{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T19:17:29Z","timestamp":1792005449054,"version":"4.4.0"},"posted":{"date-parts":[[2025,8,15]]},"group-title":"Biochemistry","reference-count":23,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T00:00:00Z","timestamp":1755216000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"award":["R35GM138362"],"award-info":[{"award-number":["R35GM138362"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,30]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>We present a multi-organism, ground-truth metaproteomic dataset generated using data-dependent acquisition Parallel Accumulation-Serial Fragmentation (ddaPASEF) and data-independent acquisition (diaPASEF) on a trapped ion mobility mass spectrometer. The dataset comprises 28 species (30 strains) spanning Archaea, Bacteria, Eukarya, and bacteriophages, assembled into an uneven mock community with a 400-fold dynamic range of organismal abundance. Four biological replicates were processed using a standardized sample preparation workflow and analyzed using described LC-MS conditions. Raw data, search outputs, protein coverage metrics, quantitative abundance estimates, and strain-specific peptide evidence are provided. The dataset enables evaluation of proteome depth, proteome coverage, quantitative reproducibility, and strain-level resolution across acquisition strategies. diaPASEF yielded broader peptide and protein detection and deeper sequence coverage, while both methods accurately quantified high-abundance organisms. Detection evidence for low-abundance bacteriophages and single-amino-acid-variant peptides is included to support benchmarking of taxonomic and strain-resolved analyses. This dataset provides a comprehensive reference for developing and validating metaproteomic workflows, protein inference strategies, and ion mobility-aware computational tools.<\/jats:p>","DOI":"10.1101\/2025.08.13.670166","type":"posted-content","created":{"date-parts":[[2025,8,16]],"date-time":"2025-08-16T04:25:24Z","timestamp":1755318324000},"source":"Crossref","is-referenced-by-count":1,"title":["Evaluation of Parallel Accumulation-Serial Fragmentation methods for metaproteomics using a model microbiome"],"prefix":"10.64898","author":[{"given":"Ruben","family":"Shreshta","sequence":"first","affiliation":[{"name":"Bruker Scientific LLC, Billerica, MA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5119-8075","authenticated-orcid":false,"given":"Andrew T.","family":"Rajczewski","sequence":"additional","affiliation":[{"name":"University of Minnesota, Minneapolis, 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