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In general, all samples in a given sub-experiment were processed on the same day in parallel. For each condition (either WT and MB-COMT-/- cells, either untreated, treated with DA, or treated with H2O2) 3 bio-replicates were used.   Briefly, cell pellets were lysed in 250 μL ice cold LiP-MS buffer (100 mM NaCl, 2 mM MgCl2, 20 mM Tris-HCl pH 8.0) in a 1 mL dounce homogenizer with freshly added protease inhibitor cocktail (500 μM PMSF, 15 μM E64, 50 μM bestatin final concentration, added from 100X stocks in DMSO) and 100 μg/mL DNAse I. The lysate was clarified by centrifugation for 15 min at 15,000 rcf and allowed to sit at room temperature for at least 2 h to allow the majority of PMSF to quench, preventing significant interference with proteolysis by proteinase K (PK) or trypsin. Total protein concentration in tissue homogenates was measured by bicinchoninic acid (BCA) assay (Pierce BCA Protein Assay Kit), and normalized to 1 mg/mL. Normalized homogenates were each split into two samples, one to be used for limited proteolysis and one that serves as the trypsin-only control. To each limited proteolysis sample, proteinase K (PK) (Thermo Fisher – from 1 mg/mL stock, stored in LiP buffer and 10% glycerol at -80 °C in flash-frozen aliquots) was added to a final ratio of 1:100 (w:w) enzyme to total homogenate protein ratio. The samples were briefly mixed by vortex and incubated for a total of 1 minute at room temperature with PK, followed by termination of proteolysis by immediate submersion of sample tube in a 105°C oil bath and 5 min incubation.   Preparation of limited proteolysis samples for mass spectrometry Post heat inactivation of PK, each sample was transferred to a separate tube containing urea (f.c. 8 M urea upon full dissolution in sample). Trypsin-only samples were processed similarly, but without addition of PK. Next, samples were reduced using dithiothreitol (f.c. 10 mM, diluted from freshly made stock) and incubating for 30 min at 37°C in a thermomixer at 700 rpm. Samples were alkylated by adding iodoacetamide (f.c. 40 mM, diluted from freshly made stock), incubated for 45 min at room temperature in a dark space. Samples were then diluted to 2 M urea using a freshly prepared 100 mM ammonium bicarbonate solution, and subjected to overnight digest at 25 °C with trypsin (New England Biolabs), added to a final ratio of 1:50 (w:w) enzyme to total homogenate proteinratio . Digests were terminated by adding trifluoroacetic acid to a final concentration of 1% (v:v). Samples were then desalted using Waters Sep-pak Vac Cartridges with 50 mg sorbent. Cartridges were placed in a vacuum manifold and conditioned with 2 x 1 mL of an 80% acetonitrile, 0.1% formic acid solution (Sep-pak elution buffer) and equilibrated with 4 x 1 mL of a 0.1% (v:v) aqueous formic acid solution (Sep-pak wash buffer). After loading of digested peptides slowly under reduced vacuum, the sorbent was washed with 4 x 1 mL Sep-pak wash buffer.  The cartridges were thenremoved from the vacuum manifold, and peptides eluted from the sorbent with 1 mL of Sep-pak elution buffer. Peptides were dried by evaporation in an Eppendorf Speedvac concentrator, and stored at -80 °C until analysis by LC-MS.  LC/MS data acquisition for LiP-MS samples Digested samples were resuspended in 0.1% aqueous formic acid solution, and peptide concentrations were normalized by absorbance at 280 nm (measured by nanodrop spectrophotometer) prior to LC-MS injection. Samples were chromatographically separated using a Vanquish HPLC system (Thermo Fisher) with mobile phases consisting of 0.1% formic acid in water (Buffer A) and 0.1% formic acid in acetonitrile (Buffer B). For each sample run, 500 ng of peptides are accumulated onto a trap column (Acclaim Pepmap, 75 um x 15 cm, 3 um, 100 A) as buffer B is ramped linearly from 1% to 4% over 6 seconds, and from 4% to 9% over 8 minutes. After 24 seconds at 9% buffer B, the trap column is brought in line with the resolving column (Acclaim Pepmap RSLC, 75 µm x 25 cm, 2 µm, 100 A), and peptides