Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/MitrasamplenamesRAWfiles.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/Peptideandproteinlistminusdecoy.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/QSPECanalysisminusdecoy.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_25.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_55.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_85.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_99.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_69.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_37.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_97.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_67.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_41.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_71.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_49.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_31.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_103.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_75.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_23.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_39.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_83.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_91.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_65.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_105.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_73.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_57.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_29.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_51.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_81.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_47.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_101.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_77.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_21.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_93.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_63.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_33.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_59.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_89.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_107.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_27.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_53.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_79.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_45.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_61.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_43.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_35.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_19.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_87.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/EAA20140526_95.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD002407/soybean_tandem.zipprimaryOK2000000sanghamitra.majumdar@ct.govSanghamitra MajumdarMass SpectrometryShotgun proteomicsNot availableNanoceriaLc ms/msProteomicsKidney beanhttp://www.ebi.ac.uk/pride/archive/projects/PXD002407Plant CellSeedQuantitative proteomic analysis using 1D LC-MS/MS. Seeds harvested from plants exposed to 0-500 mg nCeO2/kg OMES were lyophilized in sets of three seeds per replicate. Seeds were pulverized in liquid nitrogen with a mortar and pestle, and were stored at -80°C until analysis. Seed proteins were extracted in triplicate according to Lee and Koh with minor modifications.52 Briefly, 150 mg of each sample was suspended in an extraction buffer of 100 mM Tris-HCl (pH 8.5) containing 5 mM DTT, 1 mM EDTA, 1% (m/v) dodecyl-b-maltoside, and 1% (v/v) plant proteinase inhibition cocktail (Sigma, MO, USA) using pulse sonication for 1 min. After 30 min of incubation at ambient temperature, the extracts were centrifuged at 14,000 x g for 15 min. Two distinct precipitation procedures were performed. One set of extracted proteins was precipitated overnight with chilled acetone, and the other with chilled 10% (v/v) TCA/acetone, followed by three acetone washes. The protein pellets were resolubilized in 400mM NH4HCO3 containing 8M urea and the protein