{
  "abstract": "Tandem mass spectrometry (MS/MS) spectral matching is increasingly performed at the repository scale, where tools such as MASST enable a query spectrum to be compared against heterogeneous public data. Unlike analogous genomic-based searches, repository-scale MS/MS matching lacks integrated false discovery rate (FDR) reporting, leaving parameter selection entirely to user discretion. Here, we evaluate how acquisition factors and analysis filters jointly affect MS/MS matching using a curated library of 40 metabolites spanning ten chemical classes. In this study, we find that normalized collision energies from 30 to 50% balance sufficient fragmentation against loss of larger diagnostic ions, producing the most structurally informative spectra and yielding the highest proportion of repository matches. Using a fragmentation-based decoy library, we show that six minimum matching peaks achieve <1% FDR across the entire cosine threshold range tested (0.7–1.0), while fewer matching peaks require increasingly stringent cosine thresholds. These findings provide practical, benchmarking guidance for user-provided acquisition and search parameters in MASST searches.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Allison J. Keys"
    },
    {
      "affs": [
        0
      ],
      "name": "Emily C. Gentry",
      "orcid": "0000-0002-0016-8132"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8zfqg45rmwvc7.bib",
  "cited_by": 0,
  "doi": "10.1021/jasms.6c00332",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13741904/",
  "id": "8zfqg45rmwvc7",
  "issns": [
    "1044-0305",
    "1879-1123"
  ],
  "landing_url": "https://doi.org/10.1021/jasms.6c00332",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Article"
    ],
    [
      "openalex",
      "1607|Mass Spectrometry Techniques and Applications"
    ]
  ],
  "openalex": "W7223269141",
  "pdf_url": "https://pubs.acs.org/jamsef/article-pdf/doi/10.1021/jasms.6c00332/68957874/jasms.6c00332.pdf",
  "pmcid": "PMC13741904",
  "pmid": "42980298",
  "published": "2026-10-23",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/8zfqg45rmwvc7.ris",
  "sources": [
    {
      "first_seen": "2026-11-10T12:22:51Z",
      "native_id": "PMC13741904",
      "source": "pmc",
      "url": "https://doi.org/10.1021/jasms.6c00332"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:1607|Mass Spectrometry Techniques and Applications",
      "subfield": "physical"
    }
  ],
  "title": "Evaluating the Effects of Acquisition and Search Parameters on Repository-Scale MS/MS Matching",
  "title_text": "Evaluating the Effects of Acquisition and Search Parameters on Repository-Scale MS/MS Matching",
  "type": "peer-reviewed",
  "updated_at": "2026-11-10T12:22:51Z",
  "url": "https://research.draconitic.com/paper/8zfqg45rmwvc7",
  "venue": "Journal of the American Society for Mass Spectrometry",
  "versions": []
}