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Mendes MaiaData-dependent acquisitionMass SpectrometryBottom-up proteomicsLipid Metabolism DisorderMitochondrial Complex I DeficiencyOrganic Acidemiahttps://www.ebi.ac.uk/pride/archive/projects/PXD048352FibroblastFirst, protein pellets were dried in a vacuum concentrator to remove all residual methanol and denatured in a buffer containing 8 M urea and 20 mM HEPES. Proteins were reduced by addition of 15 mM dithiothreitol (DTT) and incubation fo 30 minutes at 55˚C and then alkylated by addition of 30 mM iodoacetamide (IAA) for 15 minutes at room temperature in the dark. Samples were diluted with 20 mM HEPES pH 8.0 to a final urea concentration of 4 M and proteins were digested with 1 µg lysyl endopeptidase (Wako) (1/100, w/w) for 4 hours at 37°C. Samples were again diluted to 2 M urea and digested with 1 µg trypsin (Promega) (1/100, w/w) overnight at 37˚C. The resulting peptide mixture was acidified by addition of 1% trifluoroacetic acid (TFA) and desalted on a reversed phase (RP) C18 OMIX tip (Agilent). The tip was first washed 3 times with 200 µl pre-wash buffer (0.1% TFA in water/acetonitrile (ACN, 20:80, v/v)) and pre-equilibrated 5 times with 200 µl of wash buffer (0.1% TFA in water) before the sample was loaded on the tip. After peptide binding, the tip was washed 3 times with 200 µl of wash buffer and peptides were eluted twice with 100 µl elution buffer (0.1% TFA in water/ACN (40:60, v/v)). The combined elutions were dried in a vacuum concentrator. Purified peptides were re-dissolved in 20 µl loading solvent A (0.1% TFA in water/ACN (98:2, v/v), the peptide concentration was determined on a Lunatic (PMID: 32258910) spectrophotometer (Unchained Labs) and 2 µg of each sample was injected for LC-MS/MS analysis on an Ultimate 3000 RSLCnano system in-line connected to an Orbitrap Fusion Lumos mass spectrometer (Thermo Scientific) equipped with a pneu-Nimbus dual ion source (Phoenix S&T). Trapping was performed at 10 μl/min for 4 min in loading solvent A on a 20 mm trapping column (made in-house, 100 μm inner diameter(ID), 5 μm beads, C18 Reprosil-HD, Dr. Maisch) and the sample was loaded on a 200 cm long micro pillar array column (Thermo Scientific) with C18-endcapped functionality mounted in the Ultimate 3000’s column oven at 50°C. For proper ionization, a fused silica PicoTip emitter (10 µm ID, New Objective) was connected to the µPAC™ outlet union and a grounded connection was provided to this union. Peptides were eluted by a non-linear increase from 5 to 55% MS solvent B (0.1% FA in water/ACN (2:8, v/v)) over 145 minutes, first at a flow rate of 750 nl/min, then at 300 nl/min, followed by a 15-minutes wash reaching 99% MS solvent B and re-equilibration with 95% MS solvent A (0.1% FA in water). The mass spectrometer was operated in data-dependent mode, automatically switching between MS and MS/MS acquisition. Full-scan MS spectra (300-1500 m/z) were acquired in 3 s acquisition cycles at a resolution of 120,000 in the Orbitrap analyzer after accumulation to a target AGC value of 2E5 with a maximum injection time of 250 ms. Monoisotopic precursor selection (MIPS) was set to Peptide and the precursor ions were filtered for charge states (2-7 required), dynamic exclusion (60 s; +/- 10 ppm window) and intensity (minimal intensity of 5E3). The precursor ions were selected in the multipole with an isolation window of 1.2 Da and accumulated to an AGC target of 1.2E4 or a maximum injection time of 40 ms and activated using HCD fragmentation (34% NCE). The fragments were analysed in the Ion trap Analyzer with Normal scan rate. The polydimethylcyclosiloxane background ion at 445.120028 Da was used for internal calibration (lock mass). QCloud (PMID: 29324744) was used to control instrument longitudinal performance during the project.PrideLC-MS/MS runs of all 62 samples were searched together using the MaxQuant algorithm (version 1.6.2.6) with mainly default search settings, including a false discovery rate set at 1% on peptide and protein level. Spectra were searched against the human reference proteome sequences in the Uniprot database (database release version of 2020_01), containing 20.595 sequences (https://www.uniprot.org). The mass tolerance for precursor and fragment ions was set to 20 and 4.5 ppm, respectively, during the main search. Enzyme specificity was set to C-terminal of arginine and lysine, also allowing cleavage at Arg/Lys-Pro bonds with a maximum of two missed cleavages. Variable modifications were set to oxidation of methionine residues and acetylation of protein N-termini whereas carbamidomethylation of cysteine residues was set as fixed modification. In order to reduce the number of spectra that suffer from co-fragmentation, the precursor ion fraction (PIF) option was set to 75%. Only proteins with at least one unique or razor peptide were retained leading to the identification of 4,749 proteins Proteins and peptides were quantified by the MaxLFQ algorithm, integrated in the MaxQuant software. A