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KleffmannMass SpectrometrySWATH MSEndometriosisNot availableEndometriosisCervicovaginal fluidSwath-mshttps://www.ebi.ac.uk/pride/archive/projects/PXD065951Cervicovaginal FluidA total of 39 samples, (20 positive for endometriosis and 19 negative for endometriosis) were processed and analysed by SWATH-MS in two separate experiments (indicated by E1 and E2 in all file names) based on the time frame of sample collection. Low vaginal swabs were taken by the operating surgeon after the administration of anaesthesia, prior to surgical preparation. Vaginal swabs were collected first by inserting a FLOQ swab into the vagina and turning for approximately 30 seconds, then placed into a tube with 1 mL of phosphate buffered saline Each 200 µL aliquot of vaginal swab or cervicovaginal fluid was denatured in 4% SDS for protein extraction. An amount of 100 µg of extracted protein from each sample processed and digested with trypsin using S-Trap micro spin columns (Protifi, #C02-micro) according to manufacturer’s instructions. To generate a spectral library for each experiment, equal aliquots of each sample from each experiment were pooled and subjected to peptide pre-fractionation by high pH reversed phase separation. The pooled samples were fractionated into 11 fractions for each experiment. Samples were analysed on a 5600+ Triple Time-of-Flight (TOF) mass spectrometer coupled to an Ekspert NanoLC 415 system (Eksigent, AB Sciex). A spectral library was generated through data-dependent acquisition (DDA) of the fractions of each pooled sample. Each fraction was run in two technical replicates. The individual samples were analysed in technical triplicate by SWATH-MS with the mass spectrometer operated in data-independent mode. All DDA and DIA analyses used the same LC conditions over a 115 min gradient from 3% acetonitrile (ACN), 0.05% formic acid (FA) in water to 90% ACN, 0.05% FA in water followed by 5 min of column washing and re-equilibration. The mass spectrometer was operated in a mass range of 400-1250 m/z with a cycle time of 3.3 seconds for DIA.PrideProtein identification was performed by searching the raw data from the data-dependent acquisition against the human reference sequence database using ProteinPilot software version 4.5 (AB Sciex). The spectral library was built using the SWATH application (version 2.0) embedded into PeakView software (version 2.2, AB Sciex). The raw data from the data-independent acquisition of individual samples was aligned to the spectral library at a false discovery rate of 1% and confidence ≥99% for peak identification in at least one sample. Protein, peptide and fragment ion intensities were imported to the MarkerView software (AB Sciex) for further data analysis and basic statistics.ProteomicsClaire HenryDepartment of Surgery and Anaesthesia, University of Otago (Wellington)PARTIALHomo Sapiens (human)torsten.kleffmann@otago.ac.nz41906395 Paterson ESJ, Scheck S, Kleffmann T, Gill R, Bedford N, McDowell S, Girling JE, Henry CE. Proteomic Analysis of Cervicovaginal Fluid for Diagnostic Endometriosis Biomarker Discovery. Proteomics Clin Appl. 2026 20(3):e70044 10.1002/prca.70044Department of Biochemistry, University of OtagoNew Zealand<h4>Purpose</h4>Endometriosis is a prevalent inflammatory condition characterised by the presence of endometrial-like tissue outside the uterus and is associated with significant challenges, including diagnostic delays and continued reliance on laparoscopy. Although extensive research has investigated potential biomarkers in various biofluids, none have been validated for clinical use.<h4>Experimental design</h4>This pilot study explored the proteome of cervicovaginal fluid to identify biomarkers of endometriosis. SWATH-MS was performed over two experiments on cervicovaginal fluid sampled via a low vaginal swab, from people with (n = 20) and without (n = 19) surgically confirmed endometriosis. STRING, OPLS-DA modelling and ingenuity pathway analysis were used to interrogate the data. ELISA was performed validate SWATH-MS findings.