptide chains, hydrogen chloride, CEH, cobalt(II) formate dihydrate, CH3-C#N, Chronic irreversible airway obstruction, Urea, GRP8, GRP7, Barh1, Il1bc, MST131, Fluoristat, Sep, Divorced, TFIID TAF250, sarcoma of breast, 32P2-labeled cpd, sec, CAFL - Chronic airflow limitation, proteins, Divorces, IL-1BC, SNAP-25, AI047805, PA1, Wasserstoffchlorid, column, disease (COPD), ACN, sample, fused to, stage, autolysin activity, RIP14, SMDF, phosphatase, M(3)RpS17, Dimethylsulfoxid, acidum edeticum, B2AR, DMSO, BZRP, dmso, Trypsin/K, TAF200, l(2)SH0173, heregulin, GAST, CG4637, PBS, PBR, Dm1, Stickstoff, M(3)i(55), Chlorwasserstoff, sodium, leukemic reticuloendotheliosis, Airflow Obstruction, 6-trans-farnesyl-diphosphate diphosphate-lyase (germacrene-A-forming) activity, natrium, CG6829, GLYCINE-RICH PROTEIN 8, Chronic Obstructive Airways Disease, Ethylic acid, MCGF, proportionality, rate, cromium (+3), N'-1, beta Trypsin, Painful bladder syndrome, Cell Extract, F2G1.4, Drice, multipotential colony-stimulating factor, methyl cyanide, chlorane, fused, DRICE, lead (+2) salt, TAF230, hg, BPBS, Cleland Reagent, FUSED, knobbly, MULTI-CSF, nickel formate dihydrate, lead formate, sarcoma of the breast, chlorure d'hydrogene, DrIce, aluminum salt, CAO - Chronic airflow obstruction, Fused, 4-dimercapto-, dimethylsulfoxyde, Carbamide, protein-containing complex, thomson, CG5529, and RNA binding 1, EDTA tetraanion, RNF47, CG42273, CG6625, Carmol, T6K12_14, proportion, 2-Ethane diylbis-(N-(carboxymethyl)glycine), ethylenediamine tetraacetic acid tetraanion, NDF, beta-Trypsin, l(3)dtOA4, methanoic acid, D230005F13Rik, Solution, dimetil sulfoxido, bar-3, NEC, Kochsalz, M(3)i[55], Chromatographies, decahydrate, caspase 3, dApaf-1, barh1, COAD, Clelands Reagent, BG:DS00004.13, chloridohydrogen, potassium formate, CE-2, anhydrous sodium pyrophosphate, backward, acetonitrile, Cell, chronic, B930045J24, polypeptide, hrr-1, tetrasodium salt, Natriumchlorid, TAF[[II]]250/230, (COPD), CAL - Chronic airflow limitation, Sodium Ion Level, T6K12.14, lithium formate, underdeveloped, P-cell-stimulating factor, Dark/Dapaf-1/HAC1, IL-1 beta-converting enzyme, mDRC, ME-IV, Cleland's Reagent, fxr, MeCOOH, anon-WO0182946.19, hydrochloric acid, chronic obstructive pulmonary disease, ethylenediaminetetraacetate tetraanion, Hac-1/Dark, determination, and rna binding 2, SEC9, RPS17, Essigsaeure, Hydrogenchlorid, lysis, sodium diphosphate, M(3)67, halite, sodio, BANF, Glacial Acetic Acid, kinky, chronic obstructive airways disease NOS (disorder), NL1, Min, 2', NL2, Mir, present in fewer numbers in organism, ARK, alpha-SNAP, DmelCG42273, Edetic acid, 2-diyldinitrilo)tetraacetate, reference sample, ion(4-), l(3)67BDo, 2610510L13Rik, Acetic Acid, min, analyzer, copper, SCAN, cloruro sodico, fSAP152, 6030402G23Rik, necrosis, dApaf1, glycine-rich RNA-binding protein 8, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, ratio, rock salt, hematopoietic growth factor, dimethyli sulfoxidum, ice, methylsulfinylmethane, M(3)67C, {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID, classic hairy cell leukemia, ur, PSF, pulmonary disease (COPD), any method, carbamide, Ionen, drICE, Fluorides, ADRBR, low temperature, bar3, chronic obstructive pulmonary disease and allied conditions, HCL, Chronic airway disease, NOS, COPD NOS, Mnb, parent ion, Chronic airway obstruction, l(3)neo56, l(3)neo57, cold, HCl, Rp S17, hac1, MASS, gas, natrii chloridum, organ system, dapaf-1S, Chronic Airflow Obstruction, nanospray, H2NC(O)NH2, dapaf-1L, precursor ion, SR3-5, Acetamide, chronic obstructive airways disease, Eph2, Polypeptide, obstructive pulmonary disease (COPD), 7N, COLD, chronic obstructive