JPOST 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KurodaMus Musculus (mouse)https://repository.jpostdb.org/entry/JPST003082University of TokyojPOSTMus musculus, 3.4.22.-, Caspase-14 subunit p10, Laboratory, Swiss, mice, Mus domesticus, Swiss Mouse, CASP14, mouse, total expressed protein, mini-ICE, House Mice, Swiss Mice, Caspase-14 subunit p19, CASP-14, MICE, House Mouse, Laboratory Mice, domesticus, jecur, iecur., Livers, House, Mus, Mini-ICE, Mus musculus domesticus, Mouse, Mice, Proteomes, Laboratory MouseWater, Methane, sodium salt, 70zpep, CDF, ammonium formate, PEP/X4, 13C-labeled, PP14, MeCN, cadmium salt, Materials, anon-WO0172774.86, Raw, Product, Laboratory, anon-WO0172774.87, LYP2, LYP1, Powder, DmelCG14121, AI326280, H(2)O, A4, BOUND WATER, anon-WO0172774.89, 2-(indol-3-yl)ethanoic acid, magnesium formate, oxidane, mg/ml, CG3629, House Mouse, zinc salt, DmelCG6143, trichloro-, WATER, HOH, Bca, 5730420M11Rik, 2-Propanone, Polypeptides, hydrogen chloride, MSK16, cobalt(II) formate dihydrate, Method, Biological, CH3-C#N, B1, AGM4, Capcell, AGAMOUS-like 61, germacrene A synthase activity, Software Engineering, Biological Product, WMS, DiA, bca, treatment, gamma sarcoglycan, LyP, SET, Biologic Drugs, K, Ushercell, HardwareType, T6G21.3, DIASP, DIA, Dia, EG:196F3.2, Ba, AI047805, DmelCG4299, isolation and purification, PA1, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, LYP, set, Wasserstoffchlorid, Lymphoid phosphatase, Biological Medicine, LYS, Lys, column, Propanon, scientific observation, Lysin, D1, sample, Medicine, Half Cystine, F12B17_170, Biologic Drug, Lzm, nickel salt, SGS, Lzp, Stars, Bonin Islands, protein biosynthetic process, dl, Biologic Products, Zinc Cysteinate, cobalt (+2) salt, acid, CASP14, Procedure, PEPINO, Software Tools, ACMICD, l(2)01092, Computer Applications, H2O, (Indol-3-yl)acetate, sodium (4:1:1) salt, Pyroacetic ether, Dm1, magnesium salt, Computer Applications Software, Chlorwasserstoff, protein formation, sarcoglycan, shell, 6-trans-farnesyl-diphosphate diphosphate-lyase (germacrene-A-forming) activity, Hydrogen Oxide, Acid, DLL, Software Applications, bcgn, h., HLA-DR-associated protein II, Caspase-14 subunit p10, Standard, instrument, DI-2, LY57, Biological Medicines, Source Software, I-2Dm, Biological Drug, F27C12_24, Swiss Mouse, formate, F27C12.24, F20B18_110, cromium (+3), Caspase-14 subunit p19, INSDC_feature:gene, Biologics, alpha, Methodological, E(Arp), Agc, GD, I-2PP1, Lysm, Applications, dll, heteroauxin, TAF-IBETA, protein synthesis, Material, 35kD dystrophin-associated glycoprotein, spirit of wood, DIANA, ammonium (4:1) salt, Mouse, TAF-Ibeta, methyl cyanide, chlorane, DmelCG32810, lead (+2) salt, STARS, PEP, glutamic acid side-chain, Methyl Alcohol, Computer Software Applications, 3.4.22.-, nickel formate dihydrate, lead formate, Biologic Pharmaceuticals, chlorure d'hydrogene, Biocatalysts, aluminum salt, 2-trans, mini-ICE, CH3OH, precursor, protein-containing complex, thomson, pep, CG7826, agua, jecur, mass-to-charge ratio, fs(2)eo6, propanone, CG30170, l(2)387, isolation, Ly57, dimethylcetone, Gene Products, CG7835, HILDA, Mus musculus domesticus, CG42273, Half-Cystine, MAM, gamma-SG, PH3, Technique, Application, Biologicals, Open Source Softwares, anatomical systems, Hydrogen chloride, thallium (+1) salt, L Cysteine, Software