<h4>Results</h4>There were 29 proteins in experiment one and 47 proteins in experiment two identified as differentially abundant between cases and controls. No proteins were identified as differentially abundant in both experiments. Legumain (LGMN) measured via ELISA was significantly increased in the cervicovaginal fluid of people with endometriosis.<h4>Conclusions and clinical relevance</h4>Cervicovaginal fluid proteins sampled via vaginal swab may have limited biomarker potential for endometriosis. A larger and more diverse cohort would be required to confirm the promise of cervicovaginal fluid LGMN as a candidate biomarker of endometriosis.Proteomic Analysis of Cervicovaginal Fluid for Diagnostic Endometriosis Biomarker Discovery.Paterson Emily S J ESJ, Scheck Simon S, Kleffmann Torsten T, Gill Roopi R, Bedford Nicholas N, McDowell Simon S, Girling Jane E JE, Henry Claire E CEfalseProteomic analysis of cervicovaginal fluid for endometriosis biomarker discoveryEndometriosis is a gynaecological disease facing significant diagnostic challenges, contributing to an extensive diagnostic delay. Non-invasive diagnostic biomarkers of endometriosis could expedite diagnosis and minimise the reliance on surgery to confirm endometriosis. This pilot study aimed to identify candidate protein biomarkers of endometriosis from cervicovaginal fluid i) collected from consenting people having surgery for suspected endometriosis and ii) sampled via low vaginal swab. Samples from people with (n=20) and without (n=19) endometriosis across were analysed by data independent acquisition mass spectrometry using the Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH)-MS approach. Samples were measured and analysed in two experimental runs (E1 and E2) based on time periods of sample collection. ELISA was performed to validate SWATH-MS findings.2026-04-062025-07-09PXD065951NEWT:6945NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2042546NEWT:45351NEWT:43179NEWT:4513NEWT:5722NEWT:55153NCBITaxon:10407NEWT:1736309NEWT: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:10029NEWT:1000589NEWT:85962NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT: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: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:935293NEWT:64152NEWT:4924NEWT:749200NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NCBITaxon:1313NEWT:43330NEWT:408169NEWT:44544NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:990119NEWT:408172NEWT:408170NEWT:493760NEWT:260710NEWT:257313NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:1432138NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:9598NEWT:8030NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:432359NEWT:46835NEWT:2711NEWT:376686NEWT:95486NEWT:9103NEWT:29159NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:3635NEWT:5811NEWT:235443NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:169963NEWT:499175NEWT:476272NEWT:3747NEWT:367830NEWT:178616NEWT:410289NEWT:373153NEWT:352472NEWT:360094NEWT:470NEWT:1313NEWT:411469NEWT:84023NEWT:559292NCBITaxon:5811NEWT:411464NEWT:411460NEWT:2762NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:28038NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:327159NEWT:178876NEWT:327160NEWT:573NEWT:9031NEWT:7091NEWT:241368NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:5180NEWT:256737NEWT:115104NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:13076NEWT:1249668NEWT:317NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:415540NEWT:4081NEWT:554NEWT:98334NEWT:426428NEWT:7574NEWT:7215NEWT:575412NEWT:29204NEWT:2172103NEWT:507601NCBITaxon:6157NEWT:746360NEWT:6239NEWT:470150NEWT:216257NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NCBITaxon:2NEWT:985076NEWT:1215323NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:2829NEWT: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: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:373995NEWT:5689NEWT: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:749906NEWT:418985NEWT:146479NEWT:1911079NEWT: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:58334NEWT:1193501NEWT:3055NEWT:58331NEWT:6326NEWT:6689NEWT:5476NEWT:1274432NEWT:1274426NEWT:70448NEWT:9825NEWT:1274423NEWT:393765NEWT:698936NEWT:39946NEWT:9823NEWT:9940NEWT:521001NEWT:39947NEWT:1274420NEWT:578458419063950000-0001-9305-5980