are eluted by linear increment of buffer B to 25% over 30 minutes, and to 40% over 26 minutes. The column is then washed by increasing from 40% to 90% buffer B over 2.5 minutes, and held at 90% for 3 minutes. The effluent was analyzed with an Orbitrap Ascend mass spectrometer (Thermo Fisher) in data-independent acquisition mode. MS1 spectra were collected with a scan range of 380-980 m/z, a resolution of 120,000, a maximum injection time of 251 ms, and an AGC target of 1E6. Data-independent MS2 spectra were acquired across the 380-980 m/z precursor scan range in isolation windows of 12 m/z units. Precursors were fragmented with an HCD collision energy of 30%.  MS2 spectra were collected with a scan range of 150-2000 m/z, a resolution of 30,000, a maximum injection time of 59 ms, and an AGC target of 2.5E5."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["To assess quality of individual LiP and trypsin-only sample runs, raw LC-MS data files were searched independently for identifications using the Fragpipe suite of analysis software (ver. 22.0). Database searches were performed using Fragpipe’s default workflow. The mouse reference proteome was used (Uniprot UP0000000589, downloaded 2025/04/19). Decoy and contaminant masses were added to all searches through Fragpipe’s user interface. Default settings were used except where stated otherwise. Briefly, semi-specific searches were done with MSFragger DIA using strict tryptic cleavage rules. The data were searched for peptides 7-50 residues long, with up to 2 missed cleavages, with a peptide mass range of 500-5000 Da. Precursor and fragment mass tolerances were 20 ppm. Dynamic modifications included up to 3 methionine oxidations, and acetylation at the protein N-terminus. Carbamidomethylation at cysteine residues was included as a static modification. Identifications were validated using Philosopher, and filtered for an FDR of 0.01 at the PSM and protein level. Protein and peptide IDs were quantified with an in-house Python script that reads the Protein and Peptide TSV files from each sample’s output directory, counts identifications, and determines whether peptide IDs are fully tryptic or half tryptic. Percent half-trypticity was determined by calculating the percentage of peptide IDs corresponding to half-tryptic peptides. A peptide was considered fully tryptic if its C-terminal residue was a lysine or arginine, and its N-terminal residue was preceded in the protein’s full sequence by a lysine or arginine. A peptide was considered half tryptic if either of those two conditions was false.   For each of the three LiP-MS sub-experiments, two separate label-free quantifications (LFQ) were run: One including all trypsin-only samples, and one including all LiP samples. These were all run using the ‘DIA Speclib Quant’ preset in Fragpipe. Briefly, a database search is done as described in the previous subsection to identify peptides from the LC-MS data. These are validated with Philosopher, and used to construct a DIA-based empirical spectral library. Precursor abundances are quantified using the DIA-NN node (ver. 2.1.0) in Fragpipe, set to high-accuracy QuantUMS quantification strategy, and an FDR cutoff of 0.01.  Structural alteration of LiP-MS sites was assessed using an in-house Python script based on code from FLiPPR. Precursor QuantUMS intensities were taken directly from the DIA-NN precursor matrix output for the LFQ corresponding to LiP samples. First, precursors are filtered based on missing intensity values. If a precursor missing more than 1 intensity value, it is excluded from LiP analysis. If a precursor is missing exactly 1 intensity value, that single values is dropped (not imputed), and summary statistics for that precursor are computed using the remaining 5 intensity values. If a precursor has intensity values for all members of one group, and no members of the other, it is considered ‘all or nothing’, and intensity values are imputed by Gaussian imputation from a distribution with a mean of 104 and a standard deviation of 103. Fold-change and p-values from the t-test