Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD002773/1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD002773/3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD002773/2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD002773/8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD002773/7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD002773/6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD002773/4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD002773/5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD002773/Uniprot_OSjaponica_ref_39947.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD002773/MaxQuant_output.zipprimaryOK200001680zp7@BCH.msstate.edujun zhuMass SpectrometryShotgun proteomicsNot availableOryza sativaLc-ms/msLysine acetylationhttp://www.ebi.ac.uk/pride/archive/projects/PXD002773Whole BodyTrypsin Digestion For digestion, the protein solution was reduced with 10 mM DTT for 1 h at 37 °C and alkylated with 20 mM IAA for 45 min at room temperature in darkness. For trypsin digestion, the protein sample was diluted by adding 100 mM NH4CO3 to urea concentration less than 2M. Finally, trypsin was added at 1:50 trypsin-to-protein mass ratio for the first digestion overnight and 1:100 trypsin-to-protein mass ratio for a second 4 h-digestion. HPLC Fractionation The sample was then fractionated into fractions by high pH reverse-phase HPLC using Agilent 300Extend C18 column (5 μm particles, 4.6 mm ID, 250 mm length). Briefly, peptides were first separated with a gradient of 2% to 60% acetonitrile in 10 mM ammonium bicarbonate pH 10 over 80 min into 80 fractions, Then, the peptides were combined into 8 fractions and dried by vacuum centrifuging. Affinity Enrichment To enrich Kac peptides, tryptic peptides dissolved in NETN buffer (100 mM NaCl, 1 mM EDTA, 50 mM Tris-HCl, 0.5% NP-40, pH 8.0) were incubated with pre-washed antibody beads (PTM Biolabs) at 4°C overnight with gentle shaking. The beads were washed four times with NETN buffer and twice with ddH2O. The bound peptides were eluted from the beads with 0.1% TFA. The eluted fractions were combined and vacuum-dried. The resulting peptides were cleaned with C18 ZipTips (Millipore) according to the manufacturer’s instructions, followed by LC-MS/MS analysis.PrideNot availableiodoacetamide derivatized residuemonohydroxylated residueacetylated residueThe resulting MS/MS data was processed using MaxQuant with integrated Andromeda search engine (v.1.4.1.2). Tandem mass spectra were searched against UniProt_Oryza sativa (63,195 sequences) database concatenated with reverse decoy database. Trypsin/P was specified as cleavage enzyme allowing up to 4 missing cleavages, 5 modifications per peptide and 5 charges. Mass error was set to 10 ppm for precursor ions and 0.02 Da for fragment ions. Carbamidomethylation on Cys was specified as fixed modification and oxidation on Met, acetylation on lysine and acetylation on protein N-terminal were specified as variable modifications. False discovery rate (FDR) thresholds for protein, peptide and modification site were specified at 1%. Minimum peptide length was set at 7. All the other parameters in MaxQuant were set to default values. The site localization probability was set as > 0.75.ProteomicsZhaohua PengQ ExactiveUniversity of Mississippi , Department of BiochemistryPARTIALOryza Sativa (rice)29235492 Meng X, Xing S, Perez LM, Peng X, Zhao Q, Redoña ED, Wang C, Peng Z. Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds. Sci Rep. 2017 7(1):17486 10.1038/s41598-017-17756-6jun_zhu@ptm-biolab.comBiologicalPH.D studentLysine 2-hydroxyisobutyrylation is a recently identified protein post-translational modification that is known to affect the association between histone and DNA. However, non-histone protein lysine 2-hydroxyisobutyrylation remains largely unexplored. Utilizing antibody-based affinity enrichment and nano-HPLC/MS/MS analyses of 2-hydroxyisobutyrylation peptides, we efficaciously identified 9,916 2-hydroxyisobutyryl lysine sites on 2,512 proteins in developing rice seeds, representing the first lysine 2-hydroxyisobutyrylome dataset in plants. Functional annotation