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_sample-03_S1-C3_1_7836.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075039/20230214_klaupman_schizophrenia-cells_DIA_sample-11_S1-C11_1_7844.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075039/20230216_klaupman_schizophrenia-ACM_DIA_sample-05_S1-C5_1_7873.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075039/20230214_klaupman_schizophrenia-cells_DIA_sample-12_S1-C12_1_7845.d.zipprimaryOK200guus.smit@vu.nlFrank KoopmansMass SpectrometryData-independent acquisitionProtein secretionAstrocytesIpscProteomicsSchizophreniahttps://www.ebi.ac.uk/pride/archive/projects/PXD075039Cell CultureMS sample preparation of astrocytes Astrocyte pellets were extracted and reduced in Laemmli sample buffer, containing 5 mM tris(2-carboxyethyl)phosphine (TCEP), by incubation at 55 °C for 15 minutes in a thermomixer set to 1250 RPM. Free sulfhydryl groups were alkylated by incubation with 20 mM methyl methanethiosulfonate (MMTS) for 15 minutes at RT. Next, the lysates were cleared of insoluble debris by centrifugation at 15000x g for 1 minute at RT, loaded onto a 10% SurePAGE polyacrylamide gel (Genscript) and resolved for 1 cm. The gels were fixed overnight and stained with colloidal Coomassie Blue G-250. Sample lanes were cut into 1 mm3 cubes, transferred to a MultiScreen HV 96-well filter plate (Millipore) and destained until clear using repeated applications of 50 mm NH4HCO3 in 50% acetonitrile. After dehydration with 100% acetonitrile, each well was supplemented with 0.4 µg MS grade Trypsin/Lys-C (Promega) in 50 mM NH4HCO3 and tryptic digestion was performed overnight at 37 °C within a humidified incubator. Tryptic peptides were extracted and pooled by two incubations with 0.1% TFA in 50% acetonitrile, dried by SpeedVac and stored at -80 °C. MS sample preparation of astrocyte conditioned medium MS sample preparation of astrocyte conditioned medium was performed following the DNA micro spin column suspension trapping (S-Trap) protocol73, with some minor adaptations. Medium was mixed with S-trap lysis buffer up to a final concentration of 5% SDS, 100 mM Tris-HCl pH 8.0 and 2 mM tris(2-carboxyethyl)phosphine (TCEP), and incubated in a thermomixer for 30 minutes at 65°C. Free sulfhydryl groups were alkylated by incubation with 8 mM methyl methanethiosulfonate (MMTS) for 5 minutes at RT. Next, the samples were acidified to a final concentration of 1.1% phosphoric acid (12% stock solution), mixed with six volumes of binding/washing buffer (90% methanol and 100 mM Tris-HCl pH 8.0), and loaded onto a plasmid DNA micro column (HiPure from Magen Biotechnology). The protein particulate was retained on the column upon centrifugation at 1400x g for 1 minute and the columns were washed four times with binding/washing buffer. Columns were transferred to new LoBind tubes (Eppendorf), supplemented with 0.4 μg Trypsin/Lys-C (Promega) in 50 mM NH4HCO3 and incubated overnight at 37°C in a humidified incubator. Tryptic peptides were eluted and pooled by subsequent addition of 50 mM NH4HCO3, 0.1% formic acid and 0.1% formic acid in acetonitrile. Collected peptides were dried by SpeedVac and stored at -80°C. LC-MS analysis Each sample of tryptic digest was redissolved in 0.1% formic acid and the peptide concentration was determined by tryptophan-fluorescence assay74; 75 ng of peptide was loaded onto an Evotip Pure (Evosep). Peptide samples were separated by standardized 30 samples per day method on the Evosep One liquid chromatography system, using a 15 cm × 150 μm reverse-phase column packed with 1.5 µm C18-beads (EV1137 from Evosep) connected to a 20 µm ID ZDV emitter (Bruker Daltonics). Peptides were electro-sprayed into the timsTOF Pro 2 mass spectrometer (Bruker Daltonics) equipped with CaptiveSpray source and measured with the following settings: Scan range 100-1700 m/z, ion mobility 0.65 to 1.5 Vs/cm2, ramp time 100 ms, accumulation time 100 ms, and collision energy decreasing linearly with inverse ion mobility from 59 eV at 1.6 Vs/cm2 