Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_6-combinationMdomestica_196_v1.0.proteiniRT__FDR.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_M_2_SWATH.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_M-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_CK_2_SWATH.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_CK-1.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_M_3_SWATH.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_M-1.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_CK_2_SWATH.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_CK-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_CK-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_M-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_CK-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_M-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_CK_1_SWATH.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_M_1_SWATH.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_M-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_M_3_SWATH.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_CK_3_SWATH.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_M_1_SWATH.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_CK-1.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_M-1.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_M_2_SWATH.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_CK_1_SWATH.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180413_CK_3_SWATH.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_CK-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD011132/20180211_ZFY_6-combinationMdomestica_196_v1.0.proteiniRT.groupprimaryOK200fyzhu@njfu.edu.cnChuan-Qi ZhongMass SpectrometrySWATH MSNot availableAppleSwath-mshttp://www.ebi.ac.uk/pride/archive/projects/PXD011132Approximately 1g of apple skin was grind in a mortar by liquid nitrogen. The tissues were homogenized with the 10X vol of solution A (10% trichloroacetic acid (TCA)/ acetone) and then centrifuged at 16000g for 5 mins. After removed the supernatants, the pellets were washed by the 10X vol of solution B (80% MeOH/0.1M NH4OAc) and then centrifuged again and followed by the 10X vol of washing solution C (80% acetone). After centrifugation and the supernatants removing, the pellets were dissolved into the 8ml SDT buffer (4% SDS, 0.1M DTT, 0.1M MOPS/Cl, pH 8.0). Thereafter, the dissolved samples were incubated at 95oC for 10mins and cooled on ice immediately for 5mins. After centrifugation twice again, the final supernatants were obtained with the addition of 4X vol of chilled 80% acetone for protein precipitation overnight at -20oC. At the end, the protein pellets were dissolved into 1-2ml urea buffer (6M urea in 200mM MOPS-Cl/ 4mM CaCl2, pH 8.0) according to the size of pellet. The protein concentration was determined based on the Bradford method (Bio-Rad). Each protein sample (100μg) was reduced by 10mM DTT at 50oC for 40mins and then alkylated by 40mM IAA (iodoacetamide) in the dark at room temperature for 30mins. Subsequently, each sample was further diluted by distilled water for decreasing urea concentration below 2M and sample peptides were acquired by a trypsin digestion (enzyme/protein, 1:50 w/w) at 37oC overnight. These peptides were acidified by 10% trifluoroacetic acid (TFA) and further desalted by SepPak C18 cartridges (Waters). Moreover, the desalted peptide samples were speed-dried in vacuum concentrator and directly dissolved into the water with 0.1% formic acid for LC-MS/MS analysisPrideNot availableNo PTMs are included in the datasetPeptides samples were analyzed by a Triple TOF 5600 mass spectrometer (SCIEX, USA) coupling