Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-HCD-S01-S15_Trypsin_S_cerevisiae_cs.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-EThcD-S01-S15_Trypsin_S_cerevisiae_cs.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-EThcD-03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-EThcD-13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-HCD-11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-EThcD-11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-HCD-03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-EThcD-05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-HCD-07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-HCD-05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-EThcD-09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-EThcD-07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-HCD-01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-EThcD-01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-HCD-13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-EThcD-15.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-HCD-15.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077396/EC-OT30-25-190-HCD-09.rawprimaryOK200m.luzarowski@zmbh.uni-heidelberg.deMarcin LuzarowskiMass SpectrometryBottom-up proteomicsPresequence processingReactive oxygen speciesMitochondrial protein biogenesisMitochondrial unfolded protein responsehttps://www.ebi.ac.uk/pride/archive/projects/PXD077396Protein samples were digested using the Single Tube Solid Phase Sample Preparation (SP3) method on a KingFisher Apex platform, as described previously [cite: Voran, J.C.; Kilian, L.S.; Martini, S.; Luzarowski, M.; Noormalal, M.I.; Müller, O.J.; Rangrez, A.Y.; Frank, D. First Glance at Myeloid Leukaemia Factor 2 in Cardiomyocytes.]. To preserve potential cysteine S-glutathionylation, both reduction and alkylation steps were omitted. After digestion, peptides were desalted using Affinisep Stage Tips 200µl C18 T2. After initial sequential washing with (i) 50% MeOH, (ii) 80% ACN, 0.1% TFA, and (iii) 0.1% TFA, acidified peptides were loaded on the stage tips. After washing with 0.1% TFA, peptides were eluted twice using 80% ACN, 0.1% TFA. NanoLC–MS/MS analysis was performed using a Vanquish Neo system coupled to an Orbitrap Eclipse Tribrid mass spectrometer (Thermo Fisher Scientific). Peptides derived from recombinant Mas1, Mas2, and Oct1 were separated using a 30-min linear gradient from 4% to 32% solvent B over 25 min, followed by an increase to 49% solvent B over 5 min and a final wash at 99% solvent B. Each sample was analyzed in two independent LC–MS/MS runs. One run employed higher-energy collisional dissociation (HCD), and the second run employed electron-transfer/higher-energy collision dissociation (EThcD). For both acquisition strategies, the instrument was operated in data-dependent acquisition (DDA) mode. For HCD runs, MS1 spectra were acquired in the Orbitrap at a resolution of 120,000 (m/z 200), with an AGC target of 1.2 × 10⁶, maximum injection time of 50 ms, RF lens of 30%, and a scan range of m/z 400–1600. Dynamic exclusion was enabled for 10 s, excluding all charge states of a given precursor. Monoisotopic peak determination was enabled, and precursors were isolated using a 0.5 m/z window. Singly charged ions and ions with charge states above 5 were excluded, and the intensity threshold was set to 5 × 10³. MS2 spectra were acquired in the Orbitrap at a resolution of 30,000, with a maximum injection time of 54 ms, a custom AGC target of 1.25 × 10⁵, and a normalized collision energy (NCE) of 30%. For EThcD runs, MS1 spectra were acquired at a resolution of 120,000, with an AGC target of 1.2 × 10⁶, maximum injection time of 246 ms, RF lens of 36%, and a scan range of m/z 500–2000. Dynamic exclusion and monoisotopic peak determination were applied as described above. Singly charged ions and ions with charge states above 6 were excluded, and the intensity threshold was set to 5 × 10⁴. Precursors were isolated using a 1.6 m/z window. MS2 spectra were acquired in the Orbitrap at a resolution of 30,000 using EThcD fragmentation with a supplemental HCD activation energy of 25%, a maximum injection time of 54 ms, and a custom AGC target of 1.0 × 10⁵.PrideNot availableMS/MS spectra were searched against the UniProt Saccharomyces cerevisiae reference proteome (UP000002311, downloaded February 2025), supplemented with custom FASTA sequences for Mas1, Mas2, and Oct1, as well as a curated contaminant database, using Proteome Discoverer 3.1 with the Sequest HT search engine. The precursor mass tolerance was set to 10 ppm, and the fragment ion mass tolerance was set to 0.02 Da. For spectra acquired using the EThcD method, b-, c-, y-, and z-type fragment ions were enabled during database searching. Trypsin was specified as the proteolytic enzyme. The following variable modifications were included: oxidation (M), glutathionylation (C), methionine loss (M), and combined methionine loss with N-terminal acetylation. Peptide quantification was performed using the precursor ion quantifier node in Proteome Discoverer, with summed precursor abundances used for protein-level quantification.ProteomicsMarcin LuzarowskiCore Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, GermanyPARTIALSaccharomyces Cerevisiae (baker's Yeast)m.luzarowski@zmbh.uni-heidelberg.deNot availableUniversity of HeidelbergGermanyfalseMitochondrial surveillance activates the primary UPRmtThe mitochondrial unfolded protein response (UPRmt) is critical for protecting mitochondria against proteotoxic stress. Current UPRmt models propose that mitochondrial defects are detected by cytosolic surveillance mechanisms after release of damage into the cytosol. However, these findings are based on models that induce rapid and severe mitochondrial dysfunction, and thus their mode of toxicity contrasts sharply from physiologically occurring mitochondrial damage, e.g. the gradual accumulation of reactive oxygen species (ROS) during age-related decline or chronic respiratory chain defects. Here, we employed a chemogenetic strategy that induces low levels of H2O2 in the mitochondrial matrix to investigate cellular responses to physiologically relevant levels of mitochondrial dysfunction. We uncover that this mild oxidative stress activates the UPRmt independently of cytosolic signals revealing a so far concealed primary surveillance mechanism within mitochondria. Moreover, we identify the mitochondrial presequence proteases MPP and Oct1 as early molecular targets of ROS: Oxidative stress induces glutathionylation of critical cysteine residues, resulting in diminished proteolytic activity and the accumulation of proteotoxic precursor aggregates in the matrix. These aggregates are detected by intramitochondrial surveillance systems, activating UPRmt signaling. Our findings uncover the primary response to mitochondrial dysfunction, and highlight the organelle's capacity for self-surveillance and its ability to initiate early and rapid protective signaling in the face of mitochondrial dysfunction.2026-04-202026-04-20PXD077396NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:43186NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:12637NEWT:59729NEWT:2164133NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:633149NEWT:10239NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1436733NEWT:460519NEWT:1247411NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:333760NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NEWT:39491NCBITaxon:5811NEWT:29491NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:272634NEWT:9031NEWT:1872122NEWT:7091NEWT:1034015NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:9557NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:725NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:74649NEWT:52638NEWT:57075NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NCBITaxon:11320NEWT:632957NEWT:11051NEWT:9925NEWT:89462NCBITaxon:9606NEWT:8839NEWT:90690NEWT:1436183NEWT:4232NEWT:2758385NEWT:11298NEWT:171101NEWT:714NEWT:5322NEWT:421932NEWT:312017NEWT:196627NEWT:200308NEWT:553470NEWT:200302NEWT:870435NEWT:284593NEWT:100392NEWT:5315NEWT:9913NEWT:265872NEWT:105841NEWT:337330NEWT:2666255NEWT:2285NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:981087NEWT:180066NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:430615NEWT:326423NEWT:4524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