to 20 eV at 0.6 Vs/cm2. Operating in dia-PASEF mode, each cycle took 1.59 s and consisted of 1 MS1 full scan and 14 dia-PASEF scans. Each dia-PASEF scan contained two isolation windows, in total covering 300-1301 m/z (1 Th window overlap) and ion mobility 0.65 to 1.50 Vs/cm2. Dia-PASEF window placement was optimized using the py-diAID tool75. Ion mobility was auto calibrated at the start of each sample (calibrant m/z, 1/K0: 622.029, 0.992 Vs/cm2; 922.010, 1.199 Vs/cm2; 1221.991, 1.393 Vs/cm2).PrideNot availableMS downstream analysis DIA-PASEF raw data were processed with DIA-NN 1.8.126,76. An in-silico spectral library was generated from the uniprot human proteome (SwissProt and TrEMBL, canonical and additional isoforms, release 2022-03) using Trypsin/P digestion and at most 1 missed cleavage. Fixed modification was set to beta-methylthiolation(C) and variable modifications were oxidation(M) and N-term M excision (at most 1 per peptide). Peptide length was set to 7-30, precursor charge range was set to 2-4, precursor m/z was limited to 280–1320, both MS1 and MS2 mass accuracy were set to 10 ppm, scan window was set to 8, double-pass-mode and match-between-runs were enabled. Protein identifiers (isoforms) were used for protein inference. All other settings were left as default. MS-DAP 1.0.9 27 was used for downstream analyses of the DIA-NN results. Filtering and normalization was applied to respective samples per statistical contrast. Peptide-level filtering was configured to retain only peptides that were confidently identified in at least 75% of samples per sample group. Peptide abundance values were normalized using the VSN algorithm, followed by protein-level mode-between normalization (MS-DAP defaults).ProteomicsAugust B. SmitPARTIALDept. of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.Homo Sapiens (human)42346080 Li WP, Laupman KE, Beekhuis-Hoekstra SD, Thanou E, Klaassen RV, Sullivan PF, Posthuma D, Smit AB, Koopmans F, Heine VM. Multimodal Proteomics Reveals Dysregulated Secretion and ECM Remodelling in Schizophrenia Patient iPSC-Derived Astrocytes. Cells. 2026 15(12):1052 10.3390/cells15121052frank.koopmans@vu.nlVrije Universiteit AmsterdamNetherlandsAstrocytes are increasingly implicated in the pathophysiology of schizophrenia (SCZ), yet how astrocytic dysfunction contributes to disease-relevant neuronal abnormalities remains unclear. Here, we used mass spectrometry-based proteomics to profile lysates (proteome) and secreted proteins (secretome) from iPSC-derived astrocytes originating from 9 SCZ patients and 8 healthy controls. Compartment-specific analyses showed that lysates were enriched for mitochondrial and nuclear pathways, whereas astrocyte-conditioned media (ACM) were enriched for extracellular matrix (ECM) and vesicle-associated proteins. Differential expression analysis revealed minimal overlap between dysregulated proteins in lysates and ACM, suggesting modality-specific effects of SCZ-associated donor background. Interestingly, ECM proteins and key secreted cues involved in synaptic development, including MFGE8 and SEMA3C, were selectively reduced in SCZ ACM, whereas RNA-processing proteins were aberrantly increased. This is in line with previously reported microRNA enrichment in extracellular vesicles (EV) derived from SCZ patients. Gene set analyses further identified the alteration in secretion and nuclear processes as well as the potential involvement of autophagy-dependent release mechanism in SCZ astrocytes. Together, these findings suggest disrupted astrocytic protein homeostasis and extracellular signalling in SCZ iPSC-derived astrocytes, providing mechanistic insight into astrocyte-mediated contributions to synaptic and circuit deficits in the disorder.Multimodal Proteomics Reveals Dysregulated Secretion and ECM Remodelling in Schizophrenia Patient iPSC-Derived Astrocytes.Li Wei-Ping WP, Laupman Karen E KE, Beekhuis-Hoekstra Stephanie D SD, Thanou Evangelia E, Klaassen Remco V RV, Sullivan Patrick F PF, Posthuma Danielle D, Smit August