concentration was quantified using a BCA kit. The aliquots containing 600 µg of protein were reduced with 5 mM DTT for 30 min at 55°C. Following the alkylation of the reduced thiol groups using 10 mM iodoacetamide in the dark for 30 min, and an 8-fold dilution to a final concentration of 1M urea/50mM NH4HCO3, the proteins were digested overnight at 37°C using sequencing grade trypsin (Sigma-Aldrich). The protein digestion was quenched with TFA to a final concentration of 0.05% TFA. Resulting tryptic peptides were then desalted using solid phase extraction cartridges (Discovery® DSC-18 SPE Tube) prior to 1D LC-MS/MS analysis. Aliquots from two different precipitation procedures were combined and run as one sample. Each replicate from 15 samples was run in triplicate, totaling 45 analytical runs using a Dionex Ultimate 3000 RSLC nano system online coupled to a Q-Exactive (Thermo Fisher Scientific). Peptides were introduced to the analytical column (Acclaim® PepMap RSLC, 75 μm × 15 cm, nanoViper, C18, 2 μm, 100 Å) and separated using a 90 min gradient from 5 to 40% solvent B at a flow rate of 300 nl/min (solvent A: 0.1% formic acid 5 % acetonitrile, solvent B: 0.1% formic acid 80% acetonitrile). The mass spectrometer was operated in a data-dependent mode. Full scan MS spectra were acquired at a mass resolution of 70,000 (mass range 400-1600 m/z and AGC target value of 1E6) in the Orbitrap analyzer. Tandem mass spectra of the 10 most abundant peaks of a full scan MS spectrum were acquired following peptide fragmentation using higher-energy collisional dissociation (HCD) at a mass resolution 17,500 (AGC target value of 2E5, NCE 28%, isolation width 4 m/z). The dynamic exclusion time was set at 15 sec. A polysiloxane ion, m/z 445.12003, was used as lock mass throughout.PrideSpectrum countingNo PTMs are included in the dataset1D LC MS/MS data processing and database search. The MS/MS spectra were searched against Phaseolus vulgaris and Glycine max UniProt sequence databases (downloaded on November 21, 2013), and contaminant proteins, comprising of keratin and porcine trypsin using the X! Tandem search engine (TPP version 2013.06.15.1). Both databases were used in this study because G. max and P. vulgaris share extensive macrosyntentic relationships and a number of phenotypes, controlled by similar sets of genes.30 Linkage mapping studies of DNA markers suggest high conservation and preservation, demonstrated by an average conserved block length of 13.9 cM between the two genomes.53 Phylogenetically, these two species belong to the same group of papilionoid legumes, referred to as the core Phaseoleae.30 In the database search, mass tolerances were set to 10 ppm and 0.02 Da for precursor and fragment ions, respectively, and up to two missed cleavages were permitted. Cysteine carbamidomethylation was included as a fixed modification. Oxidation of methionine and deamidation of asparagine and glutamine were allowed as variable modifications. Peptide and protein identification was performed using PeptideProphet and ProteinProphet in the Trans-Proteomics Pipeline respectively, with target FDR at 1%.54-55 Protein quantification was performed using a label free approach called spectral counting,56 which tallies the number of MS/MS spectra assigned to any peptide belonging to each protein.57 Spectral counting was performed using the Abacus tool,58 since the algorithm provides an automated spectral counting with robust treatment of ambiguity due to shared peptides in homologous proteins. The resulting spectral count data was analyzed using QSPEC algorithm (version 1.2.2) ,59 which performs model-based statistical analysis of differential protein expression. The spectral count data was transformed by log2 transformation and was centered by the median of the three controls in each protein. The software reports statistical significance scores (Z-statistics) and associated local and global FDRs, which was targeted at 10%. The rationale for using a rather large FDR in this study is that the total expected number of false positives is still low at 10% due to the moderate number of differentially expressed proteins.ProteomicsSanghamitra MajumdarQ ExactiveResearch ScientistPARTIALPhaseolus Vulgaris (kidney Bean) (french Bean)26488752 Majumdar S, Almeida IC, Arigi EA, Choi H, VerBerkmoes NC, Trujillo-Reyes J, Flores-Margez JP, White JC, Peralta-Videa JR, Gardea-Torresdey JL. Environmental Effects of Nanoceria on Seed Production of Common Bean (Phaseolus vulgaris): A Proteomic Analysis. Environ Sci Technol. 