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Fox"],"software":["Not available"],"tissue":["Wound Fluid"],"sample_protocol":["Wound fluid was collected from Medical Device Related Pressure Injuries from Intensive Care Patients. The wound fluid was extracted from collection swabs. 10 µg of protein was vaccum dried and treated with tetraethylammonium bromide and dithiothreitol. The samples underwent alkylation via  indole-3-acetic acid. Samples were then digested with trypsin (1:100, enzyme to total protein) at 37 °C for 18 hours. Samples desalted using a modified stage-tipping method utilising C18 membranes. A peptide spectral library was generated from the PBQC sample. The PBQC sample was subjected to Data-Dependent Acquisition (DDA) performed on a 5600+ TripleTOF mass spectrometer (Sciex) integrated with an Eksigent Ekspert HPLC system. The digested peptide samples were analysed using a Triple TOF 5600+ (SCIEX) LC-MS/MS platform, using a 95 min SWATH (data independent acquisition, DIA) method with custom variable windows. Normalising and cleaning of peptide spectral data is important to accounted for batch effects and non-biological differences to identify true data variants."],"repository":["Pride"],"labhead":["Anthony J Parker"],"instrument_platform":[""],"labhead_affiliation":["Queensland University of Technology, Australia"],"submission_type":["COMPLETE"],"publication":["42143236 Fox HA, Broszczak DA, Doubrovsky A, Levido A, Palmer J, Coyer F, Parker TJ. Wound fluid proteomics reveal elevated alpha-1 antitrypsin levels are associated with healing of medical device related pressure injury. Clin Proteomics. 2026 23(1):39 10.1186/s12014-026-09609-0"],"submitter_affiliation":["Queensland University of Technology"],"labhead_mail":["a.parker@qut.edu.au"],"technology_type":["Mass Spectrometry","SWATH MS"],"disease":["Wounds And Injuries"],"submitter_keywords":["Human","Proteome","Medical device related pressure injury","Swath-ms","Intensive care unit"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD069939"],"quantification_method":[""],"modification":[""],"data_protocol":["The spectral library file was loaded into the Sciex SWATH MicroApp 2.0 in the PeakView® 2.2 program and the spiked iRTs were utilised to calibrate the retention-time shift across samples. The process settings in PeakView® 2.2 were set to 6 peptides per protein and 6 transitions per peptide. The peptide confidence threshold was set to 99% and the false discovery rate threshold was set to 1%. Finally, the XIC extraction window was 5 min and the XIC width was 75 ppm. The raw relative protein abundance quantification data was then exported into a text file format. This yielded 231 protein IDs which was reduced to 217 in Excel 2023 by removing protein IDs with missing values across samples. The refined protein abundance data was imported into R Studio 2023.09.01 for further analysis."],"omics_type":["Proteomics"],"species":["Homo Sapiens (human)"],"submitter_mail":["foxh3@qut.edu.au"],"curator_keywords":["Human proteome project"],"submitter_country":["Australia"],"doi":["10.6019/PXD069939"],"pubmed_abstract":["The Medical Device Related Pressure Injuries (MDRPIs) are a wound type that has been extensively tracked and recorded within observational studies, with a global patient prevalence of 19.3% [Zhang N et al. in Eur J Med Res 1:425, 2024] and 28.1% in acute care patients [Brophy S et al. in J Tissue Viability 4:489-498, 2021]. Yet, despite being an injury caused directly by medical intervention, to the author's knowledge, no in-depth proteomic analysis in this wound type has been published previously. This study represents a novel proteomic analysis of clinical MDRPI samples providing initial characterization of a protein pathway significant to wound healing in the context of MDRPIs developed in an ICU setting (Fig. 1). To investigate the proteomic changes associated with the healing outcomes of medical device related pressure injuries through comprehensive proteome characterisation. Clinical wound fluid samples were collected from Intensive Care Unit (ICU) patients with MDRPIs. These samples underwent analysis using Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS) mass spectrometry. The severity and healing trajectories of the injuries were assessed using the Pressure Ulcer Scale for Healing (PUSH) scores, facilitating the comparison of protein abundances to identify key pathways involved in healing and non-healing MDRPIs. The study identified a significant inverse correlation between the severity of non-healing MDRPIs and the levels of alpha-1 antitrypsin (A1AT) (R = -0.43; P = 0.035). A1AT functions as an inhibitor of neutrophil elastase (NE), which targets kininogen-1 (KNG-1). This relationship was further substantiated by a strong positive correlation between A1AT and KNG-1 levels (R = 0.76; Q < 6.8 × 10<sup>- 10</sup>), indicating a protective function of A1AT over KNG-1 from NE. Given that KNG-1 contributes to early wound healing through its derivative, bradykinin, the misregulation of A1AT may disrupt the healing process of MDRPIs. The findings suggest that decreased levels of A1AT are associated with increased severity in non-healing MDRPIs, potentially due to the disruption of KNG-1 activity. These insights offer a foundation for further research into targeted therapeutic strategies aimed at enhancing the healing of MDRPIs."],"pubmed_title":["Wound fluid proteomics reveal elevated alpha-1 antitrypsin levels are associated with healing of medical device related pressure injury."],"pubmed_authors":["Fox Haydn A HA, Broszczak Daniel A DA, Doubrovsky Anna A, Levido Annabel A, Palmer Jennifer J, Coyer Fiona F, Parker Tony J TJ"],"additional_accession":[]},"is_claimable":false,"name":"Analysing Medical Device Related Pressure Injuries through Sequential Window Acquisition of all Theoretical Fragment Ion Spectra Mass Spectrometry","description":"This project aimed to investigate the proteome of wound fluid collected from medical device related pressure injuries.","dates":{"publication":"2026-09-07","submission":"2025-10-27"},"accession":"PXD069939","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:1131","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:57577","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:111205","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:672127","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:1584","NEWT:36630","NEWT:1585","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:29064","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:273791","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:55350","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:5516","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:33554","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:1310173","NEWT:171719","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NCBITaxon:37162","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10891","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:34878","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:926571","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:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2499525","NEWT:2853422","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:237610","NEWT:95486","EFO:0001352","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","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:1640278","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:28128","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:1290454","NEWT:906914","NEWT:28141","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:2126348","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:207340","NEWT:172271","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:49012","NEWT:6493","NEWT:10832","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:9983","NEWT:8655","NEWT:5147","NEWT:595495","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:1613","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:353153","NEWT:227377","NEWT:1774284","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:13037","NEWT:51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