Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_MTB_TMT10_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_MTB_TMT10_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_MTB_TMT10_5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_MTB_TMT10_6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_MTB_TMT10_7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_MTB_TMT10_4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_MTB_TMT10_9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_MTB_TMT10_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_MTB_TMT10_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_MTB_TMT10_8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/MTB191015.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD023788/20210123_results_txt.rarprimaryOK200xuping_bprc@126.comSun jinshuaiMass SpectrometryShotgun proteomicsMaxQuantQe-hfMycobacterium tuberculosisTmt10tagshttp://www.ebi.ac.uk/pride/archive/projects/PXD023788H37Rv, H37Ra and BCG were grown in Lowenstein-Jensen medium. The three strains were harvested at logarithmic mid-late phase and washed with phosphate buffer saline (PBS) three times. Lysis was performed in lysis buffer (9 M Urea, 10 mM Tris-HCl (pH 8.0), 30 mM NaCl, 50 mM IAA, 5 mM Na4P2O7, 100 mM Na2HPO4 (pH 8.0), 1 mM NaF, 1 mM Na3VO4, 1 mM sodium glycerophophate, 1% phosphatase inhibitor cocktail 2, 1% phosphatase inhibitor cocktail 3, 1x EDTA-free protease inhibitor cocktail. Then the total lysate was centrifuged at 13,000 rpm for 10 min at 4℃ to remove debris. The technical replicate was set in H37Rv samples as H37Rv1-1and H37Rv1-2, and we had at least three biological replicates in each strain. The same amount of proteins (120 μg) from each total sample was reduced with 5 mM of DTT, alkylated with 20 mM of iodoacetamide, precleaned with 10% SDS-PAGE (0.7 cm), and digested in-gel with final concentration of 12.5 ng/μL trypsin (Meizhiyuan, Beijing, China) at 37 ℃ for 12 h. The tryptic peptides were labeled with TMT reagents (10plex) according to the manufacturer’s instructions. The 127N, 127C, 128N and 128C TMT tags were used for the H37Rv samples, the 126, 129N and 129C tags were used for the H37Ra, and the 130N, 130C and 131 tags were used for the BCG samples, respectively.The TMT-labeled and combined samples were injected into a Durashell C18 column (150 Å, 5 μm, 4.6 × 250 mm2) and eluted with a linear gradient in 60 min. The eluent was collected every 1 min and finally combined into 10 fractions and analyzed with a Q Exactive HF mass spectrometer.PrideTMTmonohydroxylated residueacetylated residueThe raw files were searched with MaxQuant (v1.5.5.1) against the TubercuList reference proteome from M. tuberculosis H37Rv database along with 245 common contaminant protein sequences (http://www.maxquant.org/contaminants.zip). Fully tryptic peptides with as many as 2 missed were allowed. TMT 10-plex (N-Term/K) and cysteine carbamidomethyl were set as fixed modification, whereas oxidation of methionine was set as variable modification. The tolerance of the precursor and fragment ions were set to 20 ppm.ProteomicsPing XuQ Exactive HFState Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics, 38 Life Science Park Road, Beijing 102206PARTIALMycobacterium Tuberculosis H37rvsjsshuai@126.com34634997 Wang H, Wan L, Shi J, Zhang T, Zhu H, Jiang S, Meng S, Wu S, Sun J, Chang L, Zhang L, Wan K, Yang J, Zhao X, Liu H, Zhang Y, Dai E, Xu P. Quantitative proteomics reveals that dormancy-related proteins mediate the attenuation in mycobacterium strains. Virulence. 