Application, hydrogen sulfate, rubidium salt, Open Source Software, 2pp2a, methanoic acid, CG10331, CG10574, CD156, Computer Software Application, CG10330, Study, Enzyme, 2PP2A, Tools, dSET, dSet, peptidos, Dimethyl ketone, Saeure, 2.7, PTHB1, CSPG1, Biologic, Drl, Pharmaceuticals, Lyzs, measuring, Products, 1-(14)C-labeled, 35 kDa dystrophin-associated glycoprotein, Biologic Medicines, Proteins, D10Wsu136e, b(2)cgn, Methyl alcohol, chloridohydrogen, potassium formate, copper (+2) salt, acetonitrile, DRF2, (+)-(10R)-germacrene A synthase activity, SGCG, Mdu, Tool, polypeptide, Temperatures, native protein, I-2PP2A, mda, C18, cupric formate, chemical analysis, Dm I-2, proteomic analysis, Biopharmaceutical, MFS1, Sodium, MeOH, aluminum formate, Library, ami, Achromobacter protease I, AU020952, lithium formate, Col4a-1, DMDA1, ensemble, cellulose sulfate, Ptpn8, Saeuren, med, Striated muscle activator of Rho-dependent signaling, 3-Indolylessigsaeure, hydrogen phosphorus, House Mice, ethanenitrile, muscle, CD156a, ME-IV, achromopeptidase, plan specification, Computer Programs, Gene Proteins, Applications Softwares, 2-PHOSPHOENOLPYRUVIC ACID, hydrogen phosphide, Standards, PE, AI450383, [OH2], PTPN8, hydrochloric acid, Methoxide, protein translation, MGC130048, IPP2A2, Bru, NCMe, determination, DmelCG30170, b(2)gcn, Mus domesticus, instrument configuration, classic hairy cell leukaemia, zinc formate, cleavage, lead salt, CASP-14, Hydrogenchlorid, protein, CG11121, Alkylations, peptide, Techniques, old, ammonium tetraformate, POF, peptido, IAA, Pop, Min, protein aggregate, methyl ketone, Computer Program, DmelCG42273, wood alcohol, Svc, Art, l(2)k07135, peptides, TAF-I, Natural, Open, E430039A18Rik, iecur, epsilon-diaminocaproic acid, min, Computer Programs and Programming, Swiss Mice, achromobacter beta-lytic protease (blp), mAPC, X4/PEP, purification, PEPPER, copper, Biological Drugs, SO, IGAAD, lithium salt, Methodological Studies, DmelCG10574, PrEP, ppm, C16orf53, disease management, 38E.16, Therapies, gamma-sarcoglycan, dihydridooxygen, Lyw-57, TEAB, Medicines, Sodium Methoxide, house mouse, PAEG, dihydrogen oxide, GPHYSD2, Reference Standard, fs(2)eo-C, ammonium (2:1) salt, So, Therapy, phapii, (+)-germacrene A synthase activity, Standard Preparation, Standard Preparations, protein anabolism, Standardization, CG6143, Alcohol, dimethylketone, SG-gamma, mouse, aqua, Dmel_CG7826, StF-IT-1, ben(2)gcn, Th, classic hairy cell leukemia, Aceton, Source Softwares, Programs, SLP65, Program, Ly-57, ms(2)04138, Desmoplastic infantile astrocytoma, DmelCG3629, Biopharmaceuticals, Mini-ICE, 3.1.3.48, lysyl endoprotease, BcDNA:LP01770, Computer Applications Softwares, Genetic Materials, Biologic Product, median, Lzm-s1, cellulose, IES, Softwares, CG14784, GAS, nickel (+2) salt, Carbinol, Dmel_CG7835, Genetic Material, 2-(phosphonooxy)-2-propenoic acid, carbinol, CG14783, Mnb, MNB, parent ion, Mus musculus, SLP-65, ammonium salt, PEST-domain phosphatase, F20B18.110, BASH, MS/MS, mice, acide, POF2, HCl, hydrogen hydroxide, cobaltous formate, acids, L-Cysteine, AI047692, acido, CG4299, MASS, AW124434, gamma (35kDa dystrophin-associated glycoprotein), MICE, beta-Ketopropane, Methodological Study, Treatments, En(Arp), acqua, muscle element, domesticus, Trichloromethane, Wood, GdA, DMDA, precursor