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CunninghamNot availableCell CultureFibroblast10 mg of “light”, “medium” and “heavy” lysates were pooled prior to trypsin digestion. Five biological replicates were carried out; Expt1 (WT Light with PDGF, WT Medium no PDGF and LARΔP Heavy with PDGF), Expt2 (WT Heavy with PDGF, LARΔP Light with PDGF and LARΔP Medium no PDGF), Expt3 (WT Light with PDGF, LARΔP Medium no PDGF and LARΔP Heavy with PDGF), Expt4 (WT Light with PDGF, WT Medium no PDGF and LARΔP Heavy with PDGF), Expt5 (WT Light with PDGF, WT Medium no PDGF and LARΔP Heavy no PDGF). Proteins were reduced with 8 mM DTT, alkylated with 20 mM iodoacetamide in 50 mM ammonium bicarbonate and digested with trypsin Gold (1:100 enzyme: protein ratio; Promega) at 37 °C overnight. Digested samples were acidified by addition of 0.5% TFA. Peptides were desalted using Sep-Pak C18 Cartridges (Waters, Milford, MA) according to manufacturer’s instructions. Desalted and dried peptides were resuspended in 100 μL mobile phase A (10 mM KH3PO4, 20 % acetonitrile, pH 3) and loaded onto a 100×4.6 mm polysulfoethyl A column (5 μm particle size, 200 nm pore size, PolyLC). Separation used a gradient elution profile that started with 100% mobile phase A, increased from 0 to 50% mobile phase B (10 mM KH3PO4, 20 % acetonitrile, 500 mM KCl, pH 3) over 30 min, increased to 100% B over 5 min, and then returned to 100% A. Each of the 20 resulting fractions was desalted using C8 macrotrap cartridge (Michrom BioResources) according to manufacturer’s instructions. Phosphopeptides were enriched using TiO2 tips (GL Sciences), according to the manufacturer’s instructions. All resulting peptide mixtures were analysed in duplicate by liquid chromatography tandem mass spectrometry (LC-MS/MS). For proteome analysis samples from each experiment were run on an SDS PAGE gel. Lanes were cut into 10 gel slices and digested with trypsin using standard in-gel digestion protocols.PrideDebbie L CunninghamLTQ Orbitrap EliteSchool of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UKPARTIAL27074791 Sarhan AR, Patel TR, Creese AJ, Tomlinson MG, Hellberg C, Heath JK, Hotchin NA, Cunningham DL. Regulation of platelet derived growth factor signalling by LAR protein tyrosine phosphatase: a quantitative phosphoproteomics study. Mol Cell Proteomics. 2016 Apr 13. pii: mcp.M115.053652University of Birminghamd.cunningham@bham.ac.ukMass SpectrometryShotgun proteomicsDisease FreeLtq orbitrap eliteMousePhosphoproteomicsFibroblasthttp://www.ebi.ac.uk/pride/archive/projects/PXD002545SILACphosphorylated residueMass spectra were processed using the MaxQuant software (version 1.5.3.8). Data were searched, using the Andromeda search engine within MaxQuant, against the mouse Swiss-Prot database (downloaded 6.10.15). The mouse database contained 16,719 reviewed protein entries. The search parameters were: minimum peptide length 7, peptide tolerance 20 ppm (first search) and 6 ppm (second search), mass tolerance 0.5 Da, cleavage enzyme trypsin/P, and 2 missed cleavages were allowed. Carbamidomethyl (C) was set as a fixed modification. Oxidation (M), acetylation (Protein N-term), and phospho (STY) were set as variable modifications. The appropriate SILAC labels were selected and the maximum labelled amino acids was set to 3. All experiments were filtered to have a peptide and protein false-discovery rate (FDR) below 1 %. Within the MaxQuant output, phosphorylation