2021 12(1):2228-2246 10.1080/21505594.2021.1965703StudentChinaAlthough members of the <i>Mycobacterium tuberculosis</i> complex (MTBC) exhibit high similarity, they are characterized by differences with respect to virulence, immune response, and transmissibility. To understand the virulence of these bacteria and identify potential novel therapeutic targets, we systemically investigated the total cell protein contents of virulent H37Rv, attenuated H37Ra, and avirulent <i>M. bovis</i> BCG vaccine strains at the log and stationary phases, based on tandem mass tag (TMT) quantitative proteomics. Data analysis revealed that we obtained deep-coverage protein identification and high quantification. Although 272 genetic variations were reported in H37Ra and H37Rv, they showed very little expression difference in log and stationary phase. Quantitative comparison revealed H37Ra and H37Rv had significantly dysregulation in log phase (227) compared with stationary phase (61). While BCG and H37Rv, and BCG and H37Ra showed notable differences in stationary phase (1171 and 1124) with respect to log phase (381 and 414). In the log phase, similar patterns of protein abundance were observed between H37Ra and BCG, whereas a more similar expression pattern was observed between H37Rv and H37Ra in the stationary phase. Bioinformatic analysis revealed that the upregulated proteins detected for H37Rv and H37Ra in log phase were virulence-related factors. In both log and stationary phases, the dysregulated proteins detected for BCG, which have also been identified as <i>M. tuberculosis</i> response proteins under dormancy conditions. We accordingly describe the proteomic profiles of H37Rv, H37Ra, and BCG, which we believe will potentially provide a better understanding of H37Rv pathogenesis, H37Ra attenuation, and BCG immuno protection.Quantitative proteomics reveals that dormancy-related proteins mediate the attenuation in mycobacterium strains.Wang Hong H, Wan Li L, Shi Jiahui J, Zhang Tao T, Zhu Huiming H, Jiang Songhao S, Meng Shuhong S, Wu Shujia S, Sun Jinshuai J, Chang Lei L, Zhang Liqun L, Wan Kanglin K, Yang Jiaqi J, Zhao Xiuqin X, Liu Haican H, Zhang Yao Y, Dai Erhei E, Xu Ping PIPP2A2, LYNAP, Monocyte-derived neutrophil chemotactic factor, Ethylenediaminetetraacetic acid, classic hairy cell leukaemia, Basodexan, Hydrogenchlorid, 2-(indol-3-yl)ethanoic acid, protein, lysis, Neutrophil-activating factor, IL-8(6-77), (ethylenedinitrilo)tetraacetic acid, Mid(H15), 5730420M11Rik, peptide, Polypeptides, MDNCF-c, protein polypeptide chains, halite, Lymphocyte-derived neutrophil-activating factor, sodio, Bcg, BCG, hydrogen chloride, IAA, peptido, IL-8, Urea, HCL-C, DGS, 2, Min, 2', Sodium Ion, IL8|NAP1 form III, protein aggregate, MDNCF-a, present in fewer numbers in organism, MDNCF-b, DmelCG42273, Sinkiang, Edetic acid, (Ala-IL-8)77, 2-diyldinitrilo)tetraacetate, SET, sarcoma of breast, ion(4-), SDS-PAGE electrophoresis, peptides, dermoid cyst with malignant transformation, TAF-I, E927b, N, phosphatase 2A inhibitor I2PP2A, hypoplasia, min, mAPC, IBP, proteins, free, ecotype, IL8|NAP1 form IV, AI047805, DmelCG4299, cloruro sodico, salt, set, IGAAD, Wasserstoffchlorid, decreased, MDNCF, DmelCG10574, DmelCG1106, sample, IL8|NAP1 form II, Strains, autolysin activity, necrosis, (ethane-1, Bladder pain syndrome, GCP|IL-8 protein V, Reagents, MONAP, GCP|IL-8 protein I, phosphatase, Itg, acidum edeticum, reagents, phapii, Emoctakin, ethylenediaminetetraacetate, rock salt, GCP|IL-8 protein III, BZRP, IL-8(7-77), Ity, 2'', Dmel_CG7826, StF-IT-1, MM2, late, {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID, T-cell chemotactic factor, classic hairy cell leukemia, breast sarcoma, Granulocyte chemotactic protein 1, ur, PBS, PBR, Manchuria, carbamide, Sodium-23, common salt, (Indol-3-yl)acetate, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Dm1, ity, HCL, Chlorwasserstoff, sodium, bacteriocin activity, cultivar, IES, leukemic reticuloendotheliosis, reactif, natrium, Dmel_CG7835, H15r/nmr2, Mnb, MNB, Painful Bladder Syndrome, GCP|IL-8 protein IV, HLA-DR-associated protein II, Mainland China, DI-2, Interleukin-8, I-2Dm, HCl, IL8|NAP1 form