with an Eksigent NanoLC-2D plus system. In the Trap-Elute mode, each sample (2μg) was entranced into a nanaoFlexcHiPLC trap (3μm, ChromXP C18CL, 120 Å, 0.5 mm × 200μm) under the 95% solvent A (water with 0.1% formic acid) and 5% solvent B (acetonitrlile with 0.1% formic acid) at a stable flow rate of 500 nL/min for 15 mins, then separated through a linear gradient from 5% to 35% of solvent B at 300 nL/min for 120 mins. The positive ion mode with an ion spray voltage of 2300V was used in the Triple TOF 5600 mass spectrometer. The spectral ion library based on SWATH-MS was firstly generated by using data-dependent acquisition (DDA). In the DDA mode, the complete MS1 spectra was collected by a survey scan of 250ms in the range of 350-1250 m/z. The top 40 precursor ions were selected for further MS2 fragmentation and MS/MS spectra was acquired in the range of 100-1800 m/z. In the SWATH analysis, the same peptide samples were analyzed using the cyclic DIA (Data-Independent Acquisition) mode under the similar methods as above described. All precursor ions in the range of 400-1250Da were collected for further fragmentation. All of DDA data files were used to set up a reference spectral library by the software ProteinPilot 4.5 (Sciex) against the searching from the UniProt Swiss-Prot Malus domestica protein database (28797 proteins, July 2015 release). The parameters including the digestion, alkylation, biological modification and ID search were set up during the database search and a false discovery rate (FDR) of <1% was accepted as the criteria for the peptides assignments and protein identification. Subsequently, all DIA data and spectral library were loaded into the software PeakView v.1.2 (Sciex) under restricted criteria and settings such as eight peptides, six transitions, 99% peptide confidence and ion library mass tolerance (50 ppm). The output of quantified proteins and corresponding peptides by the MarkerView (Sciex) was generated three quantitative files including the extracted peak area for individual fragment ion, sum of fragment ion areas for each as well as the sum of peptide areas for each protein. The exported raw peak intensity data of proteins was normalized and analyzed using z-transformation as described in (Cheadle et al., 2003; Haverland et al., 2014). Protein differential expression between Fuji_Apple and Fuji_M was expressed in z value as >2 or < -2 with p value < 0.05 to be up-regulation or down-regulation respectively.ProteomicsFuyuan ZhuTripleTOF 5600PARTIALNanjing Forestry UniversityMalus DomesticaNot availableandyzcq@gmail.comCollege of life ScienceChinasodium salt, liquid chromatography tandem mass spectroscopy, Hac-1/Dark, the integument, ammonium formate, 13C-labeled, IL1BC, cadmium salt, pelt, determination, Skn-li, DmelCG6829, CASP-1, zinc formate, Ter94, CG7788, crice, rad, lead salt, SDH, protein, Basodexan, 2-(indol-3-yl)ethanoic acid, magnesium formate, CG15720, 10X, Apaf-1, zinc salt, trichloro-, ter, DmelCG2331, 2-Propanone, peptide, Trifluoroacetate, Malus pumila auct., SDS, Polypeptides, protein polypeptide chains, ammonium tetraformate, IAA, peptido, ClvPrd, cobalt(II) formate dihydrate, B1, Urea, Apaf1, protein aggregate, 10x, Il1bc, present in fewer numbers in organism, ARK, DmTER94, integumentum commune, wood alcohol, rsh, LCMSMS, I, 10x single cell library construction, hac-1, peptides, Rubidium, N, E927b, weight-weight percentage, dvcp, Tissue, dermoid system, hypoplasia, entire skin, arc, chemical analysis., proteins, CaCl2, copper, ark, Trichloroacetic, IL-1BC, T1, decreased, lithium salt, l(2)03775, SOLO DANCERS, 22.26, ICE, sample, trifluoro-, D1, ter94, Otf11, Fam91a1, dVCP, Sodium