2015 49(22):13283-13293 10.1021/acs.est.5b03452majumdarsm@gmail.comBiologicalResearch ScientistUnited StatesThe rapidly growing literature on the response of edible plants to nanoceria has provided evidence of its uptake and bioaccumulation, which delineates a possible route of entry into the food chain. However, little is known about how the residing organic matter in soil may affect the bioavailability and resulting impacts of nanoceria on plants. Here, we examined the effect of nanoceria exposure (62.5-500 mg/kg) on kidney bean (Phaseolus vulgaris) productivity and seed quality as a function of soil organic matter content. Cerium accumulation in the seeds produced from plants in organic matter enriched soil showed a dose-dependent increase, unlike in low organic matter soil treatments. Seeds obtained upon nanoceria exposure in soils with higher organic matter were more susceptible to changes in nutrient quality. A quantitative proteomic analysis of the seeds produced upon nanoceria exposure provided evidence for upregulation of stress-related proteins at 62.5 and 125 mg/kg nanoceria treatments. Although the plants did not exhibit overt toxicity, the major seed proteins primarily associated with nutrient storage (phaseolin) and carbohydrate metabolism (lectins) were significantly down-regulated in a dose dependent manner upon nanoceria exposure. This study thus suggests that nanoceria exposures may negatively affect the nutritional quality of kidney beans at the cellular and molecular level. More confirmatory studies with nanoceria along different species using alternative and orthogonal "omic" tools are currently under active investigation, which will enable the identification of biomarkers of exposure and susceptibility.Environmental Effects of Nanoceria on Seed Production of Common Bean (Phaseolus vulgaris): A Proteomic Analysis.Majumdar Sanghamitra S, Almeida Igor C IC, Arigi Emma A EA, Choi Hyungwon H, VerBerkmoes Nathan C NC, Trujillo-Reyes Jesica J, Flores-Margez Juan P JP, White Jason C JC, Peralta-Videa Jose R JR, Gardea-Torresdey Jorge L JLBio-magnification, Biological Markers, Viral Marker, Food Plants, Surrogate Endpoints, Laboratory, Bio-concentration, Biomagnifications, Parasite Chains, Biochemical, Endpoint, protein, GRO:0005339, Serum, composed of, Productivity, cerium oxide, protein polypeptide chains, Laboratory Markers, string bean, exact), Biological, responsivity, Edible Plants, Elaiosome, protein aggregate, seed, me75, kidney bean, Bio Accumulation, Moods, Bioamplifications, Predator Chains, Plant Embryo, composition, plants, proteins, D17Mit170, T1, retention, Food, Immune, Markers, Diaspores, Viral Markers, Therapies, associated, reniculate kidney, Bio-amplifications, Therapy, nanoceria, Saprophytic Chains, Viral, Surrogate Endpoint, Isolectins, land plants, Biochemical Markers, Tl3, Tl2, Biologic Marker, Literatures, 種子 (Japanese, Bioconcentrations, Marker, margin of safety, Seed, Bio Concentration, Saprophytic, Diaspore, carbohydrate metabolism, maintenance of localization, End Points, content, Food Chains, Plant, pooled, Plant Zygote, Predator Chain, Bio-amplification, Immunologic, Laboratory Marker, cerium oxide (CeO2), Treatments, Edible, Kidneys, higher plants, Parasite, Biochemical Marker, Food Web, Bio Amplification, Lectin, Saprophytic Chain, Clinical Markers, Clinical Marker, diaspore (broad), number, Gene, protein-containing complex, presence, Surrogate End Points, Surrogate Markers, French bean, polypeptide chain, Plants, Metabolism, Peat, susceptible, single-organism carbohydrate metabolic process, Gene Products, Mood, Web, Low, Animal, Animal Lectin, Chain, reactivity, study, Biomarker, ceric oxide (CeO), multicellular organismal carbohydrate metabolic