VI, SDS polyacrylamide gel electrophoresis, RGAG2, GCP|IL-8 protein II, reagent, CG4299, inhibitor of granzyme A-activated DNase, N'-1, AW124434, natrii chloridum, lysed material, beta Trypsin, CG1106, I-2PP1, Neutrophil-activating protein 1, H2NC(O)NH2, Indole-3-acetic acid, lysin activity, Painful bladder syndrome, heteroauxin, TAF-IBETA, Acetamide, Indicator, bacteriolytic toxin activity, NAP1, NAF, TAF-Ibeta, Polypeptide, chlorane, Strains and Sprains, i2pp2a, TMT, 1728, Bladder Pain Syndrome, BPBS, Calmette-Guerin Bacillus, NAP-1, sarcoma of the breast, chlorure d'hydrogene, Reagent, Gene, Carbamide, ethylenediaminetetraacetic acid, protein-containing complex, SDS polyacrylamide gel electrophoresis of proteins, EDTA tetraanion, CG7826, PHAPII, MA2, Buffer, Ion Level, Karbamid, template-activating factor I, polypeptide chain, reduced, Protein 3-10C, subnumerary, Acide ethylenediaminetetracetique, Harnstoff, IL-8(1-77), CG7835, technical_replicate, Gene Products, CG42273, tiny, Carmol, Sprains, IL-8(8-77), Level, cloruro de hidrogeno, Reagents and Indicators, acide edetique, 2'''-(ethane-1, GCP|IL-8 protein VI, 2-Ethane diylbis-(N-(carboxymethyl)glycine), reactivo, Hydrogen chloride, ethylenediamine tetraacetic acid tetraanion, gel, ipp2a2, los, beta-Trypsin, chlorure de sodium, inhibiteur, 2pp2a, pk18, Indoleacetic acid, decreased number, MBR, CG10574, Indicators, Nramp1, IL-8(5-77), Chemokine (C-X-C motif) ligand 8, edta, 2-diyldinitrilo)tetraacetic acid, DmelCG6634, lysate, hairy cell leukemia, inhibidor, 2PP2A, (indol-3-yl)acetic acid, Peking, taf-ibeta, EDTA, Kochsalz, dSET, dSet, PTBR, peptidos, IL8, 2-iodo-, thiol methyltransferase activity, small, inhibitors, 1H-indol-3-ylacetic acid, CXCL8, DYRK1, LECT, DBI, protein complex, Sprain, GCP-1, Proteins, igaad, inhibitor, chloridohydrogen, Monocyte-derived neutrophil-activating peptide, LUCT, (Ser-IL-8)72, buffer, GCP1, People's Republic of China, Peptide, acido edetico, Lsh, strain, polypeptide, [HCl], IL8|NAP1 form I, Inner Mongolia, H15r, native protein, PKBS, Natriumchlorid, IL8|NAP1 form V, natural protein, carbonyldiamide, I-2PP2A, ME-IV., Dm I-2, Protein, Strain, I2PP2A, Hydrochloride, table salt, Sodium, IL-8(9-77), Dyrk1, NaCl, teratoma with malignant transformation, Sodium Ion Level, AU020952, technical replicate, holin, underdeveloped, uree, nmr2, urea, sodium dodecyl sulphate–polyacrylamide gel electrophoresis, CC1, H4edta, 3-Indolylessigsaeure, Tripcellim, CG6634, Na, Natrium, phosphoric monoester hydrolase activity, TBX20, extra, mDRC, sample population, UREA, ME-IV, Nramp, Protein Gene Products, Gene Proteins, Trypure, dSET/TAF-Ibeta, 11Na, 2610030F17Rik, C-X-C motif chemokine 8, concentration, Peptid, edetic acid, Sodium 23, AA407739, hydrochloric acid, sodium chloride, ethylenediaminetetraacetate tetraanionPeptidomics, protein complex, Proteins, Sprain, number, Gene, dormancy, proteins, protein, protein-containing complex, presence, Protein Gene Products, Gene Proteins, count in organism, protein polypeptide chains, Mycobacteria, native protein, natural protein, polypeptide chain, lethargus, Protein, Mycobacterium Lehmann and Neumann 1896 (Approved Lists 1980), Gene Products, Strain., Strains, quantitative, diapause, protein aggregate, Sprains, Strains and Sprains, presence or absence in organismZIP, Zip, Bru, IPP2A2, Cysteine Hydrochloride, 2-amino-4-(methylsulfanyl)butanoic acid, Raw, MHC, ion, AI461847, GPATCH6, L Isomer, Myo-II HC, protein, precursor, protein-containing complex, PHAPII, zip, ter, 5730420M11Rik, Myo, peptide, Polypeptides, protein polypeptide chains, L-Isomer Methionine, Methionine, Dm nmII, peptido, polypeptide chain, template-activating factor I, L-Methionine, Kochs disease, Tuberculosis, Pgi, Del(8)44H, Half-Cystine, protein aggregate, Gpi-1, Pedameth, CG15792, Koch's Disease, ZIPK, Svc, Koch