Trichloroacetate, dApaf1, AV220772, skin and subcutaneous tissue, ammonium (2:1) salt, Dmel_CG4346, Calcium chloride anhydrous, nickel salt, symmetric dyschromatosis of the extremities, LC-MS2, Caspase-1 subunit p10, Malus domestica, ice, iCE, D-Apaf-1, drice, cobalt (+2) salt, anon-53Fa, LC-MS/MS, AI836084, l(2)SH0173, CG2331, integumental organ, 10x sequencing, cultivated apple, Pyrus malus, not genetically inherited, ur, DmelCG7788, dmTERA, carbamide, (Indol-3-yl)acetate, sodium (4:1:1) salt, Tera, Stickstoff, magnesium salt, drIce, drICE, DmelCG42628, BC033609, BcDNA:GM02885, Raps, IES, nickel (+2) salt, END, CG6829, Acetic acid, Hydrogen Oxide, carbinol, dark/hac-1/dapaf-1, Acid, calcium chloride, reticulate acropigmentation of Dohi, ammonium salt, ribosome-associated degradation, P45, apple, familial reticulate acropigmentation of Dohi, Trifluoroacetic, formate, dyschromatosis symmetrica hereditaria 1, cobaltous formate, Dmel_CG15720, ribosome-associated ubiquitin-dependent protein degradation, cromium (+3), hac1, anon-WO2004063362.65, anon-WO2004063362.67, beta Trypsin, mKIAA0493, w/w, REM3, dapaf-1S, METHANOL, H2NC(O)NH2, Indole-3-acetic acid, vertebrate epidermis, apaf-1, nitrogen, dapaf-1L, heteroauxin, VCP/p97, Cesium, Acide, spirit of wood, Acetamide, liquid chromatography-tandem mass spectroscopy, Drice, copper salt, p45, ammonium (4:1) salt, Apple, Polypeptide, entire integument, 7N, DRICE, lead (+2) salt, dermal system, RAD1, 1728, Malus sylvestris var. domestica, dermis plus epidermis plus hypodermis, F10B6_15, region of skin, Acide trichloracetique, nickel formate dihydrate, Dapaf-1/HAC-1, lead formate, Otf-11, DrIce, DrICE, aluminum salt, cesium salt, rapsyn, dyschromatosis symmetrica hereditaria, CH3OH, Carbamide, Methylalkohol, protein-containing complex, DmelCG5692, F10B6.15, apple tree, epidermis, LC-MS-MS, Buffer, formic acid, 7.12, Dark/Hac-1/dApaf1, Karbamid, method, Hac1, potassium salt, Dark/Hac-1/dApaf-1, polypeptide chain, reduced, subnumerary, 14C-labeled, method used in an experiment, Harnstoff, LC-MSMS, tiny, Carmol, VCP ATPase, trichloracetique, Skn-1a, calcium dichloride, Cesium Trifluoroacetate, VCP, Vcp, skin, pins, thallium (+1) salt, PCE-2, dapaf-1, beta-Trypsin, rubidium salt, 4733401P19Rik, Indoleacetic acid, dapaf, methanol, dark, decreased number, calcium formate, methanoic acid, SKIN, PINS, Solution, calcium chloride anhydrous, skin organ, (indol-3-yl)acetic acid, Caspase-1 subunit p20, DARK, wood naphtha, dTERA, ribosome-associated ubiquitin-dependent protein catabolism, peptidos, liquid, cromium (+3) salt, 10X sequencing, dArk, Dapaf-1, HHT1, 2-iodo-, sodium formate, PTHB1, small, 1H-indol-3-ylacetic acid, dark/dapaf-1/hac-1, cdc48, mass percentage, Oct-11a, CG42628, CG5692, nickel formate, caspase 3, protein complex, dApaf-1, p97, strontium formate, skin zone, Methyl alcohol, apaf1, acropigmentation of Dohi, potassium formate, CE-2, DSH, DSH1, copper (+2) salt, strontium salt, buffer, ribosome-associated ubiquitin-dependent protein breakdown, Peptide, Methanol, polypeptide, skin plus hypodermis, APAF1, LC/MS/MS, skin region, Oct11, native protein, Temperatures, natural protein, carbonyldiamide, Hac-1, C18, cupric formate, Protein, Trichloroacetate, pTER94, Sodium, Rubidium Trichloroacetate, MeOH, Skin-1a, CES2A1, Dark, Vacuums, BcDNA.GM02885, tegument, aluminum formate, Skin, Pins, Dark/Apaf-I, lithium formate, underdeveloped, uree, urea, vertebrate integument, 3-Indolylessigsaeure, Tripcellim, SWDS, Dark/Dapaf-1/HAC1, CDC48, IL-1 beta-converting enzyme, azote, Interleukin-1 beta-converting enzyme, CGI-97, dApaf-1/DARK/HAC-1, sample population, chromic formate, l(2)46Ch, UREA, Epoc-1, nitrogeno, Interleukin-1 