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Stein"],"software":[""],"tissue":["Heart","Cardiac Muscle Cell"],"sample_protocol":["Lysates were subjected to an in-solution tryptic digest, following a modified version of the Single-Pot Solid-Phase-enhanced Sample Preparation (SP3) technology (PMID: 25358341, PMID: 29565595). 20 µl of a slurry of hydrophilic and hydrophobic Sera-Mag Beads (Thermo Scientific, #4515-2105-050250, 6515-2105-050250) were mixed, washed with water and were then reconstituted in 100 µl water. 5 µl of the prepared bead slurry were added to 50 µl lysate containing 10 µg of protein. 55 µl of acetonitrile were added. All further steps were prepared using the King Fisher Apex System (Thermo Scientific). After binding to beads, beads were washed three times with 100 µl of 80% ethanol before they were transferred to 100 µl of digestion buffer (50 mM Hepes/NaOH pH 8.4 supplemented with 5 mM TCEP, 20 mM chloroacetamide (Sigma-Aldrich, #C0267), and 0.25 µg trypsin (Promega, #V5111)). Samples were digested overnight at 37°C, beads were removed and the remaining peptides were dried down and subsequently reconstituted in 10 µl of water. 50 µg of TMT16pro (ThermoFisher, #A44520 and #A52045) label (dissolved in 4 µl of acetonitrile) were added. Excess TMT reagent was quenched by the addition of 4 µl of an aqueous 5% hydroxylamine solution (Sigma, 438227). Peptides were reconstituted in 0.1 % formic acid and equal volumes were mixed. Mixed peptides were purified by a reverse phase clean-up step (OASIS HLB 96-well µElution Plate, Waters #186001828BA). Peptides were subjected to an off-line fractionation under high pH conditions (PMID: 25358341) yielding 12 fractions.  Peptides were separated using an Ultimate 3000 nano RSLC system (Dionex) equipped with a trapping cartridge (Precolumn C18 PepMap100, 5 mm, 300 μm i.d., 5 μm, 100 Å) and an analytical column (Acclaim PepMap 100. 75 × 50 cm C18, 3 mm, 100 Å) connected to a nanospray-Flex ion source. The peptides were loaded onto the trap column at 30 µl per min using solvent A (0.1% formic acid) and eluted using a gradient from 2 to 80% Solvent B (0.1% formic acid in acetonitrile) over 2 h at 0.3 µl per min (all solvents were of LC-MS grade). The Orbitrap Fusion Lumos was operated in positive ion mode with a spray voltage of 2.2 kV and capillary temperature of 275 °C. Full scan MS spectra with a mass range of 375–1500 m/z were acquired in profile mode using a resolution of 120,000 with a maximum injection time of 50 ms, AGC operated in standard mode and a RF lens setting of 30%.  Fragmentation was triggered for 3 s cycle time for peptide like features with charge states of 2–7 on the MS scan (data-dependent acquisition). Precursors were isolated using the quadrupole with a window of 0.7 m/z and fragmented with a normalized collision energy of 34%. Fragment mass spectra were acquired in profile mode and a resolution of 30,000. Maximum injection time was set to 94 ms and AGC target to custom. The dynamic exclusion was set to 60 s. Acquired data were analyzed using FragPipe (PMID: 28394336) and a Uniprot Mus musculus C57BL (UP000000589, ID10090, 21.968 entries, data: 27.10.2022, downloaded: 11.01.2023) or Homo sapiens (UP000005640, ID9606, 20.594 entries, date: 26.10.2022, downloaded: 11.01.2023) fasta database that included common contaminants. The following modifications were considered: Carbamidomethyl (C, fixed), TMT16/18plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT16/18plex (N-term, variable). The mass error tolerance for full scan MS spectra was set to 10 ppm and for MS/MS spectra to 0.02 Da. A maximum of 2 missed cleavages were allowed. A minimum of 2 unique peptides with a peptide length of at least seven amino acids and a false discovery rate below 0.01 were required on the peptide and protein level (PMID: 25987413)."],"repository":["Pride"],"labhead":["Prof. Dr."],"instrument_platform":[""],"labhead_affiliation":["Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA Stanford Genome Technology Center, Palo Alto, CA, USA Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany"],"submission_type":["PARTIAL"],"publication":["Not available"],"submitter_affiliation":["EMBL"],"labhead_mail":["Lars.Steinmetz@stanford.edu"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"disease":["Dilated Cardiomyopathy"],"submitter_keywords":["Heart failure","Human ipsc-derived cardioids","Mitochondrial dysfunction","Solubility profiling","Rbm20","Mice","Dcm"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD057195"],"quantification_method":[""],"modification":[""],"data_protocol":["For soluble proteomes: The raw output files of FragPipe were processed using the R programming language (ISBN 3-900051-07-0). Contaminants and reverse proteins were filtered out and only proteins that were quantified with at least 2 razor peptides (Razor.Peptides >= 2) were considered for the analysis. 