process, Clinical, Bio-accumulations, nutrients, Biological Marker, Humus, Bio-concentrations, Zygote, susceptibility., nutritional quality, Immunologic Markers, Edible Plant, Bio Amplifications, Soils, Zygotes, Isolectin, toxic potential, species, Immunologic Marker, Biologic, Biomagnification, Elaiosomes, nutrient, Bioamplification, cou, protein complex, Affects, Bio Magnification, Proteins, Serum Markers, End Point, Webs, function, compositionality, Food Webs, Immune Marker, cerium dioxide, count in organism, uptake, Bio-accumulation, Lr, Parasite Chain, native protein, natural protein, Surrogate End Point, Embryos, Food Plant, Protein, proteomic analysis, Lectins, Biologic Markers, Embryo, ceric oxide (Ce2O3), Serum Marker, Exhibit, Chains, storage, Surrogate, Bioconcentration, Endpoints, Bio-magnifications, Plant Embryos, Carbohydrate, Surrogate Marker, mg/kg, Protein Gene Products, Gene Proteins, semilla (Spanish, Therapeutic, Plant Zygotes, structure, Animal Lectins, Bra, Treatment, response, quantitative, sequestering, earth, Predator, pyrene (narrow), presence or absence in organism, Immune MarkersIPP2A2, Materials, dmMOF, ion, Mbp1, protein, L-(+)-glutamine, DmelCG9648, 5730420M11Rik, peptide, Polypeptides, protein polypeptide chains, L-Isomer Methionine, string bean, L-glutamine, Methionine, L-Glutaminsaeure-5-amid, ClvPrd, peptido, dMOF, 2, L-2-aminoglutaramic acid, Software Engineering, protein aggregate, myd, WMS, Computer Program, average, DL-Asparagine, SET, thymus nucleic acid, me75, asparagina, F, kidney bean, reference sample, peptides, Genomes, asparagine, Soybean, TAF-I, M, dMax, N, phosphatase 2A inhibitor I2PP2A, L-Asparagine, Open, Soy Beans, D-Glutamine, Q, Computer Programs and Programming, Statistic, Mbp-1, proteins, number of, ASN, free, D17Mit170, Asn, T1, DmelCG4299, set, IGAAD, DmelCG10574, ppm, Double-Stranded DNA, deoxyribonucleic acids, Half Cystine, DNAn, associated, GPHYSD2, Racemethionine, SGS, phapii, Soybeans, Zinc Cysteinate, gyltl1b-b, 2-Amino-4-(methylthio)butyric acid, CG9648, StF-IT-1, Search, extra or missing physical or functional parts, Double-Stranded, Normalcy, Tl3, Gene Mapping, Tl2, Chromosome Mappings, Source Softwares, Software Tools, bHLHd7, ACMICD, Programs, Soy Bean, bHLHd6, (Deoxyribonucleotide)n+m, bHLHd9, bHLHd8, Program, Computer Applications, bHLHd5, bHLHd4, batch, count, Ionen, MDDGA6, Algorithm, mKIAA0609, Computer Applications Software, dmax, Computer Applications Softwares, Genetic Materials, Methionin, median, methionine, Hmet, Softwares, desoxyribose nucleic acid, Gene Mappings, Genetic Material, L Glutamine, parent ion, fg, Software Applications, gyltl1b, HLA-DR-associated protein II, DI-2, Phaseolus max, Source Software, I-2Dm, mdc1d, expanded, L-Cysteine, MASS, CG4299, inhibitor of granzyme A-activated DNase, 2-amino-3-carbamoylpropanoic acid, (S)-2, beta Trypsin, I-2PP1, L-glutamic acid gamma-amide, cv. Wye, Phenotypes, data analysis, MDC1D, Applications, MOF, Mof, Health, TAF-IBETA, precursor ion, enr, Chromosome, enlarged, Material, ds DNA, Cistron, Mappings, TAF-Ibeta, Polypeptide, DNA, i2pp2a, Liquimeth, Gruppe, Computer Software Applications, big, GLUTAMINE, Cysteine Hydrochloride, 2-amino-4-(methylsulfanyl)butanoic acid, DNS, Linkage Mappings, (Deoxyribonucleotide)n, Peptidomics, False, 5-diamino-5-oxopentanoic acid, nucleocapsid, number, L Isomer, FBN, Levoglutamide, Gene, Hasp, Linkage Mapping, precursor, Computer, (2S)-2-amino-4-carbamoylbutanoic acid, protein-containing complex, Deoxyribonucleic acids, PHAPII, froggy, Gyltl1a, large, French bean, DmelCG3025, polypeptide chain, Deoxyribonucleic Acid, template-activating factor I, ECTOL1, Gene Products, L-Methionine, Low, Half-Cystine, Pedameth, Application, Normalities, study, Open Source Softwares, Search Engines, MAX, Genetic, iones, L Cysteine, (2S)-2, Software Application, MDDGB6, soybeans, ipp2a2, beta-Trypsin, Open Source Software, Double Stranded, 2pp2a, TPP, Deoxyribonucleic acid, ions, CG10574, Computer Software Application, soybean, OCTD, Asparagin, BPFD#36, Linkage, max, data processing, 2PP2A, 2-amino-4-(methylthio)butanoic acid, 10^[-6], Tools, Genome