with Welch’s correction for unequal population variances are computed for each precursor. If multiple charge states are detected for a given peptide, and the direction of fold-change is in agreement between all, they are combined into a single row whose fold-change is the median of the peptide’s detected precursors, and whose p-value is a combined p-value obtained by Fisher’s method. If the direction of fold-change between a peptide’s charge-states does not agree, the peptide is excluded from analysis. To account for the effect of a protein’s abundance on the measured abundance of its LiP peptides, abundance values from the pg-matrix DIA-NN output from the LFQ corresponding to trypsin-only samples were used. If a protein’s abundance had a fold-change of at least 2 and a p-value < 0.01, its fold-change value is used to normalize the fold-change of all of its detected peptides for LiP-MS analysis. After filtering and normalization, peptide-level p-values are corrected by Benjamini-Hochberg method on a per-protein basis, to account for the fact that proteins with more detected peptides have more propensity for type I statistical error. Peptides are called structurally altered if their fold-change exceeds 2, and their adj. p-value is < 0.05. Proteins are called structurally altered if they have at least 2 peptides that are altered. To assess false-positive rate for the LiP-MS comparisons, the same workflow was applied to equivalent LFQs where group-assignment was randomized. Randomization was done such that each group had the same N as the non-null comparisons, and no more than half of each group belonged to the same original group."],"omics_type":["Proteomics"],"labhead":["Stephen D. Fried"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Department of Chemistry, Johns Hopkins University"],"species":["Rattus Norvegicus (rat)"],"publication":["42748150 Tripathi SJ, Chakraborty S, Wood NB, Hoopes D, Barker S, Vázquez-Rosa E, An J, Ma C, Hou Y, Sharma SM, Cheng F, Thomas B, Orsburn BC, Fried SD, Snyder SH, Pieper AA, Paul BD. Catechol-&lt;i&gt;O&lt;/i&gt;-methyltransferase connects dopamine homeostasis to redox signaling, metal homeostasis, and protein folding in schizophrenia. Proc Natl Acad Sci U S A. 2026 123(38):e2606205123 10.1073/pnas.2606205123"],"submitter_mail":["nwood11@jh.edu"],"submitter_affiliation":["Johns Hopkins University"],"submitter_country":["United States"],"pubmed_abstract":["Dysregulated dopamine (DA) signaling and redox homeostasis contributes to multiple neuropsychiatric and neurodegenerative disorders. Polymorphisms that influence the activity of catechol-O-methyltransferase (COMT), an enzyme critical for degrading DA in the dorsolateral prefrontal cortex, have been implicated in behavioral and neuropsychiatric alterations associated with schizophrenia (SCZ). Adverse neuropsychiatric effects have also been reported in Parkinson's disease (PD) patients administered COMT inhibitors in combination with other DA-enhancing therapies. COMT exists as two isoforms: a soluble short isoform (S-COMT) and a membrane-bound long isoform (MB-COMT). These variants differ in their N-terminal domains, with MB-COMT being the predominant brain isoform. Here, unbiased proteomic and biochemical analyses show that genetic loss of MB-COMT disrupts DA signaling and perturbs pathways governing synaptic and mitochondrial function, iron and copper homeostasis, and redox balance. Limited proteolysis mass spectrometry (LiP-MS) further revealed that MB-COMT deficiency triggers widespread protein structural alterations, a molecular event commonly occurring in neurodegenerative conditions but not as well studied in neuropsychiatric diseases. Our results show that MB-COMT is a molecular hub that connects multiple cellular pathways whose differential dysregulation underlies the pathophysiology of complex neuropsychiatric diseases such as SCZ. Thus, MB-COMT is identified as a key regulator of brain DA biology, loss of which activates cellular stress response pathways, revealing potential targets for therapeutic