beta convertase, plan specification, Trypure, portion of skin, l(2)46CFs, integument, concentration, velocity, wood spirit, 3.4.22.36, [CaCl2], CG4346, calcium salt, Malus pumila var. domestica, liquid chromatography tandem mass spectrometry, Peptid, RAD, Rad, assay, 10x Genomics, ORW1, l(2)46CFf, dAPAF-1sodium salt, CDF, ammonium formate, 13C-labeled, cadmium salt, ion, Raw, FEZL, magnesium formate, zinc salt, Downregulation, Solvent, RP11-508D10.1, ter, 5730420M11Rik, Polypeptides, Malus pumila auct., protein polypeptide chains, Drug Tolerance, cobalt(II) formate dihydrate, Method, AGAMOUS-like 61, Software Engineering, DmTER94, WMS, DiA, ASD2, SET, type 5 acid phosphatase, Divorced, F, I, phosphatase 2A inhibitor I2PP2A, dvcp, Divorces, proteins, procedures, T6G21.3, DIASP, DIA, Dia, AI047805, DmelCG4299, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, set, T-cell antigen Gp39, sample, ter94, dVCP, TNFSF5, drug tolerance, nickel salt, SGS, Stars, Malus domestica, cobalt (+2) salt, immune system tolerance, Tnfrsf5, Up-Regulation (Physiology), CG2331, Procedure, not genetically inherited, Software Tools, hCD40L, ACMICD, dmTERA, Computer Applications, sodium (4:1:1) salt, Tera, magnesium salt, Dm1, Computer Applications Software, IMD3, Hydrogen Oxide, Software Applications, HLA-DR-associated protein II, DI-2, Upregulation, Source Software, I-2Dm, F27C12_24, NKTL, formate, F27C12.24, proportionality, cromium (+3), rate, Methodological, inhibitor of granzyme A-activated DNase, I-2PP1, Applications, TAF-IBETA, Self Tolerance, DIANA, ammonium (4:1) salt, Apple, TAF-Ibeta, lead (+2) salt, STARS, Computer Software Applications, nickel formate dihydrate, lead formate, False, Ly62, TAPK, aluminum salt, number, precursor, thomson, protein-containing complex, TR-AP, body system, CG7826, mass-to-charge ratio, Down Regulation., TOF, GP39, CG7835, HILDA, Gene Products, CG42273, system, Technique, ZNF312, Application, gp39, CD154, Open Source Softwares, proportion, anatomical systems, GKLP, CATC4, thallium (+1) salt, Receptor Up-Regulation, Software Application, rubidium salt, Open Source Software, 2pp2a, methanoic acid, ions, Pyrus malus var. domestica, CG10574, CD156, Computer Software Application, Study, PCTAIRE2-binding protein, MGC:45012, 2PP2A, Tools, dSET, dSet, peptidos, NTKL, Proteins, potassium formate, copper (+2) salt, ACP5, DRF2, SPENCDI, Tool, polypeptide, Down-Regulation, native protein, Immune Tolerance, I-2PP2A, Down-Regulation (Physiology), cupric formate, chemical analysis, Dm I-2, MFS1, aluminum formate, BcDNA.GM02885, Library, AU020952, lithium formate, Col4a-1, Separations, Striated muscle activator of Rho-dependent signaling, CDC48, CD156a, ME-IV, Computer Programs, Gene Proteins, ZFP312, Malus communis, Applications Softwares, quotient, TRACP, Receptor, quantitative, Immunological Tolerance, IPP2A2, Bru, determination, zinc formate, Ter94, lead salt, Malus x domestica, protein, Alkylations, peptide, DmelCG2331, Tnfsf5, Techniques, ammonium tetraformate, POF, peptido, ClvPrd, Min, protein aggregate, Computer Program, DmelCG42273, T-BAM, Svc, tartrate-resistant acid ATPase, l(2)k07135, peptides, TAF-I, TACHD, Open, E430039A18Rik, min, Computer Programs and Programming, mAPC, copper, SCAN, TRAP3, IGAAD, Tudor repeat associator with PCTAIRE-2, lithium salt, l(2)03775, Methodological Studies, DmelCG10574, 22.26, ppm, 38E.16, T5ap, MGC - 45012, GPHYSD2, ammonium (2:1) salt, ratio, CD40L, phapii, Cd40l, Dmel_CG7826, StF-IT-1, Th, cultivated apple, Pyrus malus, Source Softwares, Programs, Program, ms(2)04138, Desmoplastic infantile astrocytoma, Ionen, Receptor Down-Regulation, Computer Applications