3827 proteins passed the quality control filters. Log2 transformed raw TMT reporter ion intensities ('channel' columns) were first cleaned for batch effects using the 'removeBatchEffect' function of the limma package (v. 3.54.2, PMID: 25605792) and further normalized using the 'normalizeVSN' function of the limma package (VSN - variance stabilization normalization - PMID: 12169536). Proteins were tested for differential expression using a moderated t-test by applying the limma package ('lmFit' and 'eBayes' functions). The replicate information was added as a factor in the design matrix given as an argument to the 'lmFit' function of limma. The t-value output of limma for certain statistical comparisons was analyzed with the 'fdrtool' function of the fdrtool packages (v. 1.2.17, PMID: 18441000) in order to extract p-values and false discovery rates (q-values were used)A protein was annotated as a hit with a false discovery rate (fdr) smaller 0.05 and an absolute log2 fold-change of greater 0.5. GO analysis was done using the clusterProfiler R package (v. 4.6.2) and org.Mm.eg.db annotation (v. 3.16.0) a. A full list of detected proteins with their differential expression statistics is provided as Supplementary Data 3. Annotation of mitochondrial proteins was done using MitoCarrta3.0. For total proteomes from iPSC-derived cardioids, the processing was same as above. A full list of detected proteins with their differential expression statistics is provided as Supplementary Data 5. For solubility profiling: The raw output files of FragPipe were processed using the R programming language (ISBN 3-900051-07-0). Contaminants and reverse proteins were filtered out and only proteins that were quantified with at least 2 razor peptides (Razor.Peptides >= 2) were considered for the analysis. 5138 proteins passed the quality control filters. Log2 transformed raw TMT reporter ion intensities ('channel' columns) were first cleaned for batch effects using the 'removeBatchEffect' function of the limma package (v. 3.54.2, PMID: 25605792) and further normalized using the 'normalizeVSN' function of the limma package (VSN - variance stabilization normalization - PMID: 12169536). Solubility of each protein was calculated as a ratio of normalized protein expression in the soluble fraction divided by the normalized protein expression in the total fraction. Proteins were tested for differential solubility using a moderated t-test by applying the limma package ('lmFit' and 'eBayes' functions). The replicate information was added as a factor in the design matrix given as an argument to the 'lmFit' function of limma. The t-value output of limma for certain statistical comparisons was analyzed with the 'fdrtool' function of the fdrtool packages (v. 1.2.17, PMID: 18441000) in order to extract p-values and false discovery rates (q-values were used). A protein was annotated as a hit with a false discovery rate (fdr) smaller 0.1 and an absolute log2 fold-change of greater 0.5. GO analysis was done using the clusterProfiler R package (v. 4.6.2) and org.Mm.eg.db annotation (v. 3.16.0). Protein-protein interaction enrichment analysis was performed using Merascape (v3.5.20240101). A full list of detected proteins with their differential expression statistics is provided as Supplementary Data 2. Annotation of mitochondrial proteins was done using MitoCarta3.0."],"omics_type":["Proteomics"],"species":["Homo Sapiens (human)","Mus Musculus (mouse)"],"submitter_mail":["frank.stein@embl.de"],"curator_keywords":["Human proteome project","Biology/disease-driven human proteome project (b/d-hpp)","Cardiovascular (b/d-hpp)"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Gain-of-function RBM20 variants linked to severe dilated cardiomyopathy impair mitochondrial function.","description":"We first performed solubility profiling in RBM20-WT, -P635L+/+ and -R636Q+/+ mice. We lysed murine ventricular tissues using either a mild detergent (NP-40) to extract only the soluble fraction of the proteome, or a strong detergent (SDS) to extract total proteomes, within the same experiment. Solubility is quantified as a proportion of the protein amount identified in the soluble fraction divided by the protein amount in the total fraction. The solubility values of proteins interacting within the same cellular compartment are then expected to be similar. For this experiment, we used N = 3 mice per genotype, with two fractions (total and soluble) for each mouse.  