lung disease, d230, E-260, DISEASE (COPD), Reagent, GGFII, FBN, circadian rhythm, ACINUS, EfW1, presence, [NH4](+), Buffer, formic acid, Dark/Hac-1/dApaf1, Karbamid, method, potassium salt, Dark/Hac-1/dApaf-1, Pulmonary Disease, reduced, Taf230, HGL, Acide ethylenediaminetetracetique, method used in an experiment, Harnstoff, Level, Separated, HCGF, cloruro de hidrogeno, acide edetique, CH3CO2H, S(O)Me2, Taf200, HRGA, iones, diphosphoric acid, Mrt, chlorure de sodium, inhibiteur, Taf1p, dark, decreased number, Chronic Obstructive, OCTD, edta, lysate, DARK, EDTA, SELP, liquid, cromium (+3) salt, HRG1, mKIAA1278, dArk, Dapaf-1, sodium formate, COPD, disodium pyrophosphate, l(3)hh, data, ng/ml, nickel formate, DBI, 3H-labeled, not elsewhere classified, strontium formate, inhibitor, apaf1, PULM DIS CHRONIC OBSTRUCTIVE, Peptide, Chronic obstructive pulmonary disease finding (finding), sep5, capillary vessel, Phosphopeptide, PKBS, natural protein, Protein, Hydrochloride, TFIID, table salt, GLYCINE-RICH RNA-BINDING PROTEIN 7, Dark/Apaf-I, BA/F3, cyanomethane, WMS2, chronic obstructive airway disease, Separation, E 260, uree, Dops, urea, H4edta, DmelCG2916, TAF[II]250, UREA, CG3922, nitrogeno, NRG1-IT2, Trypure, trisodium pyrophosphate, 11Na, Zymafluor, Ion, Sodium fluoride (NaF), SNAP, joined with, Peptid, BAR, assay, acetic acid, dimethyl sulfur oxide, SCH, coalesced, BarHI, snapprojections, Forms, malignant Growth, Erbb-3, extracellular signal-regulated kinase activity, GrpL, PRKBA, pp44mapk, GRPL, Akt/PKB, Kinship, CRKII, DAKT1/PKB, Elp-B1, der, Elp-1, Errb1, AKT1, p38-alpha, phosphorylation, p38MAPK, p38a, PIG61, ErbB-3, Hog, p38ALPHA, Receptor Mediated Signal Transduction, dmTAF[[II]]230, Pro-NRG1, Polypeptides, LeMPK3, epidermal growth factor-activated receptor activity, p44mpk, hnRNP A2/B1, Dp38, Life Cycle, Analysis, Cell Signaling, Work Flow, SAPK2, Mpk34C, MST131, p38B, p38A, average, Neuregulin 1, mapk14a, Kinship Network, TFIID TAF250, NDF Protein, Analyses, pp42, cel, hrp40, Tissue, Pathways, hnRNP36, Dm p38b, Hrb87Fa, flb, CA, Hrb85CD, RacPK, hrp36, Grf40, dMKK3, 9030024J15Rik, Signal Transduction Pathways, SMDF, HRG, GRBLG, ESTS:186F5S, single organism signaling, DmMPK2, malignancy, Ligand, dTAF[[II]]230, Pathway, anatomical protrusion, Elp, DEgfr, 6.3.2.-, csbp, ERK-2, TAF200, integral to membrane, heregulin, Normalcy, PMK-2, RAC-PK-alpha, PMK-1, p85-sErbB3, Spectrum Analysis, signal transduction by trans-phosphorylation, PMK-3, Hrb87f, CSBP, torpedo/egfr, AKT/PKB, LCCS2, Workflows, Double ring-finger protein, shelf, Cellular, p-Akt, D-MPK2, GRAP-2, egfr, DmelCG5475, HRGalpha, Mek3, MEK3, DMEK3, HD-33, El, Sensory and motor neuron-derived factor, EGFR, DER/EGFR, EGfr, EgfR, Spectrometry, DER flb, Torpedo/Egfr, c-Crk, projection, dAKT/dPKB, PKB/dAKT, ridge, Degfr, CSBP2, CSBP1, signaling pathway, Taf250, MITOGEN-ACTIVATED PROTEIN KINASE, Proliferation, DEGFR, l(2)05351, Csbp2, Mouse, Csbp1, mitogen-activated protein kinase 1, cancer, Work Flows, humans, TAF230, RAC-ALPHA, D-p38 MAPK, DmelCG4006, localised, D-Egf, proto-oncogene c-ErbB-1, lamellae, cell type cancer, number, F14N23.9, ARIA, mENA, EK2-6, Isotope-Coded Affinity, Normalcies, Exip, process of organ, NRG1 Protein, Erbb3r, lamella, PRKM15, Signal Transduction, dMPK2, p38 MAPK, PRKM14, EGFr, Egfr, sapk2a, torpedo/Egfr, TOP, Number Growth, Isotopically-Coded Affinity, neoplasm, EXIP, malignant tumour, ERK, Normalities, PRKM1, p38beta, PRKM2, Hrp36, dTAF[[II]]250, JTV1, Differentiation Factor, p38Ka, cell, ligand, p38Kb, NDF, Signal, top, Signal Pathways, AI848995, BC023857, Signal Transduction Pathway, D230005F13Rik, GRB2L, dTAF250, CG12749, AKT, Akt, peptidos, HRP36, STK26, p38-2, laminae, Signal