Mappings, grupos, taf-ibeta, great, has or lacks parts of type, dSET, dSet, Beans, L-Glutamine, peptidos, (Deoxyribonucleotide)m, species, metionina, Soy, statistical analysis, Controlled, Applications Software, Gene., Open Source, Controlling, data, grupo, Computer Software, cou, Mapping, DL-Methionine, protein complex, DNAn+1, Proteins, CG3025, igaad, L-2-Aminoglutaramic acid, L-Isomer, Cistrons, Peptide, Engine, group, Tool, AI875693, mereological quality, polypeptide, Software Tool, Lr, native protein, natural protein, I-2PP2A, Protein, Dm I-2, I2PP2A, sequence, core, Glutamic acid 5-amide, MFS1, L-Glutamin, ds-DNA, Software, Data Base, WMS2, Met, Glutamic acid amide, Normality, Bean, Engineering, Tripcellim, Rest, 4-diamino-4-oxobutanoic acid, primary structure of sequence macromolecule, Protein Gene Products, Computer Programs, Gene Proteins, Trypure, dSET/TAF-Ibeta, 2610030F17Rik, Genome Mapping, Applications Softwares, D Glutamine, Ion, Glycine max, AA960152, cardinality, SSKS, Desoxyribonukleinsaeure, alpha-amino-gamma-methylmercaptobutyric acid, Bra, Peptid, variable, AA407739, groupe, Genomereactivity, Elaiosomes, Embryo, ceric oxide (Ce2O3), ceric oxide (CeO), seed, Diaspore, nanoceria, kidney bean, diaspore (broad), pyrene (narrow)., Plant, Plant Embryo, Plant Zygote, Zygote, GRO:0005339, Plant Embryos, cerium oxide (CeO2), cerium oxide, 種子 (Japanese, cerium dioxide, string bean, French bean, exact), semilla (Spanish, Plant Zygotes, Diaspores, responsivity, Embryos, Zygotes, response, Seed, ElaiosomeElaiosomes, Embryo, ceric oxide (Ce2O3), ceric oxide (CeO), seed, Diaspore, nanoceria, kidney bean, Bean, diaspore (broad), proteomic analysis., Plant, Plant Embryo, common, Plant Zygote, Zygote, Brain-expressed protein associating with Nedd4, GRO:0005339, Plant Embryos, cerium oxide (CeO2), Brain-expressed protein associating with Nedd4 homolog, cerium oxide, 種子 (Japanese, cerium dioxide, string bean, French bean, exact), semilla (Spanish, Plant Zygotes, Diaspores, Embryos, BEAN, Zygotes, Seed, Elaiosome, SCA31, pyrene (narrow)sodium salt, ammonium formate, 13C-labeled, cadmium salt, MeCN, ion, Ethylenediaminetetraacetic acid, Basodexan, magnesium formate, Apaf-1, zinc salt, Solvent, (ethylenedinitrilo)tetraacetic acid, Long Term, 5730420M11Rik, Bca, 2-Propanone, Polypeptides, protein polypeptide chains, KL receptor activity, hydrogen chloride, cobalt(II) formate dihydrate, CH3-C#N, B1, SCO5, SEC, HCL-C, Urea, 2, AGM4, SCO1, Gsfsow3, WMS, bca, SET, Divorced, hac-1, N, phosphatase 2A inhibitor I2PP2A, sec, Plant Embryo, proteasome endopeptidase activity, proteins, Divorces, W, AI047805, DmelCG4299, set, NOR-1, Wasserstoffchlorid, decreased, column, anatomical tube, sample, Solid Phase Extractions, D1, n, Bs, DIC60, acidum edeticum, nickel salt, SGS, LC-MS2, elastase activity, Degradations, CHN, cobalt (+2) salt, land plants, anon-53Fa, 2'', Longterm Effect, l(2)SH0173, not genetically inherited, ACMICD, 種子 (Japanese, PBT, sodium (4:1:1) salt, Stickstoff, Dm1, magnesium salt, Chlorwasserstoff, leukemic reticuloendotheliosis, CG6829, dark/hac-1/dapaf-1, CG9071, pbt, HLA-DR-associated protein II, DI-2, LY57, I-2Dm, Protein Digestions, formate, dsc1, HT-CP, Plant Zygote, cromium (+3), inhibitor of granzyme A-activated DNase, exposed, N'-1, beta Trypsin, Solid Phase, I-2PP1, higher plants, nitrogen, TAF-IBETA, liquid chromatography-tandem mass spectroscopy, duct, ammonium (4:1) salt, TAF-Ibeta, methyl cyanide, chlorane, lead (+2) salt, krk1, DSC4, CG34405, nickel formate dihydrate, lead formate, Effects, chlorure d'hydrogene, aluminum salt, number, DSCI, Carbamide, protein-containing complex, thomson, body system, EDTA tetraanion, CG7826, mass-to-charge ratio, period, CDHF3, Ly57, LC-MSMS, Gene Products, CG7835, CG42273, system, Carmol, DSC1, DSC2, plantae, T6K12_14, anatomical systems, 2'''-(ethane-1, 2-Ethane diylbis-(N-(carboxymethyl)glycine), 2310061K05Rik, Hydrogen chloride, thallium (+1) salt, Longterm, ethylenediamine tetraacetic acid tetraanion, beta-Trypsin, rubidium salt, 2pp2a, Zygote, Extractions, Long-Term, methanoic acid, ions, CG10574, extruding from, hairy cell leukemia, 