minimum ratio count of two unique or razor peptides was required for quantification. Next, the proteinGroups.txt file containing the aggregated protein intensities obtained from MaxQuant was processed using the PaDuA python package (PMID: 30525654) that is optimized to work with MaxQuant output data and follows closely typical Perseus workflows. Reverse database hits, potential contaminants and proteins only identified by site were first removed. Then LFQ intensities were log2 transformed and replicate samples were grouped. Proteins with valid values in at least 2 out of 3 replicates from at least one patient sample were retained (3140 proteins in total). Missing values were then imputed from a normal distribution with default width of 0.3 and down shift of 1.8. Column-wise imputation was applied, where imputation is applied to each expression column separately. To compare protein intensities in different sample groups, statistical testing for differences between the two-group means was performed, using two-sample independent t-tests.ProteomicsSimon DevosVIB Proteomics Core, VIB, Ghent, BelgiumPARTIALHomo Sapiens (human)teresa.maia@vib-ugent.be42034643 Guharoy M, Adant I, Bird M, Botzki A, Collier J, Dehairs J, Derveaux S, Devos S, Goeminne G, Impens F, Jáñez Pedrayes A, Janky R, Maes R, Magalhães P, Maia TM, Meersseman W, Rymen D, Swinnen JV, Van Haver D, Verdegem D, Witters P, Cassiman D, Ghesquiere B. The complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in disease. NPJ Syst Biol Appl. 2026 12(1):121 10.1038/s41540-026-00716-0VIB Proteomics CoreBelgiumAnalyzing single omics and integrating multimodal omics datasets to capture functional dysregulation in disease remains challenging. Here, we propose a bioinformatics framework that leverages curated datasets of protein complexes ('complexome') as a foundation for proteomics data integration. Available for human and other model organisms, the complexome provides a global view of cellular function, enabling queries with proteomics datasets. We first benchmarked how protein abundances across human tissues shape distinct complexomic profiles, serving to fingerprint biological activity. Next, we analyzed complexome remodeling using disease versus control proteomics quantifications. Using proteomics data from fibroblasts of patients with genetically confirmed metabolic defects, we identified significant perturbations in mitochondrial oxidative phosphorylation complexes and additional complexes involved in wider mitochondrial functions. The complexome provides a systems-wide approach to dissect mechanisms underlying disease-related functional and phenotypic changes by mapping measured protein-level perturbations to specific molecular complexes. The software is available as a Python notebook at https://github.com/mguharoy/Complexome .The complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in disease.Guharoy Mainak M, Adant Isabelle I, Bird Matthew M, Botzki Alexander A, Collier James J, Dehairs Jonas J, Derveaux Stefaan S, Devos Simon S, Goeminne Geert G, Impens Francis F, Jáñez Pedrayes Andrea A, Janky Rekin's R, Maes Ruth R, Magalhães Pedro P, Maia Teresa M TM, Meersseman Wouter W, Rymen Daisy D, Swinnen Johannes V JV, Van Haver Delphi D, Verdegem Dries D, Witters Peter P, Cassiman David D, Ghesquiere Bart BfalseThe complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in diseaseProteins organize into functional assemblies that drive diverse biological activities. Leveraging a comprehensive dataset of manually curated annotations for the human protein complexome, we investigated biological perturbations at the protein complex level. Using proteomics and transcriptomics data from fibroblasts of patients with inborn errors of metabolism (IEM) and control samples, we globally mapped information onto complex subunits to discern affected processes. Across the patient cohort, mitochondrial oxidative phosphorylation emerged as the most perturbed pathway, identified through proteomics datasets. Simultaneously, metabolomics measurements highlighted significant regulation of phospholipids in patients with Fatty Acid and Mitochondrial IEM. Notably, proteomics analysis revealed the regulation of protein complexes involved in histone (de)acetylation, a finding validated through Western Blot analysis measuring histone acetylation levels. This introduces a novel epigenetic dimension to IEM and metabolic research, suggesting avenues for further exploration. Our study demonstrates a multiomics integration concept by mapping proteomics and transcriptomics onto model organism complexomes. This integrative approach extends to metabolomics and lipidomics, associating information with complexes having metabolic functions, such as enzymatic complexes. This global strategy for identifying disease-relevant perturbations offers a systems-wide perspective on molecular-level physiological and pathological changes. Such insights are crucial for devising clinical intervention strategies and prioritizing druggable pathways and complexes. The