analyses indicated that a wide variety of vital biological processes were preferably targeted by lysine 2-hydroxyisobutyrylation, including glycolysis/gluconeogenesis, TCA cycle, starch biosynthesis, lipid metabolism, protein biosynthesis and processing. Our finding showed that 2-hydroxyisobutyrylated histone sites were conserved across plants, human, and mouse. A number of 2-hydroxyisobutyryl sites were shared with other lysine acylations in both histone and non-histone proteins. Comprehensive analysis of the lysine 2-hydroxyisobutyrylation sites illustrated that the modification sites were highly sequence specific with distinct motifs, and they had less surface accessibility than other lysine residues in the protein. Overall, our study provides the first systematic analysis of lysine 2-hydroxyisobutyrylation proteome in plants, and it serves as an important resource for future investigations of the regulatory mechanisms and functions of lysine 2-hydroxyisobutyrylation.Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds.Meng Xiaoxi X, Xing Shihai S, Perez Loida M LM, Peng Xiaojun X, Zhao Qingyong Q, Redoña Edilberto D ED, Wang Cailin C, Peng Zhaohua Zprojections, protein translation, glucose biosynthetic process, Ribosomal Peptide, posttranslational modification, Lysine Hydrochloride, determination, Embden-Meyerhof, Ribosomal Protein, protein, B-cell receptor complex, Embden Meyerhof Parnas Pathway, starch anabolism, peptide, Polypeptides, protein polypeptide chains, Lysine Acetate, peptido, Associations, Rices, 2, Embden-Meyerhof Pathway, protein aggregate, Elaiosome, L Lysine, integumentum commune, Ribosomal, posttranslational amino acid modification, thymus nucleic acid, peptides, mRNA Translation, K, membrane bound, Moods, epsilon-diaminocaproic acid, Plant Embryo, Pathways, proteins, plants, number of, HPLC, LYS, Diaspores, Lysin, papilla, n, Double-Stranded DNA, deoxyribonucleic acids, house mouse, DNAn, B-lymphocyte receptor complex, Asian cultivated rice, protein anabolism, Pathway, anatomical protrusion, protein biosynthetic process, wide/broad, Data Set, external covering of organism, Krebs cycle, land plants, lamina, mouse, anaerobic glycolysis, flanges, organism surface, extra or missing physical or functional parts, Double-Stranded, antibodies, Embden-Meyerhof-Parnas, (Deoxyribonucleotide)n+m, Embden-Meyerhof-Parnas Pathway, Lipid, shelf, lysine, red rice, protein formation, Seed, desoxyribose nucleic acid, Ribosomal Protein Synthesis, Diaspore, PTM, mice, shelves, Plant, Plant Zygote, alpha, projection, ridge, Embden-Meyerhof pathway, human, Rice, Protein Synthesis, immunoglobulin, wide, higher plants, Protein Translation, B cell receptor accessory molecule complex, glycolysis, protein synthesis, spine, integumentary system, post-translational modification, rice, ds DNA, B lymphocyte receptor complex, Mouse, Polypeptide, DNA, starch synthesis, dermal system, Embden-Meyerhof Pathways, Proteomes, Protein Biosynthesis, human being, DNS, (Deoxyribonucleotide)n, lamellae, starch formation, number, Synthesis, Gene, broad, protein-containing complex, process of organ, Deoxyribonucleic acids, protrusion, lamella, Translation, antibody, surface, BCR complex, polypeptide chain, Deoxyribonucleic Acid, Metabolism, Gene Products, citric acid cycle, Mood, starch biosynthesis, Lysine, immunoglobulin complex, Genetic Translations, study, lipid metabolism, Genetic, Ribosomal Protein Biosynthesis, Peptide Biosynthesis, Double Stranded, Zygote, Deoxyribonucleic acid, ridges, posttranslational protein modification, man, has or lacks parts of type, Zygotes, peptidos, Ribosomal Peptide Biosynthesis, (Deoxyribonucleotide)m, laminae, Genetic Translation, modifed Embden-Meyerhof pathway, mRNA Translations, Elaiosomes, Embden Meyerhof Pathway, protein complex, Affects, DNAn+1, anatomical process, Proteins, total expressed protein, Peptide, mereological quality, polypeptide, native protein, natural protein, Mus, Acetate, Embryos, Protein, chemical analysis, epsilon-diaminocaproic acid., sequence, protein biosynthesis, ds-DNA, L-Lysine, flange, organ process, opsonin activity, Embryo, 10^[-9], distinct, Biosynthesis, mRNA, body