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Pérez PañedaMass SpectrometryBottom-up proteomicsData-independent acquisitionhttps://www.ebi.ac.uk/pride/archive/projects/PXD075583HeartWild-type and Lrpprc knockout mitochondria purified from mouse heart was run on BN-PAGE in triplicate, and each lane was cut into 24 equal-sized bands with a sharp scalpel and further chopped into small pieces. The gel pieces were subjected to in-gel digestion. Briefly, the gel pieces were washed and reduced by incubation in reduction buffer (6.5 mM DTT, 50 mM AMBIC, pH 8.5) for 1h at 60°C. The reduction buffer was removed, the gel pieces were dehydrated with 100% ACN, and alkylated by incubation in alkylation buffer (55 mM IAA, 50 mM AMBIC, pH 8.5) for 30min at room temperature. The alkylation buffer was removed, the gel pieces were dehydrated with 100% ACN, and subsequently washed two times with 50mM AMBIC and 100% ACN. The dehydrated gel pieces were incubated in cold trypsin solution (3 ng/μL in 50 mM AMBIC cold, pH 8.5) for 90 min on ice, the excess of trypsin was removed, and the gel pieces were incubated overnight at 37°C in 50mM AMBIC. The supernatant was collected, the gel pieces were dehydrated with 100% ACN, and both supernatants were combined. The peptide samples were analyzed using a Exploris 480 (ThermoFisher) mass spectrometer coupled to an Ultimate3000 UHPLC system (ThermoFisher). The fractions were injected at 3 µL/min for 1 min into a trap column (Acclaim Pepmap 100 C18, 5 mm x 0.3 mm, 5 µm, Thermo Fisher Scientific). The peptide separation was performed in a 50 cm long analytical column with a 75 µm inner diameter packed in house with C18 beads (Reprosil C18, 1.9 µm) at a column temperature of 32°C. Peptides were eluted at 300 nL/min with a total run time 60 min with gradient separation on the analytical column: 4 % B for 1 min, from 4 % to 11 % B in 2 min, from 11 % to 30 % in 32 min, from 30 % to 44 % in 5 min, from 44 % to 55 % in 4 min, from 55 % to 99 % in 1 min and 99 %B for 4 min, and 4 % B for 10 min. The MS acquisition method was a data-independent acquisition (DIA) mode using the Orbitrap analyzer at 60K mass resolution in the scan range 375-1600 m/z. The DIA experiment was acquired with a precursor mass range within 400-1000 m/z with 20 m/z isolation window. Peptides were fragmented with HCD 28 %.PrideThe raw files were analyzed with DIA-NN (version 1.8.1) using the FASTA file generated for the crosslinking experiments (PXD071441) and known contaminants. Library-free search was performed with tryptic digestion with a maximum of two misscleavages and mass accuracy of 20 ppm. Carbamidomethyl (C) was set as a static modification, and oxidation (M) as variable modifications. The maximum FDR was set to 1%.ProteomicsAlbert J. R. HeckUtrecht UniversityPARTIALMus Musculus (mouse)l.perezpaneda@uu.nlNot availableUtrecht UniversityNetherlandsfalseComplexome Profiling of Lrpprc KO and WT mouse heart mitochondriaComplexome profiling was performed to address the changes in composition of ATP synthase assemblies upon knockout of Lrpprc in mouse heart.2026-05-202026-03-13PXD075583NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:150475NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:115104NEWT:1081927NEWT:67825NEWT:13076NEWT:1249668NEWT:317NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:4081NEWT:876138NEWT:554NEWT:98334NEWT:237561NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:746360NEWT:6239NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:8782NEWT:1000589NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:931281NEWT:7029NEWT:1283300NEWT:334747NEWT:61235NCBITaxon:79824NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NCBITaxon:6191NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:83332NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:44685NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:1123869NEWT:7370NEWT:83906NEWT:6282NEWT:1134506NEWT:575584NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:10090NEWT:935293NEWT:749200NEWT:4120NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:632957NEWT:373995NEWT:5689NEWT:544404NEWT:3702NEWT:129249NEWT:8839NEWT:4232NEWT:990119NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:106592NEWT:1117957NEWT:9913NEWT:1432138NEWT:10312NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:180066NEWT:67767NEWT:46835NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:10306NEWT:1911079NEWT:8022NEWT:145943NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:59202NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:1147787NEWT:72407NEWT:9606NEWT:367830NEWT:157295NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:1450511NEWT:470NEWT:84023NEWT:9838NCBITaxon:9615NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:33952NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:9940NEWT:573NEWT:9031NEWT:1274420NEWT:70910009-0008-3217-284X