Pathway, p180erbB4, myelin basic protein kinase activity, Elp-B1RB1, Dp38b, signalling., Dp38a, RING finger protein 19A, Individual Health, SAPK2A, Family Research, nrg1-A, akt, TGF-alpha receptor activity, ERBB, dEGFR1, anatomical process, Breast cancer cell differentiation factor p45, Phosphorylations, Receptor-Mediated Signal Transductions, Glial Growth Factor, MAP-2 kinase activity, DAkt1, BG:DS00004.13, DAKT1, Cell, neu, dTAF230, Family Members, polypeptide, DmMKK3, PKB, MT, CWS6, Stable Isotope, p38MAPKK, GGF2, chemical analysis, PKB-ALPHA, TAF[[II]]250/230, p45-sErbB3, CG4006, DER/top, signalling cascade, p38 beta, Mass Spectrum Analyses, organ process, Dakt1, Taf[[II]]250, C76256, primary cancer, c-erbB3, P42MAPK, Crk1, Crk3, wa-2, Isotope Labeling, CSPB1, malignant tumor, Isotopically-Coded, signalling, processes, 38 kDa DNA polymerase delta interaction protein, dAkt/PKB, signalling process, D-MKK3, CRK1, Families, Erbb, regulation, quantitative, Relatives, Data Analyses, thymoma viral proto-oncogene, DER/faint little ball, Networks, Signal Transductions, ALS19, determination, sapk2, Mpk2, Mpk3, Crko, p42mapk, D-p38, Cell Growth in Number, Crk-II, p38 alpha, peptide, ClvPrd, peptido, AI552599, MDA-BF-1, kinase-related transforming protein, Cell Number Growth, mitogen-activated protein kinase activity, Q14, Q16, d-egf-r, RK, mpk2, Isotopically-Coded Affinity Tagging, Family Life Cycle, signal transduction by protein phosphorylation, Mass Spectrum Analysis, Growth, DMKK3, peptides, MEK3/MKK3, neoplasm (disease), membrane region, PKB|Akt, MP kinase activity, Dmp38a, AHA1, malignant neoplasm, Dmp38b, papilla, signaling process, erbB3-S, MBP kinase II activity, DmelCG12749, P11, RCB0805, D-EGFR, Transductions, 6030402G23Rik, house mouse, Family Life Cycles, CG5475, Tagging, Stable Isotope Labeling, NISBD2, DER1, PKB alpha, MAP kinase 2 activity, dakt, Wa5, l(2)09261, lamina, mouse, signal transduction by conformational transition, flanges, ERK1, ERK2, Erk2, A230093K24Rik, Hrb2, TAFII-250, membranous organ component, l(3)89Bq, TAF250/230, CG10079, D-P38a, GrbX, AKT1 kinase, Spectroscopy, D-p38b, D-p38a, signaling cascade, PKB/Akt, PKB/AKT, TAFII250, protein kinase B alpha, p41mapk, dAkt, dAKT, wa2, Syn, MAPK, organ system cancer, Acetylcholine receptor-inducing activity, P38, Individual, Filiation, C14orf3, DAkt, Transduction, CG12244, HRB87F/hrp36, l(3)04226, DPKB, membrane of organ, GADS, pAkt, JTV-1, mice, shelves, System, dEgfr, HRB87F, Neuregulin-1, Mona, p38alpha, p38, Prkm15, proto-oncogene c-Akt, CG17603, TAF[[II]], Prkm14, protein kinase B, Proto-oncogene c-Crk, Life Cycles, Health, Dakt, spine, SR3-5, p41, p40, dPKB, l(2)57DEFa, Cell Number, dEGFR, DmelCG12304, Polypeptide, DmHD-33, 186F5S, receptor tyrosine-protein kinase erbB-1, F14N23_9, DRAC-PK85, Signal Transduction Systems, biological signaling, d230, l(1)G0252, Family Member, Heregulin, CG7393, C-erb, GGFII, Receptor-Mediated, mor1, Signal Transduction System, dTAFII250, Network, Spectrum Analyses, EfW1, presence, protrusion, CrkIII, p38Hog, Dpkb, dp38a, dp38b, Gads, dmTAF1, Taf230, integral component of membrane, Hgl, HGL, c-erbB, Mass, EGF receptor activity, Egf-r, p42-MAPK, Mass Spectroscopy, TAF250, Mkk3, MKK3, EGF-R, Taf200, HRGA, Research, DmelCG12244, neu Differentiation Factor, Torpedo/DER, Taf1p, ridges, p42 mitogen-activated protein kinase activity, Crk-III, ATP:protein phosphotransferase (MAPKK-activated) activity, top/flb, signalling pathway, cell proliferation, GGF, GRID, Glial growth factor, Stable, l(2)57EFa, Isotope-Coded Affinity Tagging, region of membrane, DRAC-PK, signal transduction by