Softwares, Immunologic Tolerance, BcDNA:GM02885, TNF-related activation protein, Softwares, nickel (+2) salt, Ly-62, Dmel_CG7835, Mnb, MNB, parent ion, ammonium salt, MS/MS, POF2, apple, cobaltous formate, AW743063, CG4299, MASS, AI326936, AW124434, anon-WO2004063362.65, Methodological Study, anon-WO2004063362.67, organ system, precursor ion, VCP/p97, Tolerance, TrATPase, IGM, copper salt, CD40LG, Polypeptide, i2pp2a, Malus sylvestris var. domestica, Procedures, TRAP, p50, cesium salt, FBN, Gene, Computer, presence, PHAPII, apple tree, formic acid, 7.12, potassium salt, template-activating factor I, polypeptide chain, Ms1, ECTOL1, 14C-labeled, DmelCG1768, Studies, Del(8)44H, CD40-L, VCP ATPase, Separated, Vcp, VCP, MS1, iones, MS2, Up Regulation, ipp2a2, calcium formate, OCTD, 10^[-6], TEIF, Trap, taf-ibeta, male sterility 1, dTERA, HIGM1, cromium (+3) salt, DIA2, FEZ, sodium formate, C78062, Applications Software, P105, Open Source, DYRK1, data, cdc48, Computer Software, nickel formate, protein complex, PCTAIRE2BP, Desmoplastic astrocytoma of infancy, p97, igaad, strontium formate, Bp50, CG1768, strontium salt, Peptide, count in organism, Software Tool, natural protein, MLPLI, Protein, I2PP2A, pTER94, Dyrk1, techniques, connected anatomical system, Dias, Software, tandem MS, Data Base, WMS2, VSD1, Separation, MALE STERILITY 1 PROTEIN, CC1, Engineering, sample population, chromic formate, l(2)46Ch, Protein Gene Products, dSET/TAF-Ibeta, 2610030F17Rik, Ion, l(2)46CFs, SSKS, calcium salt, Malus pumila var. domestica, Peptid, assay, AA407739, l(2)46CFf, methodology, presence or absence in organismextracellular signal-regulated kinase activity, GrpL, pp44mapk, GRPL, CRKII, p38-alpha, p38MAPK, p38a, ter, Mutations, Hog, p38ALPHA, Malus pumila auct., Berries, rat, LeMPK3, Method, 芽 (Japanese, p44mpk, hnRNP A2/B1, indehiscent fruit (broad), Dp38, Analysis, SAPK2, Carbon Fixation, Mpk34C, DmTER94, integumentum commune, p38B, p38A, mapk14a, I, Analyses, pp42, anabolism, hrp40, HAND, dvcp, Lrbp, Plant Capsule, entire skin, hnRNP36, bHLHa28, proteins, W, procedures, Dm p38b, Hrb87Fa, multiple fruit (broad), Hrb85CD, hand, coenocarp (narrow), Skin Colors, hrp36, Grf40, ter94, Otf11, Fam91a1, dMKK3, RED, Red, dVCP, LRBP, AV220772, skin and subcutaneous tissue, GRBLG, ESTS:186F5S, DmMPK2, Malus domestica, 6.3.2.-, p63Mapk, csbp, familial, ERK-2, CG2331, Calvin Benson Cycle, terminal segment of free upper limb, ERK-4, PMK-2, PMK-1, Procedure, Spectrum Analysis, CSA2, HMG-CoAR, PMK-3, Hrb87f, CSBP, dmTERA, dehiscent fruit (broad), Tera, Color, Double ring-finger protein, Pigmentations, frucht (exact, D-MPK2, GRAP-2, Skin Pigmentations, DmelCG5475, Mek3, MEK3, DMEK3, MVLK, Spectrometry, Capsules, pooled, Legume Pods, Calvin Benson Bassham Cycle, Methodological, c-Crk, human, CSBP2, CSBP1, Breedings, MITOGEN-ACTIVATED PROTEIN KINASE, hand region, Pigmentation, p63MAPK, fore paw, Csbp2, Apple, entire integument, Csbp1, forefoot, mitogen-activated protein kinase 1, forelimb autopodium, D-p38 MAPK, advanced, region of skin, multicellular organismal biosynthetic process., Peptidomics, Otf-11, number, F14N23.9, propagule (broad), Reductive Pentose Phosphate Cycle, biosynthesis, Exip, Leucoanthocyanidins, PRKM15, Berry, Aril, dMPK2, Prkm4, p38 MAPK, PRKM14, Prkm6, Gene Products, CG18144, sapk2a, Colors, EXIP, Technique, Skn-1a, ERK, PRKM1, p38beta, PRKM2, Hrp36, JTV1, skin, p38Ka, p38Kb, LH receptor mRNA-binding protein, AI848995, Anthocyanidin, BC023857, SKIN, Mapk63, Dhand, PRKM4, GRB2L, AI414037, synthesis, Study, skin organ, CG12749, S cerevisiae, hand-C, MvK protein, HRP36, STK26, p38-2, constitutitional genetic, myelin basic protein kinase activity, Dp38b, Dp38a, RING