{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:06:40Z","timestamp":1787162800284,"version":"build-2736575974"},"reference-count":46,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T00:00:00Z","timestamp":1776211200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T00:00:00Z","timestamp":1776211200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteomics"],"published-print":{"date-parts":[[2026,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>In biomarker discovery phases clinical proteomics provides large\u2010scale identification and quantification of proteins in donor samples. For these studies plasma is the most frequently used biofluid, as it reflects both physiological and pathological states of the circulating proteome. However, the vast dynamic range of proteins in plasma remains a significant challenge, where low\u2010abundance biomarkers are suppressed by high\u2010abundance proteins, despite substantial technological improvements. Often the focus of improving outcomes in plasma proteomic workflows are within the biofluid's sample preparation, although adjusting MS methods dramatically improves detection and sampling of lower abundance proteins. Herein we have benchmarked various liquid chromatography (LC) and data\u2010independent acquisition (DIA) methods across three generations of mass spectrometry instruments: timsTOF Pro (2017), Orbitrap Eclipse (2020), and Orbitrap Astral (2023). This study explored 27 combinations of LC\u2010MS methods across 200 hours of instrument acquisition time, encompassing varying LC and MS settings. While each instrument generation significantly improved performance, each instrument also revealed a unique and different tuneable range to improve performance in plasma samples, highlighting the benefit of investing in plasma\u2010specific method development for any mass spectrometer. We also evaluated the detection and quantification capabilities of each instrument via a unique approach of mixing paired platelet poor plasma (PPP) and platelet rich plasma (PRP), introducing linear contamination markers for quantitative assessment. This approach tested each instrument's sensitivity to detect low\u2010abundance peptides and evaluated their quantitative accuracy. Lastly, we performed testing of the Orbitrap Astral's parallel ion processing capabilities with the aim of improving low\u2010abundance protein identifications using gas\u2010phase enrichment (GPE). More specifically, we show that optimisation of MS2 AGC targets and injection time enhanced GPE of low\u2010abundance peptides, improving detection in plasma samples.<\/jats:p>","DOI":"10.1002\/pmic.70127","type":"journal-article","created":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T06:18:07Z","timestamp":1776320287000},"page":"131-145","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Plasma Proteomics Across Three Generations of Mass Spectrometry Instruments: Lessons for Biofluid Method Optimisation"],"prefix":"10.1002","volume":"26","author":[{"given":"Jack","family":"Edwards","sequence":"first","affiliation":[{"name":"Advanced Technology and Biology Division Walter and Eliza Hall Institute  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Melbourne Victoria Australia"},{"name":"CSL Seqirus  Parkville VIC Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dylan H.","family":"Multari","sequence":"additional","affiliation":[{"name":"Advanced Technology and Biology Division Walter and Eliza Hall Institute  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Melbourne Victoria Australia"},{"name":"Monash Proteomics &amp; Metabolomics Platform Department of Biochemistry and Molecular Biology Department of Biochemistry and Molecular Biology Biomedicine Discovery Institutew Monash University  Clayton Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toby","family":"Dite","sequence":"additional","affiliation":[{"name":"Advanced Technology and Biology Division Walter and Eliza Hall Institute  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Melbourne Victoria Australia"},{"name":"CSL  Parkville VIC Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steve","family":"Binos","sequence":"additional","affiliation":[{"name":"Advanced Technology and Biology Division Walter and Eliza Hall Institute  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clare","family":"Shugg","sequence":"additional","affiliation":[{"name":"Department of Diagnostic Haematology Royal Melbourne Hospital  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew I.","family":"Webb","sequence":"additional","affiliation":[{"name":"Advanced Technology and Biology Division Walter and Eliza Hall Institute  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Melbourne Victoria Australia"},{"name":"Mass Dynamics  Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura F.","family":"Dagley","sequence":"additional","affiliation":[{"name":"Advanced Technology and Biology Division Walter and Eliza Hall Institute  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha J.","family":"Emery\u2010Corbin","sequence":"additional","affiliation":[{"name":"Advanced Technology and Biology Division Walter and Eliza Hall Institute  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Melbourne Victoria Australia"},{"name":"Monash Proteomics &amp; 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