sites were considered to be localised correctly if the localisation probability was at least 0.75 (75 %) and the score difference at least 5. For MaxQuant analysis an exoerumental template was used in order to seoarate biological and technical repeats into distinct experiments for data analysis. Replicates 1, 3, 4, and 5 were grouped and assigned the following labels for MaxQuant analysis: Heavy R0K0, Medium R6K4, Light R10K8. Replicate 2 was assigned the following labels: Heavy R10K8, Medium R6K4, Light R0K0.ProteomicsMus Musculus (mouse)d.cunningham@bham.ac.ukBiologicalUnited KingdomIntracellular signaling pathways are reliant on protein phosphorylation events that are controlled by a balance of kinase and phosphatase activity. Although kinases have been extensively studied, the role of phosphatases in controlling specific cell signaling pathways has been less so. Leukocyte common antigen-related protein (LAR) is a member of the LAR subfamily of receptor-like protein tyrosine phosphatases (RPTPs). LAR is known to regulate the activity of a number of receptor tyrosine kinases, including platelet-derived growth factor receptor (PDGFR). To gain insight into the signaling pathways regulated by LAR, including those that are PDGF-dependent, we have carried out the first systematic analysis of LAR-regulated signal transduction using SILAC-based quantitative proteomic and phosphoproteomic techniques. We haveanalyzed differential phosphorylation between wild-type mouse embryo fibroblasts (MEFs) and MEFs in which the LAR cytoplasmic phosphatase domains had been deleted (LARΔP), and found a significant change in abundance of phosphorylation on 270 phosphosites from 205 proteins because of the absence of the phosphatase domains of LAR. Further investigation of specific LAR-dependent phosphorylation sites and enriched biological processes reveal that LAR phosphatase activity impacts on a variety of cellular processes, most notably regulation of the actin cytoskeleton. Analysis of putative upstream kinases that may play an intermediary role between LAR and the identified LAR-dependent phosphorylation events has revealed a role for LAR in regulating mTOR and JNK signaling.Regulation of Platelet Derived Growth Factor Signaling by Leukocyte Common Antigen-related (LAR) Protein Tyrosine Phosphatase: A Quantitative Phosphoproteomics Study.Sarhan Adil R AR, Patel Trushar R TR, Creese Andrew J AJ, Tomlinson Michael G MG, Hellberg Carina C, Heath John K JK, Hotchin Neil A NA, Cunningham Debbie L DL355projections, para Tyrosine, Signal Transductions, 2610315D21Rik, nucleocytoplasm, SAPKa, Activity, determination, plant germ, FKBP12-rapamycin complex-associated protein, A4, protein, JTK12, l(2)k03905, BSK, Bsk, phosphorylation, DmTOR, dmTAF[[II]]230, Receptor Mediated Signal Transduction, protein polypeptide chains, Cytoskeletons, Roles, Concepts, Ly-5, Kinase, RAFT1, pdgf-a, Mammalian target of rapamycin, protein aggregate, Cell Signaling, SAPK1, JNK-46, signal transduction by protein phosphorylation, reference sample, TFIID TAF250, Pdgfr, DBSK/JNK, cel, Junk, Receptor Like, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, AI528809, Pathways, LARS, proteins, number of, PDGFR, AI849689, Y, dtor, Receptor Like Protein Tyrosine Phosphatases, signaling process, Tyr, papilla, Role Concepts, c-Jun, Signal Transduction Pathways, Transductions, Microfilaments, DmelCG10443, house mouse, ATP