finger protein 19A, SAPK2A, Oct-11a, Proteins, MAP-2 kinase activity, skin zone, p63-MAPK, AI256848, D130053K17Rik, MK, Anthocyanin, adventitious bud (narrow), DmMKK3, skin plus hypodermis, p38MAPKK, chemical analysis, Calvin-Benson Cycle, Tone, BcDNA.GM02885, Skin, p38 beta, Mass Spectrum Analyses, Anthocyanidins, increased number, P42MAPK, DmelCG18144, Crk1, CDC48, Crk3, CSPB1, REDK, Mvk protein, Epoc-1, Hands, Gene Proteins, 38 kDa DNA polymerase delta interaction protein, D-MKK3, Calvin Cycle, CRK1, German), Plant Capsules, forepaw, Tones, ERG12 protein, regulation, quantitative, compound fruit (broad), hereditary, MAPK 4, the integument, pelt, determination, sapk2, Skn-li, Mpk2, Mpk3, Ter94, Crko, p42mapk, D-p38, MVK protein, Crk-II, p38 alpha, Photosynthetic Carbon Fixation, DmelCG2331, Pod, Techniques, primordia, exact), forelimb autopod, Capsule, kinase-related transforming protein, Skin Color, mitogen-activated protein kinase activity, Q14, Q16, mevalonate 5-phosphotransferase, RK, mpk2, multicellular organismal biosynthetic process, Mass Spectrum Analysis, increased, single-organism biosynthetic process, DMKK3, MEK3/MKK3, dermoid system, Calvin-Benson-Bassham, genetic, MP kinase activity, l(2)03775, Dmp38a, Methodological Studies, AHA1, 22.26, Dmp38b, Plant Arils, bud, MBP kinase II activity, DmelCG12749, P11, Calvin, Arils, CG5475, forefoot of quadruped, mevalonate kinase protein, MAP kinase 2 activity, wide/broad, mouse, ERK1, ERK2, Erk3, Erk2, A230093K24Rik, ERK3, ERK4, integumental organ, future organ, Erk4, Hrb2, cultivated apple, Pyrus malus, D-P38a, GrbX, Spectroscopy, D-p38b, D-p38a, RAR1 protein, p41mapk, Syn, MAPK, BC033609, precocious, BcDNA:GM02885, P38, fruto (exact, C14orf3, LHR mRNA binding protein, CG12244, HRB87F/hrp36, Pods, GADS, JTV-1, HRB87F, apple, Mona, Plant, p38alpha, p38, Prkm15, anon-WO2004063362.65, anon-WO2004063362.67, Prkm14, Methodological Study, mKIAA0493, early, Proto-oncogene c-Crk, wide, vertebrate epidermis, VCP/p97, syncarp (narrow), p41, p40, Japanese), inherited genetic, DmelCG12304, 186F5S, dermal system, Proteomes, accessory, Malus sylvestris var. domestica, Skin Tones, dermis plus epidermis plus hypodermis, F14N23_9, l(1)G0252, bioformation, Procedures, CG7393, Plant Aril, Fruits, Mapk4, Gene, broad, Spectrum Analyses, presence, supernumerary, apple tree, epidermis, 7.12, CrkIII, p38Hog, dp38a, dp38b, Gads, Photosynthesis Dark Reactions, Cycle, Mass, Studies, p42-MAPK, VCP ATPase, Mass Spectroscopy, A330097D03Rik, VCP, Vcp, Mkk3, MKK3, hYAK3-2, diaspore (broad), formation, DmelCG12244, dHand, Spanish), 2310010A05Rik, p42 mitogen-activated protein kinase activity, Crk-III, ATP:protein phosphotransferase (MAPKK-activated) activity, GRID, dTERA, Skin Tone, Legume, yema (Spanish, dHAND, 2610021I23Rik, Calvin-Benson-Bassham Cycle, ATMPK1, rudiment, Dark Reactions of Photosynthesis, DYRK5, cdc48, aggregate fruit (broad), DMPK2, ATP-mevalonate 5-phosphotransferase, Photosynthetic, p97, Photosynthesis Dark Reaction, anon-sts23, total expressed protein, P11/Hrb87F, Legume Pod, Crk-I, DMKK3/lic, DmelCG7393, p38delta, count in organism, skin region, Oct11, fore-paw, group 2, Protein, MBP kinase I activity, pTER94, Skin-1a, techniques, tegument, forefeet, LRBP protein, Mass Spectrum, POROK3, mitogen activated kinase activity, Mxi2, vertebrate integument, Sapk2A, placode, MAPK2, l(2)46Ch, dp38, Dorfin, Protein Gene Products, present in greater numbers in organism, portion of skin, mxi2, l(2)46CFs, integument, ERT1, fore foot, 果実 (exact, Malus pumila var. domestica, BG:DS00797.3, assay, Calvin-Benson, l(2)46CFf, MAP kinase 1 activity, methodology, presence or absence in organismcdc48, wide/broad, aggregate