surface, Oryza sativa, glucose biosynthesis, Plant Embryos, Embden-Meyerhof-Parnas pathway, primary structure of sequence macromolecule, post-translational amino acid modification, Protein Gene Products, Gene Proteins, processes, process, red rice <Oryza sativa>, TCA cycle, Plant Zygotes, cardinality, Desoxyribonukleinsaeure, B cell receptor activity, processus, Peptid, assay, 6-diaminohexanoic acid, EnisylIPP2A2, 2-amino-4-(methylsulfanyl)butanoic acid, ion, Hgfr, Lysine Hydrochloride, False, region or site annotation, cleavage, FBN, 5730555F13Rik, protein, precursor, protein-containing complex, PHAPII, binding site, 5730420M11Rik, peptide, Polypeptides, protein polypeptide chains, Lysine Acetate, HGF, Methionine, ClvPrd, peptido, template-activating factor I, polypeptide chain, HGFR, ECTOL1, establishment and maintenance of position, 2, F15E12.6, Lysine, establishment and maintenance of substrate location, RCCP2, protein aggregate, WMS, L Lysine, Search Engines, SET, F15E12_6, proportion, positional, F, i2pp2a., peptides, TAF-I, MUB3_18, K, scatter factor receptor, iones, M, phosphatase 2A inhibitor I2PP2A, ipp2a2, Acetylations, epsilon-diaminocaproic acid, 2pp2a, proteins, MUB3.18, ions, CG10574, AUTS9, Probabilities, OCTD, DmelCG4299, set, IGAAD, 2PP2A, 2-amino-4-(methylthio)butanoic acid, LYS, 10^[-6], DmelCG10574, taf-ibeta, ppm, Lysin, dSET, dSet, site, peptidos, AI838057, RG7MT1, GPHYSD2, metionina, Racemethionine, Asian cultivated rice, SGS, ratio, phapii, establishment and maintenance of substance location, data, proto-oncogene c-Met, DL-Methionine, PRO, protein complex, T5E21.12, acetylation, igaad, 2-Amino-4-(methylthio)butyric acid, StF-IT-1, Search, 9130215G10Rik, CYS, Peptide, Engine, ACMICD, polypeptide, single organism localization, native protein, Ionen, natural protein, I-2PP2A, Acetate, Dm I-2, Protein, I2PP2A, red rice, lysine, MFS1, Methionin, establishment and maintenance of localization, methionine, Hmet, and GLY protein 2, L-Lysine, region, WMS2, Data Base, ATCMPG1, MET, Met, T5E21_12, ATCMPG2, parent ion, HGF receptor, HGF/SF receptor, and GLY protein 1, CHARGES, HLA-DR-associated protein II, positional polypeptide feature, DI-2, INSDC_feature:misc_binding, I-2Dm, tyrosine-protein kinase Met, proportionality, rate, MASS, CG4299, alpha, single-organism localization, inhibitor of granzyme A-activated DNase, hCMT1c, c-Met, I-2PP1, dSET/TAF-Ibeta, red rice <Oryza sativa>, 2610030F17Rik, TAF-IBETA, localisation, precursor ion, binding_or_interaction_site, Ion, rice, SSKS, alpha-amino-gamma-methylmercaptobutyric acid, quotient, Peptid, TAF-Ibeta, Polypeptide, Par4, variable, AA407739, 6-diaminohexanoic acid, i2pp2a, 5730455C01Rik, Enisyl, SF receptor, establishment and maintenance of cellular component locationliquid chromatography tandem mass spectroscopy, LC-MS2, LCMSMS, Lysine Hydrochloride, K, acetylation, LC-MS/MS, epsilon-diaminocaproic acid, Acetylations, alpha, red rice <Oryza sativa>, Lysine Acetate, LC/MS/MS, LYS, Acetate, liquid chromatography-tandem mass spectroscopy, rice, Lysin, LC-MSMS, red rice, lysine, 2, liquid chromatography tandem mass spectrometry, LC-MS-MS., Lysine, 6-diaminohexanoic acid, L-Lysine, Enisyl, Asian cultivated rice, L LysineElaiosomes, Embryo, Diaspore, wide/broad, determination, Lysine Hydrochloride, K, Oryza sativa, Plant, total expressed protein, epsilon-diaminocaproic acid, Plant Embryo, Plant Zygote, Zygote, alpha, broad, Plant Embryos, Rice, Plant., wide, Lysine Acetate, red rice <Oryza sativa>, LYS, Plant Zygotes, Acetate, Diaspores, Lysin, rice, Embryos, chemical analysis, Rices, lysine, red rice, Zygotes, 2, assay, Lysine, Seed, Elaiosome, 6-diaminohexanoic acid, L-Lysine, Proteomes, Enisyl, Asian cultivated rice, L Lysineliquid chromatography tandem mass spectroscopy, CPD photolyase activity, posttranslational modification, MeCN, NCMe, PhrB photolyase activity, determination, Ethylenediaminetetraacetic acid, classic hairy cell leukaemia, protein, 2-(indol-3-yl)ethanoic acid, Basodexan, Hydrogenchlorid, B-cell receptor complex, pigmented epithelium, (ethylenedinitrilo)tetraacetic acid, peptide, Polypeptides, protein polypeptide