Phosphotransferases, phosphatase, intracellular, ATP, dTOR, dTor, single organism signaling, FK506-binding protein 12-rapamycin complex-associated protein 1, Mechanistic target of rapamycin, D-junk, dTAF[[II]]230, Pathway, anatomical protrusion, embryo, dJNK, 2-Amino-3-(p-hydroxyphenyl)propionic acid, mouse, lamina, TAF200, signal transduction by conformational transition, Platelet Derived Growth Factor, flanges, dlar, extra or missing physical or functional parts, para-Tyrosine, developing organism, TAFII-250, DLar, DLAR, TAF250/230, signal transduction by trans-phosphorylation, Tyrosine, JNK21B1/2, signaling cascade, TAFII250, Role Concept, Playthings and Play, Lymphocyte antigen 5, 3.1.3.48, shelf, Role, Plaything, internal to cell, Platelet-Derived Growth, Transduction, tyrosine, Actin Microfilament, RAPT1, CD45, Transphosphorylases, PDGFR-1, absence, lymphocyte antigen 5, mice, System, shelves, Rapamycin and FKBP12 target 1, L-isomer, Toys, Actin, Filaments, BNAH2, CG17603, TAF[[II]], projection, ridge, L isomer, DJNK, DMDA, signaling pathway, Taf250, spine, SR3-5, 5092, IMF1, L-Tyrosine, Mouse, platelet-derived growth factor receptor ligand, T200, Dlar, BSK/DJNK, TAF230, Fibroblast, Signal Transduction Systems, biological signaling, d230, PDGFR binding, Plays, platelet-derived growth factor, lamellae, CG5092, number, Receptor-Mediated, Gene, dTAFII250, Signal Transduction System, protein-containing complex, EfW1, presence, process of organ, l(2)k17004, TYPE, protrusion, DAGA4, protein amino acid phosphorylation, lamella, Filament, Signal Transduction, Prkm8, polypeptide chain, dmTAF1, Ptp38A, Taf230, Gene Products, Growth Factor, TOR, MAM, SCG3, Phosphotransferase, IBGC4, DmelCG5680, TAF250, Platelet-Derived, Toy, DmelCG8274, protoplasm, DJNK/bsk, study, Taf200, dTAF[[II]]250, Bx34, protoplast, Actin Microfilaments, Playthings, cell, absent from organism, PDGFR1, JNK21B1|2, Signal, Taf1p, flat, tor, Signal Pathways, ridges, Tpr, TPR, c-Jun N-terminal kinase activity, Transphosphorylase, PRKM8, Signal Transduction Pathway, L-CA, CD140b, dTAF250, CG10443, signalling pathway, Actin Filaments, embryonic organism, Puppets, Microfilament, L Tyrosine, leukocyte common antigen, has or lacks parts of type, Play, signal transduction by cis-phosphorylation, PTPRC, Tyrosin, TAF, PTP38A, laminae, Frap1, Signal Pathway, CT24817, LAR, Puppet, Controlled, Leukocyte common antigen, CD140B, SAPK1c, signalling., Controlling, TAF[[II]]250, JNK, Jnk, JNK3alpha1, protein complex, RPTP-LAR, anatomical process, Proteins, Phosphorylations, Receptor-Mediated Signal Transductions, l(3)84Ab, FRAP1, BG:DS00004.13, Factor, FRAP2, mTOR, FRAP/TOR, DmelCG5092, lar, Phosphotransferases, Cell, LGMD2C, Concept, dTAF230, mereological quality, count in organism, JNK/SAPK, 2.7.11.1, jnk, native protein, JNK1, natural protein, tirosina, Mus, p230, Receptor-Mediated Signal Transduction, D-JNK, Protein, chemical analysis, Systems, JNK1A2, TAF[[II]]250/230, TFIID, signalling cascade, Cytoskeleton, flange, xptp-lar, organ process, Taf[[II]]250, TAF[[II]]230, ly-5, AA591035, DMDA1, Kinases, PDGF receptor binding, CT24745, phosphoric monoester hydrolase activity, Rapamycin target protein 1, TAF[II]250, AI327068, FRAP, signalling, Protein Gene Products, Gene Proteins, processes, process, Receptor-Like, Actin Filament, DmelCG17603, pdgf, developmental tissue, CT16317, signalling process, CG5680, CG8274, cardinality, SCARMD2, MTOR, processus, Leukocyte common antigen