Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/proteins.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/protein-peptides.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/de_novo_only_peptides.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/DB_search_psm.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/peptide.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/protein.htmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_14_CA4_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-14_1_9-12-2025_8337.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/peptides.htmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_1__NegCont_PDB_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-1_1_9-11-2025_8296.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_6_BF8_B05.10_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-6_1_9-11-2025_8310.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_9_BF8_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-9_1_9-12-2025_8322.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_4_B05.10_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-4_1_9-11-2025_8304.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_3_B05.10_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-3_1_9-11-2025_8301.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_5_BF8_B05.10_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-5_1_9-11-2025_8307.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_13_CA4_B05.10_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-13_1_9-12-2025_8334.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_2_B05.10_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-2_1_9-11-2025_8298.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_7_BF8_B05.10_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-7_1_9-12-2025_8313.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_11_CA4_B05.10_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-11_1_9-12-2025_8328.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_12_CA4_B05.10_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-12_1_9-12-2025_8331.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_8_BF8_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-8_1_9-12-2025_8319.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_10_BF8_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-10_1_9-12-2025_8325.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_15_CA4_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-15_1_9-12-2025_8340.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075355/JesusCantoral_sol791-34-25_16_CA4_DDA-PASEF_SG_0.8-1.5_Aurora25cm_30min_Slot2-16_1_9-12-2025_8343.d.zipprimaryOK200joseluis.padilla@uca.esJose PadillaMass SpectrometryBottom-up proteomicsNot availableProteomics lc-ms/ms dda-pasef peaks biocontrohttps://www.ebi.ac.uk/pride/archive/projects/PXD075355Cell CultureVegetative Cell (sensu Fungi)Protein samples were digested into peptides and analysed by nanoLC–TIMS–MS/MS. Peptide mixtures (200 ng per injection) were separated using a nanoElute UHPLC system (Bruker Daltonics) coupled to a timsTOF Pro 2 mass spectrometer equipped with a CaptiveSpray nanoelectrospray source. Peptides were loaded onto a Bruker FIFTEEN C18 column (15 cm × 75 μm ID, 1.9 μm particle size) and separated at 30 °C using a 20-min gradient at 300 nL min⁻¹ (mobile phase A: 0.1% formic acid; mobile phase B: 0.1% formic acid in acetonitrile). The elution gradient was 0–35% B for 13 min, 35–90% B from 13–15 min, followed by a wash at 90% B. Mass spectrometry acquisition was performed on a timsTOF Pro 2 in data-dependent acquisition mode using the PASEF method, acquiring MS and MS/MS spectra in the m/z range 100–1700. Ion mobility separation ranged from 0.85 to 1.30 V·s cm⁻² with a ramp time of 100 ms. Four PASEF MS/MS scans were acquired per cycle. Active exclusion was set to 0.4 min for precursors above 20,000 intensity units.PrideRaw LC–TIMS–MS/MS data were processed using PEAKS Studio ProX (Bioinformatics Solutions Inc.). MS/MS spectra were searched against a combined UniProt database containing the reference proteomes of the analysed yeast strains and Botrytis cinerea. Search parameters included a precursor mass tolerance of 15 ppm and fragment tolerance of 0.05 Da, with carbamidomethylation of cysteine as fixed modification and methionine oxidation and N-terminal acetylation as variable modifications. Protein identifications were validated using a target–decoy strategy with a false discovery rate (FDR) threshold of 1%. Proteins supported by at least two unique peptides and −10lgP ≥ 25 were retained for downstream analysis. Protein intensities were log2-transformed, normalized by median centering, and missing values were imputed using a minimum-intensity approach. Differential abundance analysis was performed using empirical Bayes linear modelling implemented in the limma package in R (v4.3.2), applying Benjamini–Hochberg