2PP2A, dSET, dSet, peptidos, PTHB1, Elaiosomes, proto-oncogene c-Kit, dark/dapaf-1/hac-1, 1-(14)C-labeled, dApaf-1, Proteins, DSC, chloridohydrogen, potassium formate, copper (+2) salt, acetonitrile, buffer, Digestions, polypeptide, APAF1, native protein, Temperatures, Proteolyses, I-2PP2A, carbonyldiamide, Hac-1, KIT ligand receptor activity, C18, endoprotease activity, cupric formate, chemical analysis, Dm I-2, Long Term Effects, proteomic analysis, MFS1, dsc, aluminum formate, dJ142L7.2, XKrk1, T6K12.14, AU020952, lithium formate, underdeveloped, Separations, Dark/Dapaf-1/HAC1, azote, ethanenitrile, CD117, Longterm Effects, SSKS., ME-IV, Gene Proteins, semilla (Spanish, C-Kit, Ssm, xkl-1, liquid chromatography tandem mass spectrometry, quantitative, hydrochloric acid, pyrene (narrow), ethylenediaminetetraacetate tetraanion, liquid chromatography tandem mass spectroscopy, Hac-1/Dark, IPP2A2, NCMe, determination, Pflanze, DmelCG6829, DmelCG34405, classic hairy cell leukaemia, zinc formate, lead salt, CSMF, protein, Hydrogenchlorid, Xkl-1, GRO:0005339, viridiplantae, Alkylations, peptide, Gsfsco1, ammonium tetraformate, exact), peptido, ClvPrd, Min, 2', Apaf1, Elaiosome, protein aggregate, Gsfsco5, present in fewer numbers in organism, ARK, Effect, DmelCG42273, Edetic acid, SOW3, 2-diyldinitrilo)tetraacetate, seed, LCMSMS, ion(4-), peptides, TAF-I, E927b, Dmel_CG18506, hypoplasia, min, arc, mAPC, plants, analyzer, copper, ark, Protein Degradation, T1, IGAAD, lithium salt, DmelCG10574, Diaspores, Lyw-57, dApaf1, (ethane-1, Sl, GPHYSD2, ammonium (2:1) salt, Long-Term Effects, phapii, Tube, ethylenediaminetetraacetate, D-Apaf-1, LC-MS/MS, Dmel_CG7826, StF-IT-1, Tr-kit, Th, {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID, classic hairy cell leukemia, ur, SLP65, TUBE, carbamide, Ly-57, HCD, Ionen, Digestion, HCL, kl1-A, Seed, KIT, nickel (+2) salt, Dmel_CG7835, Mnb, MNB, tyrosine-protein kinase Kit, SLP-65, ammonium salt, Diaspore, BASH, Sonications, HCl, Na-CP, Plant, cobaltous formate, CG4299, kit, hac1, MASS, AW124434, organ system, dapaf-1S, H2NC(O)NH2, apaf-1, dapaf-1L, Acetamide, copper salt, Polypeptide, 7N, i2pp2a, 1728, time, Dapaf-1/HAC-1, diaspore (broad), Degradation, cesium salt, SCF receptor activity, FBN, Gene, ethylenediaminetetraacetic acid, presence, PHAPII, LC-MS-MS, Buffer, formic acid, Dark/Hac-1/dApaf1, Karbamid, Hac1, potassium salt, Dark/Hac-1/dApaf-1, polypeptide chain, template-activating factor I, scfr, reduced, subnumerary, ECTOL1, 14C-labeled, Acide ethylenediaminetetracetique, Harnstoff, CT24831, tiny, SCFR, Separated, cloruro de hidrogeno, acide edetique, Pulses, Fdc, AI573420, iones, Selb, ipp2a2, dapaf-1, dapaf, dark, decreased number, calcium formate, Protein Degradations, OCTD, edta, 2-diyldinitrilo)tetraacetic acid, DARK, taf-ibeta, EDTA, Dmel_CG9071, Zygotes, smi60E, liquid, cromium (+3) salt, Long-Term Effect, dArk, Dapaf-1, 2-iodo-, sodium formate, BLNK-S, small, NOR1, DYRK1, data, Nor1, nickel formate, 3H-labeled, protein complex, exits through, igaad, strontium formate, apaf1, Protein Digestion, Extraction, strontium salt, Peptide, acido edetico, [HCl], count in organism, LC/MS/MS, CG18506, secret agent, natural protein, Embryos, Protein, I2PP2A, AI551343, Hydrochloride, Dyrk1, Dark, connected anatomical system, Dark/Apaf-I, ACETONITRILE, cyanomethane, WMS2, Embryo, Separation, c-KIT, 10^[-9], distinct, MINOR, uree, urea, CC1, H4edta, Tripcellim, Plant Embryos, dApaf-1/DARK/HAC-1, sample population, chromic formate, UREA, nitrogeno, Protein Gene Products, Trypure, dSET/TAF-Ibeta, 2610030F17Rik, c-kit, Ion, Plant Zygotes, concentration, SSKS, calcium salt, TEC, Peptid, edetic acid, proteinase, assay, AA407739, Minor, dAPAF-1, presence or absence in organismLectin, Materials, human being, Nanocrystalline, diaspore (broad), number, Gene, protein, GRO:0005339, protein-containing complex, Ximpact, composed of, presence, Downregulation, Nanocrystal, Productivity, inadequate, cerium oxide, Readability, protein polypeptide chains, string bean, French bean, exact), polypeptide chain, Metabolism, Peat, responsivity, single-organism carbohydrate metabolic process, Gene