Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/Setof12files.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063478/6.rawprimaryOK2002480111@tongji.edu.cnHanqing ZhuMass SpectrometryBottom-up proteomicsPulmonary HypertensionUsp2a，hpmvecs，tmt proteomics analysis.https://www.ebi.ac.uk/pride/archive/projects/PXD063478LungBlood Vessel Endothelial CellFor each sample, 2𝜇 of total peptides were separated and analyzed with a nano-UPLC (EASY-nLC1200) coupled to a Q Exactive HFX Orbitrap instrument (Thermo Fisher Scientific) with a nano-electrospray ion source. Separation was performed using a reversed-phase column (100 𝜇 ID ×15 cm, Reprosil-Pur 120 C18-AQ, 1.9 𝜇, Dr. Maisch). Mobile phases were H2O with 0.1% FA, 2% ACN (phase A) and 80% ACN, 0.1% FA (phase B). Separation of sample was executed with a 90 min gradient at 300 nL/min flow rate. Gradient B: 2-5% for 2 min, 5-22% for 68 min, 22-45% for 16 min, 45-95% for 2 min, 95% for 2 min. Data dependent acquisition (DDA) was performed in profile and positive mode with Orbitrap analyzer at a resolution of 120,000 (@200 m/z) and m/z range of 350-1600 for MS1; For MS2, the resolution was set to 15k with a fixed first mass of 110 m/z. The automatic gain control (AGC) target for MS1 was set to 3E6 with max IT 30 ms, and 1E5 for MS2 with max IT 96 ms. The top 20 most intense ions were fragmented by HCD with normalized collision energy (NCE) of 32%, and isolation window of 0.7 m/z. The dynamic exclusion time window was 45s, single charged peaks and peaks with charge exceeding 6 were excluded from the DDA procedure.PrideVendor’s raw MS files were processed using Proteome Discoverer(PD) software (Version 2.4.0.305) and the built-in Sequest HT search engine. MS spectra lists were searched against their species-level UniProt FASTA databases (uniprot-Homo sapiens-9606-2022-11.fasta), with Carbamidomethyl [C], TMT 6 plex(K) and TMT 6 plex (N-term) as a fixed modification and Oxi- dation (M) and Acetyl (Protein N-term) as variable modifications. Trypsin was used as proteases. A maximum of 2 missed cleavage(s) was allowed. The false discovery rate (FDR) was set to 0.01 for both PSM and peptide levels. Peptide identification was performed with an initial precursor mass deviation of up to 10 ppm and a fragment mass deviation of 0.02Da. Unique peptide and Razor peptide were used for protein quantification and total peptide amount for normalization. All the other parameters were reserved as default.ProteomicsHanqing ZhuShanghai Pulmonary HospitalPARTIALHomo Sapiens (human)2480111@tongji.edu.cn10.1038/S41418-026-01747-0Shanghai Pulmonary HospitalChinafalseEffect of depletion of USP2a on protein expression HPMVECsDifferentially expressed proteins (DEPs) in HPMVECs treated with either Vector or USP2a-OE lentivirus were screened through Tandem Mass Tag (TMT)-based quantitative proteomics analysis.2026-04-262025-04-30PXD063478NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:9778NEWT:150475NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:2042546NEWT:115104NEWT:1081927NEWT:67825NEWT:185579NEWT:43179NEWT:13076NEWT:1249668NEWT:317NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:415540NEWT:4081NEWT:876138NEWT:554NEWT:98334NEWT:426428NEWT:237561NEWT:6928NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:29204NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:3885NEWT:746360NEWT:6239NEWT:3888NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:3641NEWT:383379NEWT:8782NEWT:1263854NEWT: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:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:7029NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NCBITaxon:6191NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:185431NEWT:83332NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:44685NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:1123869NEWT:7370NEWT:75058NEWT:83906NEWT:607699NEWT:6282NEWT:1094343NEWT:208964NEWT:1134506NEWT:575584NEWT:296543NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:4006NEWT:1182590NEWT:8726NEWT:6669NEWT:10090NEWT:935293NEWT:64152NEWT:749200NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:100816NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:632957NEWT:373995NEWT:645463NEWT:544404NEWT:3702NEWT:129249NEWT:9925NEWT:8839NEWT:4232NEWT:990119NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:421932NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:128161NEWT:106592NEWT:61674NEWT:1117957NEWT:9913NEWT:1432138NEWT:10312NEWT:1424507NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:180066NEWT:67767NEWT:46835NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:146479NEWT:10306NCBITaxon:2759NEWT:1911079NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:3635NEWT:5811NEWT:1480154NEWT:235443NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:9606NEWT:367830NEWT:157295NEWT:641501NEWT:178616NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:9721NEWT:1450511NEWT:360094NEWT:470NEWT:1313NEWT:84023NEWT:9838NCBITaxon:9615NCBITaxon:5811NEWT:58334NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:33952NEWT:2094720NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:178876NEWT:9940NEWT:327160NEWT:573NEWT:9031NEWT:1274420NEWT:7091NEWT:578458