We then perfomred proteomics analysis of only soluble proteomes, to gain a deeper understanging of the mechanism causing the downregulation of soluble proteins in RBM20-mutant mice. For that, we lysed left ventricules of RBM20-WT, -P635L+/+ and -R636Q+/+ mice, total N = 6 mice per genotype, using mild detergent (NP-40). In addition, to assess whether our observed findings are specific to these gain-of-fucntion variants, we compared soluble lysates of RBM20-WT and RBM20-KO (Loss-of-function, LoF model) mice, N=4 mice per genotype. All mice for all experiments were between 14-17 weeks of age. To validate our findings in a human caridac model, we performed analyses of total (lysed with SDS)  proteomes of human iPSC-derived cardiac organoids with RBM20-WT, -P633L, -R634Q, and -KO, N = 3 biological replicates each.","dates":{"publication":"2026-07-19","submission":"2024-10-25"},"accession":"PXD057195","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:1131","NEWT:35795","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:247480","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:112509","NEWT:475174","NEWT:111205","NEWT:1599","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:12215","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:1596","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:294671","NEWT:376619","NEWT:1748418","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:1907535","NEWT:135622","NEWT:4615","NEWT:672127","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:3760","NEWT:1584","NEWT:2086595","NEWT:36630","NEWT:1585","NEWT:383379","NEWT:381198","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:3357","NEWT:111225","NEWT:7719","NEWT:29073","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:2020713","NEWT:224308","NEWT:3347","NEWT:49928","NEWT:3349","NEWT:160621","NEWT:2502409","NEWT:212790","NEWT:110368","NEWT:55350","NEWT:1916073","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:5516","NEWT:44688","NEWT:44689","NEWT:370038","NEWT:498211","NEWT:345076","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:1310173","NEWT:200795","NEWT:37919","NEWT:2579791","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:260499","NEWT:410661","NEWT:329854","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:2649329","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NCBITaxon:37162","NEWT:270643","NEWT:3715","NEWT:1538","NEWT:2065263","NEWT:199225","NEWT:177437","NEWT:717966","NEWT:10891","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:10886","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:926571","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:2714896","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:1608994","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2499525","NEWT:1122981","NEWT:2853422","NEWT:1122984","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:45972","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:2836","NEWT:376686","NEWT:237610","NEWT:95486","EFO:0001352","NEWT:119562","NEWT:1883446","NEWT:31345","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:1509","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1579","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:1922344","NEWT:108458","NEWT:5936","NEWT:85692","NEWT:321967","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:279010","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:415978","NEWT:1255228","NEWT:410289","NEWT:191701","NEWT:373153","NEWT:1640278","NEWT:9054","NEWT:472","NEWT:940825","NEWT:29459","NEWT:529507","NEWT:1071661","NEWT:1380096","NEWT:28128","NEWT:470","NEWT:41122","NEWT:5911","NEWT:1328300","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:11723","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166314","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:1547","NEWT:1290454","NEWT:3726","NEWT:906914","NEWT:81231006","NEWT:30455","NEWT:28141","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:548","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:2126348","NEWT:5180","NEWT:256737","NEWT:299467","NEWT:9541","NEWT:51350","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:542","NEWT:2903","NEWT:185579","NEWT:872227","NEWT:13076","NEWT: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