cis-phosphorylation, ATMPK1, l(2)57Ea, HRG1, Kinship Networks, TAF, Family, statistical analysis, Multiplication, membrane, data, TAF[[II]]250, Cellular Proliferation, DMPK2, malignant, anon-sts23, Ba/F3, l(3)84Ab, P11/Hrb87F, NRG-1, Labeling, Peptide, Crk-I, DMKK3/lic, DmelCG7393, p180-ErbB3, p38delta, Isotope, count in organism, epidermal growth factor receptor activity, Neu differentiation factor, DmelCG10079, Mus, Receptor-Mediated Signal Transduction, p230, group 2, malignant neoplasm (disease), Systems, nuc-ErbB3, whole membrane, MBP kinase I activity, TFIID, D-Akt, focal, flange, Isotope Coded Affinity Tagging, BA/F3, serine-threonine kinase Akt, Mass Spectrum, c-erbB-4, transmembrane, c-erbB-3, TAF[[II]]230, top/DER, akt1, Normality, MSTP131, dAkt1, mitogen activated kinase activity, DRAC-PK66, Mxi2, Sapk2A, ERBB1, TAF[II]250, MAPK2, Affinity Tagging, GGF Protein, dp38, Dorfin, process, NRG1-IT2, Egf, dakt1, EFG-R, DmelCG17603, mxi2, Errp, malignant neoplastic disease, Data, ERT1, PKBalpha, Cell Multiplication, Der, DER, Isotope-Coded, processus, Peptid, BG:DS00797.3, dAKT1, transforming growth factor-alpha receptor activity, assay, Rac, RAC, DER/torpedo, Her3, HER1, Her4, HER4, MAP kinase 1 activity, HER3, TAF1, presence or absence in organism00.00.00.00.00.15114127082048118trueQuantitative phosphoproteomics analysis of ERBB3/ERBB4 signalingThe four members of the epidermal growth factor receptor (EGFR/ERBB) family form homo- and heterodimers which mediate ligand-specific regulation of many key cellular processes in normal and cancer tissues. While signaling through the EGFR has been extensively studied on the molecular level, signal transduction through ERBB3/ERBB4 heterodimers is less well understood. Here, we generated isogenic mouse Ba/F3 cells that express full-length and functional membrane-integrated ERBB3 and ERBB4 or ERBB4 alone, to serve as a defined cellular model for biological and phosphoproteomics analysis of ERBB3/ERBB4 signaling. ERBB3 co-expression significantly enhanced Ba/F3 cell proliferation upon neuregulin-1 (NRG1) treatment. For comprehensive signaling studies we performed quantitative mass spectrometry (MS) experiments to compare the basal ERBB3/ERBB4 cell phosphoproteome to NRG1 treatment of ERBB3/ERBB4 and ERBB4 cells. We employed a workflow comprising differential isotope labeling with mTRAQ reagents followed by chromatographic peptide separation and final phosphopeptide enrichment prior to MS analysis. Overall, we identified 9686 phosphorylation sites which could be confidently localized to specific residues. Statistical analysis of three replicate experiments revealed 492 phosphorylation sites which were significantly changed in NRG1-treated ERBB3/ERBB4 cells. Bioinformatics data analysis recapitulated regulation of mitogen-activated protein kinase and Akt pathways, but also indicated signaling links to cytoskeletal functions and nuclear biology. Comparative assessment of NRG1-stimulated ERBB4 Ba/F3 cells indicated that ERBB3 did not trigger defined signaling pathways but more broadly enhanced phosphoproteome regulation in cells expressing both receptors. In conclusion, our data provide the first global picture of ERBB3/ERBB4 signaling and provide numerous potential starting points for further mechanistic studies2016-01-152015-08-05PXD0026654454417363091009010005896989361604889986388067825343052848125541773355511935018840194565795599034634751579595972970448757472155476676370911351317447562173623185962982545774896121697912646904932399461167669157463604232135588NCBITaxon:961512803218297601459432762991363261639101165759983856915693749200130763197106592408187613838039427256314595388531896067227370226745281