related, regulation, assay, PDGF, quantitative, General activity, Actin Cytoskeletons, Protein Tyrosine Phosphatases, TAF1, presence or absence in organismIPP2A2, determination, Aminosaeure, cleavage, Amino acid, Visible Light, protein, STY, Sty, phosphorylation, 5730420M11Rik, peptide, Polypeptides, protein polypeptide chains, Drug Tolerance, ClvPrd, peptido, DmelCG1921, gamma., hnu, Software Engineering, establishment and maintenance of substrate location, Analysis, protein aggregate, sty, foton, WMS, Computer Program, SET, F, amino acids, peptides, Analyses, TAF-I, Open, phosphatase 2A inhibitor I2PP2A, CLK|STY, Computer Programs and Programming, proteins, arg, DmelCG4299, dSPRY, set, IGAAD, DmelCG10574, ppm, s, house mouse, GPHYSD2, drug tolerance, SGS, gamma, ratio, phapii, establishment and maintenance of substance location, Radiation, immune system tolerance, Aminokarbonsaeure, acetylation, mouse, StF-IT-1, Light, Search, Source Softwares, alpha-amino carboxylic acids, Software Tools, CG1921, ACMICD, Programs, Program, Computer Applications, single organism localization, LIGHT, Computer Applications Software, Computer Applications Softwares, Immunologic Tolerance, Softwares, Visible Radiations, Amino Acid, Acid, Visible Radiation, Software Applications, HLA-DR-associated protein II, HVEML, Amino acids, DI-2, Source Software, mice, I-2Dm, proportionality, rate, MASS, CG4299, inhibitor of granzyme A-activated DNase, I-2PP1, Applications, light quantum, Self Tolerance, TAF-IBETA, Tolerance, Mouse, TAF-Ibeta, Acids, Polypeptide, i2pp2a, establishment and maintenance of cellular component location, Computer Software Applications, CLK, localised, False, Aminocarbonsaeure, FBN, high weight, Computer, alpha-amino acid, protein-containing complex, PHAPII, Ly113, l(3)rQ526, polypeptide chain, template-activating factor I, ECTOL1, heavy, establishment and maintenance of position, light, l(3)j5E11, Application, Open Source Softwares, Search Engines, proportion, localized, Software Application, Lichtquant, ipp2a2, spry, Open Source Software, Acetylations, Argos, 2pp2a, CG4531, Visible, CG10574, Probabilities, Computer Software Application, OCTD, 2PP2A, Tools, 10^[-6], taf-ibeta, DmAos, dSET, dSet, photon, peptidos, TR2, rlt, CS3-3, Applications Software, Open Source, data, Computer Software, protein complex, igaad, Phosphorylations, alpha-amino acids, CD258, Peptide, Engine, Tool, polypeptide, CLK/STY, Spry, l(3)rJ812, Software Tool, native protein, Immune Tolerance, natural protein, Mus, I-2PP2A, Protein, Dm I-2, chemical analysis, I2PP2A, MFS1, focal, establishment and maintenance of localization, l(3)05959, Software, WMS2, Data Base, Radiations, distinct, gil, HVEM-L, Engineering, Photoradiation, single-organism localization, Amino, Sry, l(3)05845, LTg, Computer Programs, DmelCG4531, dSET/TAF-Ibeta, Aos, 2610030F17Rik, Applications Softwares, localisation, Photoradiations, Data, SSKS, l(3)rJ472, quotient, Peptid, assay, variable, AA407739, Data Analyses, Immunological Tolerancepara Tyrosine, RPTP-LAR, protein complex, 2-Amino-3-(p-hydroxyphenyl)propionic acid, mouse, dlar, protein, para-Tyrosine, DLar, DLAR, protein-containing complex, lar, Concept, Tyrosine, protein polypeptide chains, Role Concept, native protein, natural protein, polypeptide chain, Roles, Ptp38A, tirosina, Mus, Protein, 3.1.3.48, Role, Concepts, protein aggregate, tyrosine, xptp-lar, Embryonic, AA591035, mice, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, L-isomer, LARS, phosphoric