Products, Animal, Elaiosome, protein aggregate, Animal Lectin, Normalities, average, reactivity, study, ceric oxide (CeO), seed, multicellular organismal carbohydrate metabolic process, kidney bean, FATE, nutrients, Humus, Plant Embryo, Zygote, composition, plants, proteins, man, nutritional quality, retention, Mineral, extruding from, Diaspores, Soils, Zygotes, Nanocrystals, Isolectin, associated, Nanocrystalline Material, reniculate kidney, Normalcies., Elaiosomes, Individual Health, nutrient, Nanoparticle, nanoceria, Isolectins, Nanocrystalline Materials, protein complex, exits through, land plants, Proteins, Normalcy, compositionality, impact-a, Down Regulation, 種子 (Japanese, cerium dioxide, count in organism, Down-Regulation, native protein, Receptor Down-Regulation, natural protein, Down-Regulation (Physiology), Embryos, Protein, CT43, proteomic analysis, Seed, Individual, Lectins, Foods, Embryo, ceric oxide (Ce2O3), Epistemology, Diaspore, carbohydrate metabolism, maintenance of localization, storage, Normality, content, Plant, Plant Zygote, Understanding, exposed, Plant Embryos, Carbohydrate, cerium oxide (CeO2), human, mg/kg, Protein Gene Products, Gene Proteins, Kidneys, higher plants, Health, semilla (Spanish, Material, Plant Zygotes, structure, Animal Lectins, Receptor, response, quantitative, sequestering, earth, E430016J11Rik, RWDD5, pyrene (narrow), presence or absence in organism0trueNanoceria modulates kidney bean proteomic response and compromises its seed qualityThere is inadequate understanding of the environmental fate and effects of engineered nanoparticles, including nanoceria. Also, knowledge about the influence of environmental factors on the bioavailability of these particles and resulting impacts on the nutritional quality of crops is limited. Alterations in mineral and macromolecular composition of some grains and fruits under nanoceria exposure have been reported recently; however, the cellular mechanisms associated with the effects are unknown. Here, we show that the impact of nanoceria at 62.5 to 500 mg/kg soil on kidney bean (Phaseolus vulgaris) productivity and seed quality are influenced by soil organic matter content. Seeds obtained from plants exposed to nanoceria at 125 mg/kg showed unique and contrasting response in terms of nutritional quality under varying soil organic matter content. Additionally, quantitative proteomic analysis provides evidence for dose-dependent down-regulation of some major proteins associated with nutrient storage and carbohydrate metabolism, including phaseolin and lectins in the exposed seeds. This study suggests that nCeO2 exposure negatively impacts the nutritional quality of kidney beans. This altered seed quality may have significant implications for food production and human health.2019-02-212015-06-22PXD0024074454410090641524054998638804333038783839068840199615275838575748782721513517505898507655571480468352158910306364162398031002261902691574636013558811345061464796928145943NCBITaxon:61579778118259040816329573803942725631459536123517861672272432307469928671123869NCBITaxon:2453062791292497036125180142450728481235551274432150475102999903469417694534751541554059729363299796628715754647842242954862089643174475755846282287230741114817362314896935293725126469039946727360106216595544404260710128312803395232181843183NCBITaxon:619157554787931281183657593079721908021432138242619169225910659222611117957260704618326070526070788531870294558626528173630943179698936160488209285566467825124966861923555432046NCBITaxon:10359NCBITaxon:13134565860688607699795579597044830064180222354436763107622430818543116996328104215745771216979423213562233474726970498030102392976010117381858334991312744141639101165691569313076749409833440817212816120425468761383708127442399011912744201274426992588393702100058999403430555428532189517731193501872631714505118723872487279564818822954767091115104580023055148015418006690313847562360314238596298251015109823117467349321167627596776737315344685NCBITaxon:961529722109767757349376083334191107927628086363266689833321031298382375612413687492003600943197196627960615729517110151515256737264887520000-0002-8742-4759