intervention."],"pubmed_title":["Catechol-&lt;i&gt;O&lt;/i&gt;-methyltransferase connects dopamine homeostasis to redox signaling, metal homeostasis, and protein folding in schizophrenia."],"pubmed_authors":["Tripathi Sunil Jamuna SJ, Chakraborty Suwarna S, Wood Neil B NB, Hoopes Dillon D, Barker Sarah S, Vázquez-Rosa Edwin E, An Jiu J, Ma Chunxuan C, Hou Yuan Y, Sharma Sudarshana M SM, Cheng Feixiong F, Thomas Bobby B, Orsburn Benjamin C BC, Fried Stephen D SD, Snyder Solomon H SH, Pieper Andrew A AA, Paul Bindu D BD"],"additional_accession":[]},"is_claimable":false,"name":"Catechol-O-Methyltransferase connects dopamine homeostasis to redox signaling, metal homeostasis and protein folding in schizophrenia","description":"Dysregulation of dopamine (DA) signaling and redox homeostasis contributes to multiple neuropsychiatric and neurodegenerative disorders. Polymorphisms that influence the activity of catechol‑O‑methyltransferase (COMT), an enzyme critical for degrading dopamine (DA) in the dorsolateral prefrontal cortex, have been implicated in behavioral and neuropsychiatric alterations associated with schizophrenia (SCZ). Adverse neuropsychiatric effects have also been reported in Parkinson’s disease (PD) patients administered COMT inhibitors in combination with other DA‑enhancing therapies. COMT exists as two isoforms: a soluble short isoform (S-COMT) and a membrane-bound long isoform (MB-COMT). These variants differ in their N-terminal domains, with MB-COMT being the predominant brain isoform. Here, unbiased proteomic and biochemical analyses show that genetic loss of MB‑COMT disrupts DA signaling and perturbs pathways governing synaptic and mitochondrial function, iron and copper homeostasis, and redox balance. Limited proteolysis mass spectroscopy (LiP-MS) further revealed that MB‑COMT deficiency triggers widespread protein structural alterations, a molecular signature shared with numerous neurodegenerative and neuropsychiatric conditions. Our results show that MB-COMT is a molecular hub that connects multiple cellular pathways whose differential dysregulation underlies the pathophysiology of complex neuropsychiatric diseases such as SCZ.  Thus, MB‑COMT is identified as a key regulator of brain DA biology, loss of which activates cellular stress response pathways, revealing potential targets for therapeutic intervention.  These LC-MS data are from the LiP-MS study on PC12 cells (P in experimental annotation) and PC12 cells with membrane-bound COMT knocked out (C in experimental annotation). The analyzed samples were either treated with hydrogen peroxide (H in experimental annotation), dopamine (DA in experimental annotation), or were untreated (X in experimental annotation).","dates":{"publication":"2026-09-28","submission":"2026-02-28"},"accession":"PXD075030","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:235443","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:472","NEWT:1071661","NEWT:470","NEWT:5911","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:9031","NEWT:27292","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:8655","NEWT:5147","NEWT:28104","NEWT:407821","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:6063","NEWT:1328388","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:2925","NEWT:214053","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:90690","NEWT:1436183","NEWT:4232","NEWT:416348","NEWT:11298","NEWT:196627","NEWT:200308","NEWT:242507","NEWT:200302","NEWT:870435","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:2666255","NEWT:999810","NCBITaxon:5693","NEWT:28995","NEWT:1392998","NEWT:380394","NEWT:114796","NEWT:226900","NEWT:1266738","NEWT:231490","NEWT:244704","NEWT:7725","NEWT:430615","NEWT:563041","NEWT:72664","NEWT:326423","NEWT:452467","NEWT:198822","NEWT:36111","NEWT:326424","NEWT:1678078","NEWT:749906","NEWT:418985","NEWT:749907","NEWT:150847","NEWT:431947","NEWT:69014","NEWT:142809","NEWT:130821","NEWT:27606","NEWT:1519788","NEWT:59202","NEWT:9975","NEWT:8643","NEWT:1159899","NEWT:502780","NEWT:860688","NEWT:13443","NEWT:8644"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