chains, halite, hydrogen chloride, IAA, peptido, CH3-C#N, B1, Urea, HCL-C, 2, Min, 3, 2', NUP96, outer pigmented layer of retina, protein aggregate, present in fewer numbers in organism, epithelium, WMS, DmelCG42273, Edetic acid, 2-diyldinitrilo)tetraacetate, Divorced, posttranslational amino acid modification, LCMSMS, peptides, ion(4-), membrane bound, E927b, N, hypoplasia, pigmented retina, min, chemical analysis., mAPC, proteins, Divorces, DNA cyclobutane dipyrimidine photolyase activity, HPLC, SUPPRESSOR OF AUXIN RESISTANCE 3, AI047805, cloruro sodico, salt, Wasserstoffchlorid, pigment epithelium of retina, decreased, column, sample, D1, pigmented retina epithelium, s, (ethane-1, B-lymphocyte receptor complex, GPHYSD2, acidum edeticum, SGS, ratio, LC-MS2, PRE, ethylenediaminetetraacetate, rock salt, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, LC-MS/MS, Dmel_CG7826, 2'', {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID, classic hairy cell leukemia, pigmented retinal epithelium, antibodies, ur, ACMICD, carbamide, (Indol-3-yl)acetate, common salt, Dm1, retinal pigment, HCL, Chlorwasserstoff, dipyrimidine photolyase (photosensitive), IES, leukemic reticuloendotheliosis, retinal pigment layer, Dmel_CG7835, Mnb, MNB, PTM, retinal pigmented epithelium, HCl, proportionality, rate, MASS, AW124434, N'-1, natrii chloridum, beta Trypsin, Indole-3-acetic acid, H2NC(O)NH2, phr A photolyase activity, immunoglobulin, heteroauxin, DNA-photoreactivating enzyme, B cell receptor accessory molecule complex, post-translational modification, liquid chromatography-tandem mass spectroscopy, B lymphocyte receptor complex, Polypeptide, methyl cyanide, chlorane, 1728, chlorure d'hydrogene, FBN, Carbamide, ethylenediaminetetraacetic acid, photoreactivating enzyme activity, protein-containing complex, CG7826, EDTA tetraanion, deoxyribodipyrimidine photolyase activity, stratum pigmentosum retinae, LC-MS-MS, Buffer, Karbamid, antibody, BCR complex, polypeptide chain, reduced, subnumerary, ECTOL1, Acide ethylenediaminetetracetique, Harnstoff, LC-MSMS, CG7835, Darknesses, CG42273, stratum pigmentosa retinae, tiny, Carmol, Separated, immunoglobulin complex, cloruro de hidrogeno, acide edetique, proportion, MOS3, 2'''-(ethane-1, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, 2-Ethane diylbis-(N-(carboxymethyl)glycine), PRECOCIOUS, Hydrogen chloride, ethylenediamine tetraacetic acid tetraanion, beta-Trypsin, chlorure de sodium, F23A5.3, Indoleacetic acid, posttranslational protein modification, decreased number, Solution, OCTD, edta, 2-diyldinitrilo)tetraacetic acid, hairy cell leukemia, (indol-3-yl)acetic acid, EDTA, Kochsalz, peptidos, F23A5_3, PTHB1, small, 1H-indol-3-ylacetic acid, DYRK1, 1-(14)C-labeled, 3H-labeled, protein complex, chloridohydrogen, acetonitrile, buffer, Peptide, acido edetico, polypeptide, [HCl], stratum pigmentosum (retina), MODIFIER OF SNC1, LC/MS/MS, native protein, Temperatures, natural protein, Natriumchlorid, carbonyldiamide, C18, Protein, deoxyribonucleic photolyase activity, Hydrochloride, MFS1, table salt, Dyrk1, Vacuums, NaCl, ACETONITRILE, WMS2, cyanomethane, opsonin activity, AU020952, Separation, RPE, underdeveloped, uree, photolyase activity, urea, Separations, CC1, H4edta, Tripcellim, 3-Indolylessigsaeure, ethanenitrile, retinal pigment epithelium, sample population, UREA, post-translational amino acid modification, ME-IV, p. pigmentosa retinae, Trypure, concentration, SSKS, quotient, B cell receptor activity, liquid chromatography tandem mass spectrometry, Peptid, edetic acid, deoxyribonucleate pyrimidine dimer lyase (photosensitive), assay, hydrochloric acid, sodium chloride, ethylenediaminetetraacetate tetraanionliquid chromatography tandem mass spectroscopy, LC-MS2, big, scale tissue, determination, Lysine Hydrochloride, gyltl1b-b, peltate hair, acetylation, Proteins, LC-MS/MS, Mbp1, Gene, froggy, LC-MS-MS, Gyltl1a, large, LC/MS/MS, Lysine Acetate, Acetate, MDDGA6, mKIAA0609, LC-MSMS, chemical analysis, Protein, lysine, red rice, Gene Products, 2, Lysine, scales, myd, L-Lysine, L Lysine, fg, LCMSMS, gyltl1b, scale, K, Protein., MDDGB6, plant peltate hair, mdc1d, expanded, epsilon-diaminocaproic