ion, GdF, PNBP, AGC1, Acetamide, copper salt, Biocatalyst, Cistron, Wasser, Polypeptide, GdS, i2pp2a, Proteomes, cg10331, Cysteine Hydrochloride, SGCG_HUMAN, Procedures, cesium salt, FBN, gcn, Gene, Methyl, Computer, Methylalkohol, TYPE, PHAPII, hardware, formic acid, DAGA4, method, potassium salt, DmelCG11121, House, Ms1, ECTOL1, 14C-labeled, DmelCG1768, method used in an experiment, 35DAG, Studies, Wood Alcohol, Del(8)44H, SCG3, Mice, cloruro de hidrogeno, PHOSPHOENOLPYRUVATE, Drugs, somda, Genetic, MS1, Swiss, MS2, ipp2a2, Natural Product, phosphane, Indoleacetic acid, eau, calcium formate, OCTD, Reference, (indol-3-yl)acetic acid, 10^[-6], Suspension, wood naphtha, taf-ibeta, PASTICCINO 2, male sterility 1, Mus <genus>, musculus, BGCN, cromium (+3) salt, Preparation, Azeton, DIA2, 2-iodo-, sodium formate, mouse <Mus>, TCEP, CG14121, BLNK-S, Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP, Applications Software, Open Source, Dimethylketon, DYRK1, l(3)S147910, Computer Software, nickel formate, 3H-labeled, protein complex, 6-trans-farnesyl-diphosphate diphosphate-lyase [(+)-germacrene-A-forming] activity, Desmoplastic astrocytoma of infancy, Bgcn, igaad, strontium formate, total expressed protein, CG1768, strontium salt, Cistrons, Peptide, LGMD2C, group, [HCl], Software Tool, Mus, Mus <subgenus>, water, Protein, MLPLI, I2PP2A, Hydrochloride, core, p100, protein biosynthesis, Dyrk1, Dias, Software, ACETONITRILE, tandem MS, cyanomethane, Data Base, WMS2, F12B17.170, 1479/10, MALE STERILITY 1 PROTEIN, CC1, Engineering, fs(2)eoQS2, chromic formate, sample population, Laboratory Mice, Protein Gene Products, Drug, Livers, dSET/TAF-Ibeta, Preparations, 2610030F17Rik, Therapeutic, concentration, 2-carboxyethyl, wood spirit, SCARMD2, SSKS, calcium salt, Natural Products, Peptid, Treatment, assay, AA407739, Laboratory Mouse, CG32810, UltrasonicfalseProteome data of WT and ob/ob mice liver during starvationTen-week-old wilt-type (WT) and ob/ob mice were starved for 0, 2, 4, 6, 8, 12, 16, and 24 hours and liver samples were collected. Total proteins extracted with methanol:chroloform:water (2.5:2.5:1) and subjected to the following proteomic analysis. For standardization among runs of measurement, proteins from frozen liver powder of Lys(6)-SILAC mice (Silantes) were also extracted with methanol/chloroform extraction. Protein concentration of the lysates was determined using the bicinchoninic acid (BCA) assay (23227, Thermo Fisher Scientific) and calibrated to 1 mg/mL. Then, 50 µg each of non-labeled and labeled lysates were mixed for peptide preparation. Cysteine residues were blocked by 2 mM Tris (2-carboxyethyl) phosphine hydrochloride (TCEP) (Thermo Fisher Scientific) at 37°C for 30 min followed by alkylation with 10 mM 2-iodoacetamide (IAA) at room temperature for 30 min. The proteins were precipitated with acetone for 3 hours at −30°C and the resulting pellet was dispersed in 50 mM triethylammonium bicarbonate by ultrasonic treatment (three times for 30 s with intervals of 30 s) with a Bioruptor (Diagenode). The protein suspension was subjected to digestion with lysyl endopeptidase (Wako) for 16 h at 37°C. Resulting peptides were centrifuged at 15,000 × g for 15 min at 4°C and subjected to C18-StageTip purification. Peptides were resolved in 50 µL 3% acetonitrile (can)-0.1% foromic acid prior to MS analysis. All