correction and considering proteins with FDR ≤ 0.05 and |log2FC| ≥ 0.58 as differentially abundant.ProteomicsJose Luis Padilla AgudeloDepartment of Biomedicine, Biotechnology and Public Health, University of Cádiz, SpainPARTIALPichia KluyveriPichia Kudriavzeviijoseluis.padilla@uca.es10.1016/J.FM.2026.105112University of CádizSpainfalseDistinct physiological strategies underpin antagonism of native Pichia yeasts against Botrytis cinereaProteomics dataset generated using LC-MS/MS on a Bruker timsTOF instrument with DDA-PASEF acquisition. Protein identification was performed using PEAKS software. The dataset includes raw instrument files (.d folders) and processed peptide and protein identification results.2026-04-212026-03-07PXD075355NEWT:6945NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2042546NEWT:45351NEWT:43179NEWT:4513NEWT:5722NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:1211601NEWT:876138NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:1351NEWT:1438992NEWT:2649997NEWT:272563NEWT:224326NCBITaxon:79857NEWT:1096976NEWT:95648NEWT:3885NEWT:3888NEWT:1589NEWT:135622NEWT:6915NEWT:3649NEWT:101510NEWT:3880NEWT:272559NEWT:3641NEWT:383379NEWT:466585NEWT:10029NEWT:1000589NEWT:85963NEWT:85962NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:84645NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:197NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:1270NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:286NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:1148NEWT:580240NEWT:294128NEWT:11676NEWT:55571NEWT:100226NEWT:4530NEWT:4896NEWT:75058NEWT:13616NEWT:1094343NEWT:296543NEWT:1773NEWT:1895NEWT:1182590NEWT:3712NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NCBITaxon:1313NEWT:43330NEWT:1603293NEWT:408169NEWT:44544NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:243277NEWT:990119NEWT:408172NEWT:408170NEWT:493760NEWT:260710NEWT:257313NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:460519NEWT:1187947NEWT:1432138NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:9598NEWT:8030NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:432359NEWT:46835NEWT:1182263NEWT:2711NEWT:376686NEWT:95486NEWT:9103NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:3635NEWT:5811NEWT:235443NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:169963NEWT:32644NEWT:499175NEWT:109779NEWT:476272NEWT:3747NEWT:195051NEWT:367830NEWT:1255228NEWT:178616NEWT:410289NEWT:373153NEWT:352472NEWT:357NEWT:360094NEWT:470NEWT:1313NEWT:411469NEWT:84023NEWT:559292NEWT:39491NCBITaxon:5811NEWT:411464NEWT:411460NEWT:2014887NEWT:2762NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:571256NEWT:28038NEWT:1663NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:327159NEWT:178876NEWT:327160NEWT:573NEWT:9031NEWT:7091NEWT:241368NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:303NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:5180NEWT:256737NEWT:115104NEWT:1121114NEWT:663NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:941442NEWT:220668NEWT:13076NEWT:1249668NEWT:7108NEWT:317NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:334542NEWT:554NEWT:98334NEWT:426428NEWT:7574NEWT:1715256NEWT:7215NEWT:575412NEWT:29204NEWT:2172103NEWT:507601NEWT:643680NCBITaxon:6157NEWT:746360NEWT:6239NEWT:470150NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NCBITaxon:2NEWT:985076NEWT:1215323NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:366581NEWT:216599NEWT:216595NEWT:243230NEWT:8355NEWT:9685NEWT:7029NEWT:1080772NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:260707NCBITaxon:6191NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:105231NEWT:1216981NCBITaxon:6073NEWT:884204NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NEWT:607699NEWT:6282NEWT:208964NEWT:1134506NEWT:575584NEWT:38783NEWT:8727NEWT:4006NEWT:8726NEWT:6426NEWT:6669NEWT:10090NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:5334NEWT:37334NEWT:382352NCBITaxon:10359NEWT:242619NEWT:632957NEWT:34073NEWT:373995NEWT:544404NEWT:9925NEWT:8839NEWT:4232NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:196627NEWT:5691NEWT:48479NEWT:627025NEWT:1097677NEWT:61674NEWT:1117957NEWT:9913NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:29722NEWT:380394NEWT:1692259NEWT:180066NEWT:135588NEWT:1843183NEWT:58002NEWT:326423NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:1678078NEWT:749906NEWT:418985NEWT:146479NEWT:1911079NEWT:69373NEWT:264203NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:9612NEWT:38865NEWT:51953NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:349741NEWT:9605NEWT:9606NEWT:157295NEWT:641501NEWT:7668NEWT:915099NEWT:74940NEWT:9721NEWT:137221NEWT:1450511NEWT:1143193NEWT:411901NEWT:9838NEWT:105884NCBITaxon:9615NEWT:9839NEWT:58334NEWT:1193501NEWT:3055NEWT:58331NEWT:6326NEWT:6689NEWT:5476NEWT:299767NEWT:1274432NEWT:1274426NEWT:70448NEWT:9825NEWT:1274423NEWT:393765NEWT:698936NEWT:39946NEWT:9823NEWT:9940NEWT:521001NEWT:39947NEWT:1274420NEWT:5784580000-0002-2019-2447