Disease, SET, DmelCG3533, ZC3HDC9, peptides, dermoid cyst with malignant transformation, Infections, Myo-II, Myo2, TAF-I, Gpi-1r, Nlk, Gpi-1s, L Cysteine, M, iones, zip/MyoII, phosphatase 2A inhibitor I2PP2A, Phi, ipp2a2, Gpi-1t, 2pp2a, DROMHC, ppm., proteins, Mycobacterium tuberculosis Infections, ions, CG10574, DmelCG4299, NMMII, set, IGAAD, DmelCG4216, 2PP2A, 2-amino-4-(methylthio)butanoic acid, 10^[-6], DmelCG10574, taf-ibeta, Bsg75C, TB, NMM, dSET, dSet, peptidos, Mycobacterium tuberculosis, DmnmII, Half Cystine, ZIP3, metionina, Racemethionine, Myo II, thiol methyltransferase activity, l(2)02957, NK/GPI, Gpi, GPATC6, phapii, ZC3H9, Kochs Disease, Zinc Cysteinate, DL-Methionine, protein complex, igaad, 2-Amino-4-(methylthio)butyric acid, total expressed protein, Mhc-c[1], StF-IT-1, E(br), MF, L-Isomer, Amf, myoII, Peptide, tuberculosis disease, polypeptide, S-adenosyl-L-methionine:thiol S-methyltransferase activity, native protein, mOC-X, natural protein, nmMHC, Ionen, I-2PP2A, Term, Protein, Dm I-2, I2PP2A, Infection, Mhc-c, Methionin, NK|GPI, methionine, Hmet, Tuberculoses, Data Base, NK, Met, teratoma with malignant transformation, DmelCG15792, nzip, parent ion, DLK, ORG, Org, Col4a-1, HLA-DR-associated protein II, DI-2, I-2Dm, CG4216, common, Gpi1-r, Gpi1-s, L-Cysteine, CG4299, inhibitor of granzyme A-activated DNase, Gpi1-t, KIAA1847, I-2PP1, dSET/TAF-Ibeta, Osi, 2610030F17Rik, TAF-IBETA, precursor ion, Ion, alpha-amino-gamma-methylmercaptobutyric acid, Dronm-MII, anon-WO0140519.37, CG3533, Peptid, TAF-Ibeta, Polypeptide, MyoII, Mycobacterium tuberculosis Infection, AA407739, TMT, i2pp2a, Liquimeth, Proteomes, active tuberculosis, Bglap-rs1, zpr, Gpi1s, nmy-2Intervention Strategies, other disease, Calmette-Guerin Bacillus, Peptidomics, protein complex, Ity, Luzp5, Sprain, Deficiencies, disorders, number, medical condition, protein, Procedure, protein-containing complex, infectivity, presence, Intervention or Procedure, Lsh, Oxygen Deficiency, Oxygen Deficiencies, T2SS-associated complexes, Anoxia, Sec-dependent secretion system-associated complex, protein polypeptide chains, count in organism, Bcg, BCG, native protein, diseases, natural protein, polypeptide chain, Protein, Strain, Pathogenicity, disease or disorder, condition, CAPG2, diseases and disorders, protein aggregate, Sprains, hCAP-G2, LUZP5, Intervention, viral infection, human disease, CAP-G2, interventionDescription, 5830426I05Rik, general secretion pathway-associated complex, Hypoxemia, Interventional, virus process, proteins, SURGICAL AND MEDICAL PROCEDURES, Nramp1, non-neoplastic, Nramp, Oxygen, disease, Deficiency, mCAP-G2, main terminal branch, ity., disorder, Homo sapiens disease, virulence, Strains, quantitative, Anoxemia, Mtb, MTB, Strains and Sprains, Itg, presence or absence in organismd230, Respect, Calmette-Guerin Bacillus, Mycobacterium tuberculosis variant tuberculosis, determination, Peptidomics, regulation by symbiont of host system process, modulation by organism of defense response of other organism involved in symbiotic interaction, number, positive regulation by symbiont of host non-apoptotic programmed cell death, Gene, dTAFII250, dormancy, eubacteria, protein, establishment of cell quiescence, protein-containing complex, EfW1, infectivity, presence, dmTAF[[II]]230, Personal, protein polypeptide chains, G1/G0 transition, Readability, BCG, Bcg, polypeptide chain, dmTAF1, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, Taf230, Mycobacterium tuberculosis var. hominis, responsivity, hemolysis by symbiont of host RBCs, Gene Products, pathogenesis, Kochs disease, Tuberculosis, Analysis, protein aggregate, attenuated, Sprains, upregulation by symbiont of host programmed cell death, TAF250, Koch's Disease, Bacillus tuberculosis, vegetative growth of a single-celled organism, reactivity, Bacterium tuberculosis, viral infection, Koch Disease, induction