fruit (broad), Malus domestica, p97, Plant Aril, Fruits, Ter94, propagule (broad), CG2331, broad, cultivated apple, Legume Pod, Pyrus malus, apple tree, ter, 7.12, DmelCG2331, dmTERA, Malus pumila auct., Pod, Berries, dehiscent fruit (broad), Tera, Berry, Color, Capsule, Aril, Pigmentations, indehiscent fruit (broad), Skin Color, BcDNA:GM02885, pTER94, frucht (exact, Colors, Tone, fruto (exact, VCP ATPase, BcDNA.GM02885, Skin, DmTER94, Skin Pigmentations, VCP, Vcp, diaspore (broad), Pods, I, dvcp, apple, Plant Capsule, Plant, Capsules, Spanish), Legume Pods, CDC48, anon-WO2004063362.65, anon-WO2004063362.67, multiple fruit (broad), l(2)46Ch, coenocarp (narrow), wide, Skin Colors, l(2)03775, VCP/p97, l(2)46CFs, 22.26, syncarp (narrow), dTERA, Pigmentation, ter94, German), Skin Tone, Legume, 果実 (exact, Japanese), Plant Capsules, Plant Arils, dVCP, Malus pumila var. domestica, Apple, Tones, Skin., Arils, compound fruit (broad), l(2)46CFf, Malus sylvestris var. domestica, Skin TonesfalseApple SWATH-MS - Apple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial valueApple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial value. However, the strategy on genetic breeding for red skin apple and the genetic basis of skin color differentiation is very limited and still largely unknown. Here, we reported a bud sport mutant of Fuji apple with red skin color and enhanced anthocyanins accumulation. Quantitative SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) proteomics investigations revealed proteome changes in the apple red skin bud mutation and a total of 411 differentially expressed proteins were identified in apple skin. The mutant showed significantly increased expression levels of photosynthesis-related proteins, stress-related proteins as well as anthocyanins biosynthesis pathway. On the other hand, substanial downregulation of mitogen-activated protein kinase 4 (MAPK4) and mevalonate kinase (MVK) were detected. We also hypothesize that a post-transcriptional regulation of the skin color formation occurs in the mutant through the advanced SWATH-MS analysis. Overall, our work provide important information on the application of proteomic methods for analysing proteomes changes in Fuji apple and highlights a clade of regulatory proteins potentially contributed to the fruit skin color formation.2019-06-182018-09-18PXD01113228065516460991804982953585111454224942024527872842188090368099330845811363336351524260119832758385NCBITaxon:128068888561896111430118726355557114526236493461364031952065126957366649274670738538836411354615821582310665688954762721123294422291180992323122586365458333460792519365914320597129386558195851149315242592637371250232NCBITaxon:1272111957748186614885843104300245135867221755437408169180454266834453058612668351498225058149636745855452811320814795641003923751463694204943320896420896344597413797912838440066793529367156759388036478434716052165994048321659721659545501315282693042165915627161696833218321729204277944762376454317203094980197525556978159509439843948840479NCBITaxon:2157525338551531051067439899037122857759515205968762262311210884555588845587077918178081736309431794571698936160488409859NCBITaxon:37162104782679401505907148364320421061320491381693630355543204663263331199456545351102541110321745921612928867641002642036945694101676341021076127735113165823925472793342814613584301417298174633457744491675476048932128735675684030135062191726518130194111929439367110411310239320255598632582788396591047593474951604901652998355256631758543980110243260866310245980875741755518320196447145268045796631367019083233115611415535510421932555217634981812359871069955529NCBITaxon:4751850298335476113615741465