acid, Acetylations, Mbp-1, proteins, alpha, Protein Gene Products, BPFD#36, Gene Proteins, MDC1D, red rice <Oryza sativa>, LYS, enr, enlarged, liquid chromatography-tandem mass spectroscopy, Lysin, rice, great, liquid chromatography tandem mass spectrometry, scale (sensu Metazoa), assay, 6-diaminohexanoic acid, Enisyl, Asian cultivated rice1680trueOryza sativa Lysine Acetylation LC-MS/MSBy the combination of affinity enrichment and high-resolution LC-MS/MS analysis, large-scale lysine acetylome analysis was performed in oryza sativa. Altogether, 1,003 lysine acetylation sites in 692 proteins were identified.2018-10-242015-08-21PXD0027734454464152446644991755825805931173880433309286643235983906288705108061119459932716024619624619716032933206375811363399981036358945327583851187947NCBITaxon:12805723071351225117750585557146835364916738721589103062915929158364151584938858033271591002263888691513558847518704359309451464796928123977133216413328038103430436545833398580818894621432059179392118259063295790690174934693812472725632273219286728139545132949140816918045416193453745713903634530114311402064119810871355477142450732644210435551274432149671428316669455972910039237514615754647842242208964139231744712701390114319338293550823074111481194669489693529372512646904106617275802405507216599366581216595294128213312832965431282128033952321818431832920435315228112454357554787498019575928459330797253623114367331159556444214321381849223948824261914548140479109697622615515311179573347205968798662330980058884558626528173630943179698936160488454745664162425678253175133204963035554320465650506326331299NCBITaxon:131345658606886076993894246887955453512014887519795921612941001602352642032890969456941016763107622853164351854312157457744491760445246794144242324113NCBITaxon:177321409292979310239101178709NCBITaxon:405597499079913652611227349821717018736745101161035856915693132842626587210360983341336795108944866330315819NCBITaxon:493299253068839100058987329940445861153571147161224911343053115631201755442193299358726317872366698724642615134588727421572678725476242231414611510416079129831530554689111800665564841255228562198822136162997679825102169982311746738976411676108077232642411557446894444741536776744685960039376520961182263573578458273068808637721663266689NCBITaxon:269704910312NCBITaxon:13898381920112413681089319975961230773197479465228329176196627766896059606157295137221446701711012567371233435335481052311009040544931799863878343061510429863578840193733496155087711982159739757498708782297197215407821190857075206189985076480256318418985623951655190264946454635286746360NCBITaxon:110719646375939288357461287460113450664912538458814594319722196381116752638588596NCBITaxon:6157977872379534408126338039452641145953612351786169407722724323074691123869978540979541NCBITaxon:29544243277627912924970361251804264307476792745961532848123136254264282573131504752697961029938865990346941713443386263475154155403632997966287732396440426289930629548657558462823823522862871736231399463601068842043601043994796858355859593218479968954440426071017316780781440772NCBITaxon:6191840231719931281183610036105023185579969484851908021878783749907038476641004116922596345910659212257862607046183260705334542260707NCBITaxon:780NCBITaxon:15024515166584578853187029442712115869103716478496209285747078124966842528619212638541094343197383379192875NCBITaxon:103592829126806395602959870448300641802242752266437310555242354432243081433614690081502575412983964271191364516996328104121697927262327262430085212389936436801097791356223347471821314269704958331361858030NCBITaxon:56938268830640297605277963818583342409061147787127441415368163958885813076749402243264081721281614055920425468761383708127442343427128509901191274420127442651953491137024924054373413164166081756261528235256750602853218951773119350184645145051149241215323956481882299673170915800257125614801549031384736031423166385962859631015101450520493227591428693732664179332648373153NCBITaxon:96152972210976771412621121114493760833341911079276283332518661006581237561266625555929248479148691774920036009491722617566143534073120325835247225944751750375451367830649908515151438992NCBITaxon:115523745374729235492