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  "Package": "rtmsEcho",
  "Title": "Extract and Analyze EchoMS Data from Sciex Wiff Files",
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  "Authors@R": "c(\nperson(\"Mary Ashley\", \"Rimmer\", email=\"maryashley.rimmer@stjude.org\", role = c(\"aut\")),\nperson(\"Nathaniel\", \"Twarog\", email=\"nathaniel.twarog@stjude.org\", role = c(\"aut\", \"cre\")),\nperson(\"Lei\", \"Yang\", email=\"lei.yang@stjude.org\", role = c(\"aut\")))",
  "Description": "Read raw and processed data from acoustic ejection mass\nspectrometry (AEMS) files produced by the Sciex EchoMS\ninstrument.  Includes functions to create interactive reader\nobjects, extract raw intensity measurements, mass spectra, and\nfully-processed mass-transition intensity areas.  Methods for\ndata processing and analysis are described in Rimmer et al.\n(2025) <doi:10.1021/acs.analchem.5c03730>. Supports both\nmultiple reaction monitoring (MRM) and full-scan (neutral loss\nand precursor ion) data formats.",
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    "Date": "2026-10-12 09:24:05 UTC",
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  "Author": "Mary Ashley Rimmer [aut], Nathaniel Twarog [aut, cre], Lei Yang\n[aut]",
  "Maintainer": "Nathaniel Twarog <nathaniel.twarog@stjude.org>",
  "Repository": "https://nathanieltwarog.r-universe.dev",
  "Date/Publication": "2026-01-14 18:10:02 UTC",
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    "getFullScanAreas",
    "getFullScanData",
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    "newWiffReader",
    "processAllFullScanAreas",
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      "name": "exampleWiff",
      "title": "Example wiff reader object",
      "object": "exampleWiff",
      "class": [
        "rtmsWiffReaderMRM",
        "rtmsWiffReader"
      ],
      "fields": [],
      "table": false,
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    {
      "page": "exampleWiff",
      "title": "Example wiff reader object",
      "topics": [
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      ]
    },
    {
      "page": "getAllFullScanAreas",
      "title": "Get the total area for given masses for all wells",
      "topics": [
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      ]
    },
    {
      "page": "getAllFullScanSpectra",
      "title": "Extract mass spectra for all wells",
      "topics": [
        "getAllFullScanSpectra"
      ]
    },
    {
      "page": "getAllMRMAreas",
      "title": "Extract the peak areas for MRM mass transitions for all wells",
      "topics": [
        "getAllMRMAreas"
      ]
    },
    {
      "page": "getAllTIC",
      "title": "Extract all total ion chromatograms from a Wiff file",
      "topics": [
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      ]
    },
    {
      "page": "getFullScanAreas",
      "title": "Get the total area for given masses for a particular well",
      "topics": [
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      ]
    },
    {
      "page": "getFullScanData",
      "title": "Extract raw Wiff full scan data",
      "topics": [
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      ]
    },
    {
      "page": "getFullScanSpectrum",
      "title": "Extract a full mass spectrum for a given well",
      "topics": [
        "getFullScanSpectrum"
      ]
    },
    {
      "page": "getMRMAreas",
      "title": "Extract the peak areas for MRM mass transitions for a given well",
      "topics": [
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      ]
    },
    {
      "page": "getMRMChromatograms",
      "title": "Extract full chromatograms for each mass transition",
      "topics": [
        "getMRMChromatograms"
      ]
    },
    {
      "page": "getTIC",
      "title": "Extract a total ion chromatogram (TIC) from a Wiff file",
      "topics": [
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      ]
    },
    {
      "page": "getWiffShots",
      "title": "List of Shot Names in a given Wiff File",
      "topics": [
        "getWiffShots"
      ]
    },
    {
      "page": "measureEjections",
      "title": "Measure total ion chromatogram peaks to estimate ejection time",
      "topics": [
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        "measureEjections.default",
        "measureEjections.rtmsWiffReader"
      ]
    },
    {
      "page": "newWiffReader",
      "title": "Open a Sciex EchoMS wiff File for Reading",
      "topics": [
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      ]
    },
    {
      "page": "processAllFullScanAreas",
      "title": "Fully process a Full Scan Wiff and scan File",
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      ]
    },
    {
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      "topics": [
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      ]
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