monoester hydrolase activity, proteins, BNAH2, Y, Fibroblast., L isomer, CG10443, L Tyrosine, Tyr, Role Concepts, Leukocyte common antigen related, L-Tyrosine, Mouse, DmelCG10443, Tyrosin, house mouse, PTP38A, Dlar, phosphatase, LARpara Tyrosine, biological signaling, RPTP-LAR, protein complex, postnatal development, 2-Amino-3-(p-hydroxyphenyl)propionic acid, number, growth and development, dlar, protein, para-Tyrosine, DLar, DLAR, protein-containing complex, lar, presence, Tyrosine, development, protein polypeptide chains, count in organism, native protein, natural protein, polypeptide chain, Ptp38A, tirosina, Lymphocyte antigen 5, Protein, 3.1.3.48, thrombocyte, Ly-5, protein aggregate, tyrosine, CD45, xptp-lar, lymphocyte antigen 5, ly-5, AA591035, growth pattern, non-developmental growth, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, postnatal growth, L-isomer, study., LARS, phosphoric monoester hydrolase activity, proteins, enucleate thrombocyte, BNAH2, Y, L-CA, signalling, L isomer, CG10443, signalling process, anucleate thrombocyte, L Tyrosine, signaling process, Tyr, leukocyte common antigen, blood platelet, PTPRC, Leukocyte common antigen related, regulation, L-Tyrosine, DmelCG10443, Tyrosin, quantitative, T200, PTP38A, platelet, Dlar, growth, phosphatase, LAR, single organism signaling, Leukocyte common antigen, presence or absence in organismliquid chromatography tandem mass spectroscopy, Particle Sizes, F10B6_15, polysulfoethyl A, PDGFR binding, Size, MeCN, l(1)VE614, platelet-derived growth factor, NCMe, muriate of potash, determination, Particle, Gene, high weight, KCl, Visible Light, SDH, supernumerary, CG7826, F10B6.15, LC-MS-MS, Ly113, peptide, Polypeptides, SDS, Cut, peptido, ClvPrd, reduced, Klotrix, l(1)7Ba, subnumerary, l(1)7Bb, CH3-C#N, hnu, PH 3, LC-MSMS, heavy, Gene Products, CG7835, CG42273, Min, light, tiny, pdgf-a, present in fewer numbers in organism, sylvite, foton, DmelCG42273, Pro-Mega, increased, pore, LCMSMS, peptides, Lichtquant, beta-Trypsin, hypoplasia, min, 4733401P19Rik, mAPC, Sciences, proteins, Visible, decreased number, kf, CG11387, AI047805, Sep-Pak C18, decreased, column, DmelCG11387, SOLO DANCERS, photon, CT, peptidos, TR2, polysulfoethylaspartamide, 2-iodo-, gamma, small, LC-MS2, [KCl], DYRK1, Klor-con, Radiation, 1-(14)C-labeled, potassium chloride, 3H-labeled, Proteins, LC-MS/MS, Ct, Dmel_CG7826, total expressed protein, AI836084, Light, acetonitrile, CD258, Peptide, Kaliumchlorid, polypeptide, LC/MS/MS, Experiment, LIGHT, Phosphopeptide, Dm1, Protein, chemical analysis, Sizes, Kaon-Cl 10, Dyrk1, BcDNA:GH10590, ACETONITRILE, Dmel_CG7835, cyanomethane, beta Trypsin., Visible Radiations, Radiations, Mnb, MNB, AU020952, Visible Radiation, HVEML, underdeveloped, HVEM-L, PDGF receptor binding, increased number, CC1, Photoradiation, Tripcellim, pooled, SWDS, pore-forming toxin activity, ethanenitrile, AW124434, CGI-97, beta Trypsin, LTg, ME-IV, Protein Gene Products, incised, Trypure, Gene Proteins, present in greater numbers in organism, light quantum, Photoradiations, pdgf, Acetamide, liquid chromatography-tandem mass spectroscopy, liquid chromatography tandem mass spectrometry, Peptid, platelet-derived growth factor receptor ligand, Polypeptide, assay, PDGF, methyl cyanide, Monopotassium chloride, Proteomes, accessory, channel-forming toxin activitySignal Transduction Systems, Signal Transductions, biological