{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_Final_MYC_MOCK.xlsx"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-18hr-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-18hr-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-48hr-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-4hr-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-1hr-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-1hr-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-48hr-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-18hr-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-1hr-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-1hr-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-4hr-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-4hr-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-1hr-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-18hr-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-1hr-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-4hr-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-48hr-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-48hr-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-18hr-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-18hr-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MOCK-4hr-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-48hr-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-48hr-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD043114/20220902_MYC-4hr-3.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["james.hudson@qimrberghofer.edu.au"],"submitter":["Harley Robinson"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"disease":["Cardiovascular System Disease"],"software":[""],"submitter_keywords":["Heart","Regeneration","Cardiac","Myc","Cyclin","Infarction"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD043114"],"tissue":["Heart","Stem Cell","Cell Culture"],"sample_protocol":["2D cardiomyocytes grown in 6-well plates were transfected with Lipofectamine RNAiMax with 10µg MYC-CCNT1 (M-C) modRNA or without modRNA (CTRL). At 1, 4, 18 and 48 hr timepoints, cells were lysed in RIPA Buffer (150mM NaCl, 5mM EDTA, 1% Triton X-100, 0.5% Sodium Deoxycholate, 0.1% SDS and 50mM Tris, pH 8.0) supplemented with protease inhibitor cocktail (Roche), scrapped into 1.5 mL Eppendorf tubes. Proteins were quantified by Pierce BCA Protein Assay kit (Thermo Scientific), and 35 µg were aliquoted for proteomics. Proteomics samples were reduced with 5 mM dithiothreitol (Sigma-Aldrich) at 60° C for 30 min and alkylated with 10 mM Iodoacetamide (Sigma-Aldrich) for 10 min at room temperature in the dark. Proteins were precipitated with 5x ice cold acetone (HPLC grade, Sigma-Aldrich) and centrifuged at 20 ,627 g for 10 min at 4° C. The supernatants were removed and the pellets were washed three times with acetone. Samples were then reconstituted in 40 mM Triethylammonium bicarbonate buffer (TEAB, Sigma-Aldrich) and digested overnight with Porcine trypsin (Promega) at 37° C. Digestion was quenched with trifluouroacetic acid (TFA, Thermo Scientific) and samples were cleaned using self-fabricated Empore SDB-RPS StageTips, dried by GeneVac sample concentrator, then reconstituted in 0.1% formic acid (FA, Fisher Scientific) for LC-MS analysis. Peptide concentration was determined by Pierce MicroBCA Assay kit, and all samples adjusted to 500 ng/µL.  Samples (2 µL injection) were loaded on to a Thermo Acclaim PepMap 100 trap column (5 mm x 300 um ID) for 5 min at a flow rate of 10 ul/min with 95% Solvent A (0.1% FA in water) and subsequently separated on a Thermo PepMap100 analytical column (150 mm x 300 um ID) equipped on a Thermo Ultimate 3000 LC interfaced with a Thermo Exactive HF-X mass spectrometer. Peptides were resolved using a linear gradient of 5% solvent B (0.1% FA in 80% acetonitrile) to 40% solvent B over 120 min at a flow rate of 1.5 µl/min. This was followed by column washing and equilibration for a total run time of 65 min. Mass spectrometry data was acquired in positive ion mode. Precursor spectra (350-1400 m/z) was acquired on orbitrap at a resolution of 60,000. The AGC target was set to 3x106 with a maximum injection time of 30 ms. Top 20 precursors were selected for fragmentation in each cycle and fragment spectra was acquired in orbitrap at a resolution of 15,000 with stepped collision energies of 28, 30 and 32. The AGC target was 1e5, with a maximum ion injection time of 45 ms. The isolation window was set to 1.2 m/z.  Dynamic exclusion was set to 30 sec and precursors with charge states from 2-7 were accepted for fragmentation."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Raw LC-MS data was searched against the reviewed Uniprot human database (20,399 sequences, downloaded April 19, 2021) using Sequest HT on the Thermo Proteome Discoverer software (Version 2.3), with matching between runs enabled. Precursor and fragment mass tolerance were set to 20 ppm and 0.05 Da respectively. A maximum of two missed cleavages were allowed. A strict false discovery rate (FDR) of 1% was used to filter peptide spectrum matches (PSMs) and was calculated using a decoy search. Carbamidomethylation of cysteines was set as a fixed modification, while oxidation of methionine and N-terminal acetylation were set as dynamic modifications. Protein abundance was based on intensity of the parent ions and data was normalized based on total peptide amount. Statistical significance was calculated using a t-test for summed abundance-based ratios, built into the Proteome Discoverer software."],"omics_type":["Proteomics"],"labhead":["James Hudson"],"instrument_platform":[""],"labhead_affiliation":["QIMR  Berghofer Medical Research Institute, Brisbane 4006, Queensland, Australia Faculty of Health, Queensland University of Technology, Brisbane 4000, Queensland, Australia Faculty of Medicine, The University of Queensland, Brisbane 4072, Queensland, Australia"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["harley.robinson@uqconnect.edu.au"],"publication":["Not available"],"curator_keywords":["Human proteome project","Biology/disease-driven human proteome project (b/d-hpp)"],"submitter_affiliation":["QIMR Berghofer Medical Research Institute"],"submitter_country":["Australia"],"additional_accession":[]},"is_claimable":false,"name":"Modified mRNA encoding Myc and Cyclin T1 induces transient cardiac regeneration post-myocardial infarction in the mouse","description":"Following severe myocardial injury, such as myocardial infarction (MI), cardiomyocytes perish and are never replaced. Using a combination of genetic mouse models of Myc and Cyclin T1 overexpression and experimental MI, single nuclei sequencing, human cardiac cells derived from pluripotent stem cells and treatment of wild-type mice with a prototype modified mRNA (modRNA) therapeutic, we tested the regenerative capacity of transient, localised Myc and CyclinT1 expression. Here, the proteome of 2D cardiomyocytes (from human PSC) under effect of transfected modified mRNA (with Myc-CyclinT1 co-expression \"MYC\", or without \"MOCK\") was evaluated over a time course (1, 4, 18, 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