477180066556484337677299767982510216998238976484074137351155711089725482444474153NCBITaxon:5055789969844100036465349334147147493548019467512991143597412764731370863265478765698353221599838192011106775772710348198524794640986099586157187176685991915729513722117110129292107687834974198602028091488406334249234235152335985988655974649987039202111072943311711397215987419085037117082711708284182350241451139692931902197822474636046147123749402375939723287581722532566489050794526591972211915853101774208588596NCBITaxon:615750521028307989511051989972375059576131720002634196102641088878176179212190659407121906772275885815689964975151950587244NCBITaxon:22023717NCBITaxon:17036122019998570506174767927450627249159615333554184005246432136861505964878486662941786661347515363291018194301086731018510184NCBITaxon:1763573039635586331492862876705801321650851865368595105135553482260710185687294296110091416333NCBITaxon:619184023210007348824123363630710470058127187878645159812894555663577553470951451225786260704NCBITaxon:13356262607052607076584574054163677483167233150561007133705654195NCBITaxon:305550445791399878168119011928752829126806315327341478281055524NCBITaxon:9606135858469008111167815022830519302836728593008529005NCBITaxon:569382688306401794699151011849943525815159014482428381113944260419370475927237082816772850351581990119519532673863701370249240536088385816224888175626158355837153337605726711935019980861193502167879108579137113712724071906503714759175712562745757270903113335503728142433747924910078711082NCBITaxon:96157243359463318586260799141262200298492670NCBITaxon:1263719281249212528303856838569591169266100658123756127504542666255151978837503600941293497905463224535247214012575151164990851515143899237453747445446415243235959202228870515805955365550881579327160293851578114978633892894535936479437NCBITaxon:6854412754225117159010901341673871589552101296610306129671585158451584937659393432715910022637673388990461423451287689591198332966467041464792936576164280341160221641331599280382803536909108917689462181214108034817939228788929502711313329528282944568617493468191126526997227321890382107601247190400727159736997828114311402064119810871355477436581424507229533796982042321242231291632180334708714537209164573321535815754699287770202060328114319338293550833291292211487252649997283035739087183087267271037908550717629970767892683704155737292140532941281607839563924314262654898227377596207322086595882735551693605330797255181135491597495350261159556143213840607258781414471509493349194963401614334728005936046316461046603815184547448500356709747751240174841855601335755547920427460769946881037620148871005941289093164354282688500712303831389464940838283594144242322197857742171598921409212205853939621157781154756929793244704749906604162103591905158114452749907312987779913112273170187546991103589915NCBITaxon:3729610360983341871049113079813367953164072994671034015786582645303337330638301130641399253064236365059116965478854698112116203431710337299404458620734011535711195296526117455311147161338654131316634305521323120179836025323731276125523299351299385057316317642619794011513458445772678728623219334151346186208621160791392227983516811961255228149539322323116761757312108077213487999948861856962814084341033519963218496209913924882097115338209611533920953304393755699286266447NCBITaxon:269704933986243694110312195883205092029061013068599975864486432499525297246741158343894278637894262567378639123343551419983493179986865540553435291486545147124546688925104298635712467915164135825763288401937334508771823803912903912952971974869317978911028688999513373105487712516321389850762554701193806222523256318865713034431121308516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