of non-apoptotic programmed cell death by other organism, Taf200, modification by symbiont of host biological process, Eubacteria, dTAF[[II]]250, pattern, TFIID TAF250, dermoid cyst with malignant transformation, stimulation by symbiont of host programmed cell death, Analyses, Infections, cel, cell, distribution, Taf1p, virus process, proteins, Mycobacterium tuberculosis Infections, Monera, activation by organism of programmed cell death in other organism during symbiotic interaction, Nramp1, genetic, dTAF250, Bacteria <bacteria>, Prokaryotae, Personal Respect, TB, ity., Mycobacterium tuberculosis, fungi, Procaryotae, Strains, cytolysis by organism of host cells, TAF, constitutitional genetic, thiol methyltransferase activity, Itg, Calmette Guerin Bacillus Vaccine, Calmettes Vaccine, bacteria, dTAF[[II]]230, TAF[[II]]250, disruption by symbiont of host cell, activation by organism of non-apoptotic programmed cell death in other organism, Kochs Disease, hemolysin activity, protein complex, Ity, Sprain, Proteins, familial, TAF200, cell cycle quiescence, l(3)84Ab, BG:DS00004.13, TAFII-250, TAF250/230, Calmette Vaccine, positive regulation by symbiont of host programmed cell death, Cell, tuberculosis disease, dTAF230, Lsh, count in organism, TAFII250, S-adenosyl-L-methionine:thiol S-methyltransferase activity, native protein, enhancement of host programmed cell death, natural protein, p230, Protein, chemical analysis, Strain, ity, Pathogenicity, Infection, modulation by symbiont of host system process, modulation by symbiont of host defense response, TAF[[II]]250/230, TFIID, prokaryotes, Tuberculoses, induction by organism of programmed cell death in other organism involved in symbiotic interaction, mitigation by symbiont of host defense response, diapause, haemolysis in host, teratoma with malignant transformation, Taf[[II]]250, deep, enhancement of host programmed cell death by organism, Exhibit, TAF[[II]]230, Mycobacterium tuberculosis H37Rv, Dignity, perturbation by symbiont of host defense response, Calmette's, TAF[II]250, Understanding, CG17603, TAF[[II]], induction by organism of programmed cell death in other organism during symbiotic interaction, Bacillus Calmette Guerin Vaccine, modification by symbiont of host morphology or physiology, Nramp, Protein Gene Products, Gene Proteins, stationary phase, regulation of cytolysis of host cells by symbiont, DmelCG17603, activation by organism of host programmed cell death, induction by symbiont of host programmed cell death, Taf250, Vaccine, Data, hemolysis by symbiont of host red blood cells, prokaryote, SR3-5, lethargus, Calmette's Vaccine, activation by symbiont of host programmed cell death, virulence, inherited genetic, assay, quantitative, response, Mycobacterium tuberculosis Infection, Strains and Sprains, TMT, hereditary, Data Analyses, active tuberculosis, Prokaryota, TAF230, Mycobacterium tuberculosis typus humanus, TAF1, presence or absence in organismPeptidomics, protein complex, Proteins, number, Gene, dormancy, proteins, protein, protein-containing complex, presence, Protein Gene Products, Programs, strain, Gene Proteins, count in organism, protein polypeptide chains, Mycobacteria, ecotype., native protein, natural protein, polypeptide chain, lethargus, Protein, Mycobacterium Lehmann and Neumann 1896 (Approved Lists 1980), Gene Products, cultivar, quantitative, diapause, protein aggregate, presence or absence in organismfalseQuantitative Proteomics Reveals Dormancy Related Proteins Mediated Attenuation Program in Mycobacterium StrainTo better understand the virulence difference among different MTB strains and identify new targets for therapeutic intervention under hypoxia condition, we compared the global protein expression at the protein level by quantitative proteomics among H37Rv, H37Ra and 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