{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive.ucsd.edu/v07/MSV000094570/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Benjamin C Orsburn"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=8f5a9d5ddc554da1ad82fc79d712a7a8"],"submitter_email":["borsbur1@jhmi.edu"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["375"],"ptm_modification":["UNIMOD:35 - \"Oxidation or Hydroxylation.\""],"data_protocol":[""],"omics_type":["Proteomics"],"instrument_platform":["timsTOF fleX"],"species":["Trifolium Repens (ncbitaxon:3899)"],"submitter_affiliation":["Johns Hopkins"],"name_synonyms":["Trifolium repen., white clover, Clover, creeping white clover, determination, pratenses, Trifolium pratense, Trifolium, chemical analysis, Trifolium pratenses, Red, repen, Red Clover, assay, Trifoliums, Trifolium repens L., Trifolium repens"],"description_synonyms":["Water, MeCN, NCMe, determination, H(2)O, Metabonomic, BOUND WATER, Metabonomics, Xkl-1, oxidane, Trifoliums, RP11-508D10.1, WATER, HOH, peptide, Tnfsf5, Polypeptides, KL receptor activity, Techniques, Gsfsco1, peptido, Method, CH3-C#N, SCO5, SCO1, Gsfsow3, Gsfsco5, wood alcohol, SOW3, T-BAM, type 5 acid phosphatase, tartrate-resistant acid ATPase, peptides, Trifolium pratense, hypoplasia, plants, W, procedures, TRAP3, T-cell antigen Gp39, Tudor repeat associator with PCTAIRE-2, column, Methodological Studies, Ice, Carbon, Carbon Dioxide, Red, repen, dihydridooxygen, Bs, TNFSF5, autolysin activity, necrosis, TEAB, Sodium Methoxide, dihydrogen oxide, T5ap, MGC - 45012, Sl, CD40L, c-SP3, Alcohol, land plants, Tnfrsf5, aqua, Cd40l, Tr-kit, Procedure, hCD40L, PBT, H2O, Clover, IMD3, kl1-A, bacteriocin activity, TNF-related activation protein, KIT, Carbinol, Ly-62, Hydrogen Oxide, Trifolium repens L., carbinol, tyrosine-protein kinase Kit, pbt, Dioxide Snow, Red Clover, NKTL, Plant, hydrogen hydroxide, AW743063, kit, Methodological, AI326936, beta Trypsin, Methodological Study, acqua, Wood, higher plants, Spn3, lysin activity, precipited material, spirit of wood, TrATPase, IGM, bacteriolytic toxin activity, CD40LG, Wasser, Polypeptide, methyl cyanide, Carbon Dioxide Snow, Methyl Alcohol, krk1, CG9334, Procedures, TRAP, p50, Bath, Ly62, Trifolium repen, TAPK, SCF receptor activity, Methyl, CH3OH, Methylalkohol, TR-AP, SPR2, agua, Buffer, method, reduced, scfr, method used in an experiment, GP39, Studies, Wood Alcohol, tiny, CD40-L, DmelCG9334., Metabolomic, SCFR, Technique, gp39, CD154, DmelCG2045, Fdc, anatomical systems, creeping white clover, CATC4, GKLP, beta-Trypsin, Sp3, eau, Trifolium repens, Solution, Study, PCTAIRE2-binding protein, MGC:45012, TEIF, wood naphtha, Trap, HIGM1, peptidos, SP2, SP3, sp3, C78062, small, P105, NTKL, proto-oncogene c-Kit, Snow, 1-(14)C-labeled, Dry, 3H-labeled, PCTAIRE2BP, Trifolium pratenses, Methyl alcohol, Bp50, ACP5, acetonitrile, SPENCDI, buffer, Peptide, polypeptide, SP#2, pratenses, KIT ligand receptor activity, water, chemical analysis, Sodium, MeOH, techniques, ACETONITRILE, cyanomethane, XKrk1, c-KIT, white clover, holin, PRSS, underdeveloped, Tripcellim, ethanenitrile, D130027J01Rik, CD117, plan specification, Trypure, c-kit, C-Kit, Trifolium, Ssm, wood spirit, xkl-1, Peptid, assay, TRACP, CG2045, [OH2], Methoxide, methodology"],"additional_accession":["PXD051590"]},"is_claimable":false,"name":"Proteomic and metabolomic analysis of multifoliolate mutants of Trifolium repens","description":"Quadrifoliolate and pentafoliolate mutants of Trifolium repens were collected at Pug Mountain Vineyards in Southern Pennsylvania in the summer of 2023 along with matched trifoliolate plants gathered within the same cubic yard. Stems and leaves were frozen in a dry ice bath and homogenized by beadmill in a solution of methanol, acetonitrile and water (35/35/30). The supernatants were clarified by centrifugation at 13,000 x g for 5 minutes at 4C. The supernatant was removed and dried for metabolomic analysis while the precipitate was dried by speedvac and resuspended in 1x S-Trap lysis buffer. Samples were prepared following vendor instructions using the S-Trap 96-well plate format with the exception that cysteines were not reduced and alkylated. Samples were digested for 2 hours at 47C with a 20 nanograms of trypsin in 100mM TEAB solution. Eluted peptides were dried by SpeedVac and quantified using a colorimetric peptide kit. 400 nanograms of peptides were loaded onto EvoTips and were analyzed using ddaPASEF on a TIMSTOF Flex insturment using a 15cm x 75 um column and the 15SPD and 30SPD methods. Metabolomics was performed on a Q Exactive \"Classic\" system coupled to an RSLCnano with a 15cm x 2.1mm HyperSil Gold column using a 20min method. Separate runs were performed in triplicate in positive and negative polarities. Proteomic samples were analyzed with FragPipe 21.1 and Metabolomic samples were analyzed in Compound Discoverer 3.3 SP3. ","dates":{"publication":"Fri Apr 19 14:52:00 BST 2024"},"accession":"MSV000094570","cross_references":{}}