B AB, Koopmans Frank F, Heine Vivi M VMfalseMultimodal Proteomics reveals dysregulated secretion and ECM remodeling in schizophrenia patient iPSC-derived astrocytesAstrocytes are increasingly implicated in the pathophysiology of schizophrenia (SCZ), yet how astrocytic dysfunction contributes to disease-relevant neuronal abnormalities remains unclear. Here, we use mass spectrometry–based proteomics to profile lysates (proteome) and secreted (secretome) proteins from iPSC-derived astrocytes originating from 9 SCZ patients and 8 healthy controls. Compartment-specific analyses showed that lysates were enriched for mitochondrial and nuclear pathways, whereas astrocyte-conditioned media (ACM) was enriched for extracellular matrix (ECM) and vesicle-associated proteins. Differential expression analysis revealed minimal overlap between dysregulated proteins in lysates and ACM, indicating modality-specific effects of SCZ genetic background. Interestingly, ECM proteins and key secreted cues involved in synaptic development, including MFGE8, SEMA3C, were selectively reduced in SCZ ACM, whereas RNA-processing proteins were aberrantly increased. This is in line with previously reported microRNA enrichment in extracellular vesicles (EV) derived from SCZ patients. Gene set analyses further identified altered secretion-related pathways, nuclear processes, and potential involvement of autophagy-dependent release mechanisms. Together, these findings demonstrate astrocytic protein homeostasis and extracellular signaling aberrations in SCZ iPSCs, providing mechanistic insight into astrocyte-mediated contributions to synaptic and circuit deficits in the disorder.2026-06-292026-02-28PXD075039NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:111205NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:641809NEWT:317447NEWT:4688NEWT:111225NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:1912919NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:1182590NEWT:3712NEWT:3711NEWT:270643NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1303443NEWT:9483NEWT:485NEWT:56636NEWT:2709072NEWT:2853422NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:294607NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:235443NEWT:108458NEWT:5936NEWT:320637NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:472NEWT:529507NEWT:1071661NEWT:470NEWT:5911NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:9031NEWT:27292NEWT:1050722NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:575412NEWT:28112NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:8655NEWT:5147NEWT:28104NEWT:407821NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:40674NEWT:1194669NEWT:51329NEWT:443906NEWT:519NEWT:2510939NEWT:6063NEWT:1328388NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:13489NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:4232NEWT:416348NEWT:11298NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:563041NEWT:72664NEWT:41949NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:8644NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:192222NEWT:9963NEWT:1617910NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NCBITaxon:3077NEWT:194439NCBITaxon:12637NEWT:38727NEWT:8618NEWT:70448NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2126719NEWT:118705NEWT:6945NEWT:2104NEWT:2627626NEWT:6943NEWT:157546NEWT:870726NEWT:91374NEWT:91373NEWT:474186NEWT:10136NEWT:38942NEWT:4762NEWT:307972NEWT:2102NEWT:34NEWT:38949NEWT:1299114NEWT:1590841NEWT:1276473NEWT:2282334NEWT:1247NEWT:70667NEWT:869728NEWT:6938NCBITaxon:39054NEWT:1736309NEWT:4751NEWT:194963NEWT:15819NEWT:109461NEWT:1085956NEWT:6928NEWT:1239NEWT:36745NEWT:400727NEWT:272563NEWT:11009NEWT:3885NEWT:3888NEWT:649408NEWT:6915NEWT:101510NEWT:3880NEWT:272559NEWT:216816NEWT:153151NEWT:515849NEWT:10141NEWT:95767NEWT:466585NEWT:1000589NEWT:85963NEWT:29NEWT:85962NEWT:42197NEWT:143361NEWT:1299NEWT:424718NEWT:316407NEWT:1794699NCBITaxon:183674NEWT:167387NEWT:84645NEWT:1123294NEWT:209285NEWT:211586NEWT:74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