samples were analyzed with Q Exactive HF-X (Thermo Fisher Scientific) instrument equipped with an UltiMate 3000 RSLCnano LC System (Thermo Fisher Scientific) via a nano-electrospray source with a column oven set at 50°C (AMR Inc.). Peptides were directly injected onto a 75 μm × 25 cm PicoFrit emitter (New Objective, Woburn, MA, USA) packed in-house with C18 core-shell particles (CAPCELL CORE MP 2.7 μm, 160 Å material; Osaka Soda Co., Ltd., Osaka, Japan) with a linear gradient of 7–42% B for 76 min, 42-80% B for 5 min, and 80% B for 9 min at a flow rate of 100 nL/min, where A is 0.1% formic acid and B is 0.1% formic acid and 80% acetonitrile. MS data acquisition was performed in data-independent acquisition (DIA) mode. For quantification in the DIA mode, MS1 spectra were collected in the range of m/z 423-865 at 60,000 resolution to set an AGC target of 3 × 10^6. For MS2 spectra, collections were conducted in the range of > m/z 200 at 30,000 resolution to set an AGC target of 3 × 10^6. The isolation width was configured to 8 Th with stepped normalized collision energies of 20, and 23%. Through the optimization by Skyline 4.1, isolation window patterns in m/z 428-860 were used as window placements. In the DIA mode for a spectral library, the pool of all samples was analyzed by using the above measurements and the gas-phase fractionation method. In the gas-phase fraction method, six MS ranges (m/z 426-502, 498-574, 570-646, 642-718, 714-790, and 786-862) were used, and each was measured by overlapping DIA10. MS1 spectra were collected at 120,000 resolution to set an AGC target of 3 × 10^6. MS2 spectra were collected in the range of > m/z 200 at 60,000 resolution to set an AGC target of 3 × 10^6. The isolation width was set to 2 Th with stepped normalized collision energies of 20 and 23%. Isolation window patterns in the ranges of m/z 428-500, 500-572, 572-644, 644-716, 716-788, and 788-860 were used as window placements optimized by Skyline 4.1. The spectra library was generated by searching MS data in the library against the mouse Ensembl release 97 database using Scaffold DIA (Proteome Software Inc., Portland OR, USA). The parameters were as follows: experimental data search enzyme, LysC/P; maximum missed cleavage sites, 1; precursor mass tolerance, 6 ppm; fragment mass tolerance, 8 ppm; and static modification, cysteine carbamidomethylation. The threshold for identification of peptides was a peptide false discovery rate (FDR) < 1%. To identify peptides derived from Lys(6)-SILAC mice, a library of identified peptides with a mass increase 6.020129 Da on Lys was built and added to the library obtained above. All raw data was processed with DIA-NN (ver. 1.8) using library search mode using the following parameters: reannotation, Mus_musculus.GRCm38.97.pep.all.fa; modification, UniMod188 (6.020129), and peak-translation. Using the output from DIA-NN software, the SILAC ratios of all assigned fragment ion pairs were calculated, and the median of the SILAC ratios of each protein was used for protein quantification. Proteins assigned to a single ensemble gene ID were used in the following analyses. The SILAC ratios of all the proteins were normalized by the median of the SILAC ratio in each biological sample.Note that data at 0 hour were already public (PXD048481)Tue May 20 00:00:00 BST 2025PXD05302510090