signaling, PDGFR binding, platelet-derived growth factor, determination, plant germ, Receptor-Mediated, number, A4, Signal Transduction System, protein, protein-containing complex, presence, phosphorylation, TYPE, DAGA4, Receptor Mediated Signal Transduction, protein polypeptide chains, Signal Transduction, polypeptide chain, Ptp38A, Ly-5, pdgf-a, protein aggregate, Cell Signaling, MAM, SCG3, signal transduction by protein phosphorylation, Signal, Pathways, LARS, proteins, Signal Pathways, Signal Transduction Pathway, L-CA, CG10443, signalling pathway, embryonic organism, signaling process, leukocyte common antigen, signal transduction by cis-phosphorylation, PTPRC, Signal Transduction Pathways, Transductions, DmelCG10443, house mouse, PTP38A, Signal Pathway, LAR, single organism signaling, Leukocyte common antigen, Pathway, embryo, protein complex, RPTP-LAR, mouse, signal transduction by conformational transition, Phosphorylations, Receptor-Mediated Signal Transductions, dlar, developing organism, DLar, DLAR, lar, signal transduction by trans-phosphorylation, LGMD2C, signaling cascade, count in organism, native protein, natural protein, Mus, Receptor-Mediated Signal Transduction, Lymphocyte antigen 5, Protein, chemical analysis, Systems, 3.1.3.48, signalling cascade, Transduction, CD45, xptp-lar, lymphocyte antigen 5, ly-5, AA591035, DMDA1, PDGF receptor binding, mice, System, phosphoric monoester hydrolase activity, BNAH2, signalling, DMDA, pdgf, developmental tissue, signalling process, signaling pathway, SCARMD2, Leukocyte common antigen related, Mouse, platelet-derived growth factor receptor ligand, assay, PDGF, quantitative, T200, Dlar, phosphatase., Fibroblast, presence or absence in organism1truePhosphoproteomic studies of role of LAR protein tyrosine phosphatase in mouse embryonic fibroblastsTo gain insights into the signalling pathways regulated by Leukocyte common antigen-related protein (LAR), including those that are PDGF-dependent, we have carried out the first systematic analysis of LAR-regulated signal transduction using SILAC-based quantitative proteomic and phosphoproteomic techniques. We have analysed differential phosphorylation between wild-type mouse embryo fibroblasts (MEFs) or MEFS in which the LAR cytoplasmic phosphatase domains had been deleted (LARΔP).2016-04-152016-04-04PXD00254544544100904054998638804333038783884019961575748782721513519850765557148021589103066239803100226190269157463601355881134506146479145943NCBITaxon:6157118259040813803942725631459537227243230746992867NCBITaxon:2453062791292497036125180284812355512744321504751029999034694176945347515597293632997966287157546224295486317447575584628228723074111481736231489693529372512646903994672736010621659554440426071012803218184318357559312811836575930797219080214321382426191065922261260705260707885318702945586265281736309698936160488209285678251249668619235554NCBITaxon:10359NCBITaxon:13134565860688795579597044830064123544367631076224308169963281042157457712169794232135622334747269704980301023929760101173818991312744141639101165691569313076749409833440817287613837081274423990119127442012744268839370210005899940343055542853217731193501872631714505118723872487279564818822954767091115104580023055148015490313847562360385962982510151098231174673493211676275967767373153NCBITaxon:9615297221097677573493760833341911079276280863632666898333210312983823756174920031971966279606157295171101256737270747910000-0001-7776-690X