presented methodology provides a foundation for future investigations, emphasizing the importance of integrating various omics data to comprehensively understand cellular machinery alterations and facilitate targeted therapeutic approaches.2026-09-142024-01-09PXD048352NEWT:6945NEWT:184922NEWT:6703NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2102NEWT:2042546NEWT:45351NEWT:43179NEWT:4513NEWT:5722NEWT:1247NEWT:376741NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:281395NEWT:10360NEWT:1211601NEWT:876138NEWT:47664NEWT:557436NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:272563NEWT:79220NEWT:224326NCBITaxon:79857NEWT:1096976NEWT:82688NEWT:95648NEWT:3885NEWT:3888NEWT:5821NEWT:1589NEWT:135622NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:28903NEWT:3880NEWT:272559NEWT:28909NEWT:515849NEWT:3641NEWT:383379NEWT:466585NEWT:10029NEWT:913645NEWT:1000589NEWT:85963NEWT:85962NEWT:143361NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4565NEWT:1264690NEWT:515619NEWT:31155NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:84645NEWT:626528NEWT:3347NEWT:139927NEWT:4558NEWT:209285NEWT:5888NEWT:211586NEWT:747078NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:294381NEWT:197NEWT:1390363NEWT:77133NEWT:288705NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:1270NEWT:374990NEWT:498217NEWT:156471NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:156476NEWT:286NEWT:391619NEWT:360104NEWT:287NEWT:246197NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:1148NEWT:580240NEWT:5508NEWT:294128NEWT:11676NEWT:55571NEWT:35500NEWT:1140NEWT:100226NEWT:4530NEWT:1143NEWT:4896NEWT:75058NEWT:13616NEWT:1390NEWT:1094343NEWT:1336795NEWT:172NEWT:296543NEWT:316435NEWT:1773NEWT:1895NEWT:1182590NEWT:3712NEWT:82380NEWT:105023NEWT:866628NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:375146NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NEWT:8175NCBITaxon:1313NEWT:43330NEWT:980415NEWT:1603293NEWT:408169NEWT:44544NEWT:47946NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:243277NEWT:990119NEWT:2850NEWT:408172NEWT:408170NEWT:493760NEWT:106590NEWT:260710NEWT:257313NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:1436733NEWT:460519NEWT:1187947NEWT:1432138NEWT:269796NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:9598NEWT:8030NEWT:9483NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:432359NEWT:46835NEWT:1182263NEWT:109757NEWT:943146NEWT:2711NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:9103NEWT:1883446NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:89920NEWT:3635NEWT:5811NEWT:235443NEWT:180923NEWT:108458NEWT:272623NEWT:272624NEWT:2719099NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:118499NEWT:169963NEWT:32644NEWT:527796NEWT:225117NEWT:499175NEWT:109779NEWT:1266464NEWT:476272NEWT:3747NEWT:195051NEWT:367830NEWT:1255228NEWT:178616NEWT:649908NEWT:410289NEWT:373153NEWT:375451NEWT:352472NEWT:357NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:411469NEWT:84023NEWT:559292NEWT:39491NCBITaxon:5811NEWT:411464NEWT:411460NEWT:2014887NEWT:2762NEWT:1174673NEWT:1328426NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:571256NEWT:28038NEWT:1663NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:38293NEWT:327159NEWT:178876NEWT:1660NEWT:327160NEWT:573NEWT:9031NEWT:1872122NEWT:7091NEWT:108931NEWT:241368NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:303NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:7237NEWT:5180NEWT:256737NEWT:9541NEWT:115104NEWT:1121114NEWT:663NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:941442NEWT:220668NEWT:13076NEWT:1821314NEWT:1249668NEWT:7108NEWT:317NEWT:1808362NEWT:5286NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:9644NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:334542NEWT:554NEWT:27592NEWT:98334NEWT:426428NEWT:63459NEWT:1276815NEWT:36185NEWT:588858NEWT:9639NCBITaxon:11071NEWT:242231NEWT:7574NEWT:1715256NEWT:7215NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:2172103NEWT:6494NEWT:7460NEWT:6491NEWT:507601NEWT:643680NCBITaxon:6157NEWT:42752NEWT:746360NEWT:6239NEWT:470150NEWT:162425NEWT:216257NEWT:102169NEWT:543734NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:118503NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NEWT:13164NEWT:216129NCBITaxon:2NEWT:985076NEWT:1215323NEWT:2664179NEWT:623NEWT:986NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:198618NEWT:353152NEWT:2829NEWT:366581NEWT:216599NEWT:216595NEWT:1194669NEWT:51329NEWT:243230NEWT:8355NEWT:633NEWT:9685NEWT:7029NEWT:1080772NEWT:8479NEWT:1283300NEWT:632NEWT:6183NEWT:6063NEWT:630NEWT:334747NEWT:61235NEWT:15368NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:469008NEWT:260707NEWT:256318NCBITaxon:6191NEWT:1836NEWT:185431NEWT:2925NEWT:29760NEWT:260704NEWT:1719NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:105231NEWT:1216981NEWT:52638NEWT:4097NCBITaxon:6073NEWT:884204NEWT:6279NEWT:1123869NEWT:9544NEWT:1329349NEWT:7370NEWT:83906NEWT:607699NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:426688NEW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