{
  "version": "https://jsonfeed.org/version/1.1",
  "title": "chem-bla-ics",
  "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.",
  "home_page_url": "https://chem-bla-ics.linkedchemistry.info/",
  "feed_url": "https://chem-bla-ics.linkedchemistry.info/2008/06/05/recovering-full-mass-spectra-from-gc-ms_05.json",
  "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png",
  "language": "en",
  "authors": [
    {
      "name": "Egon Willighagen",
      "url": "https://orcid.org/0000-0001-7542-0286",
      "_orcid": "0000-0001-7542-0286"
    }
  ],
  "items": [

    {
      "id": "https://doi.org/10.59350/j9rb9-ns27",
      "url": "https://chem-bla-ics.linkedchemistry.info/2008/06/05/recovering-full-mass-spectra-from-gc-ms_05.html",
      "title": "Recovering full mass spectra from GC-MS data #2",
      "content_html": "<p>Steffen reminded me over email that the particular machine only has a 1 dalton accuracy, and that the 150ppm\nparameter setting is somewhat inappropriate. As <a href=\"https://chem-bla-ics.linkedchemistry.info/2008/06/04/recovering-full-mass-spectra-from-gc-ms.html\">seen yesterday <i class=\"fa-solid fa-recycle fa-xs\"></i></a>,\nit works fine for larger peaks, but fails for low intensity peaks. So, I reran the <code class=\"language-plaintext highlighter-rouge\">centWave</code> peak detection with 750, 1000 and 1250 ppm,\nand that indeed make <a href=\"http://masspec.scripps.edu/xcms/xcms.php\">XCMS</a> recover many more metabolites, and, also important, with more\nextracted ion chromatograms per metabolite, yielding a more accurate mass spectrum. At the same time, I notice that profiles are not\nas clean as before, but that’s where the peak fitting with (Modified) Gaussians come into play.</p>\n\n<p>The original 150ppm results:</p>\n\n<p><img src=\"/assets/images/ionChromPlot4.png\" alt=\"\" /></p>\n\n<p>The 750ppm results:</p>\n\n<p><img src=\"/assets/images/map5.png\" alt=\"\" /></p>\n\n<p>And for 1000ppm (1250ppm did not further improve):</p>\n\n<p><img src=\"/assets/images/map6.png\" alt=\"\" /></p>",
      "summary": "Steffen reminded me over email that the particular machine only has a 1 dalton accuracy, and that the 150ppm parameter setting is somewhat inappropriate. As seen yesterday , it works fine for larger peaks, but fails for low intensity peaks. So, I reran the centWave peak detection with 750, 1000 and 1250 ppm, and that indeed make XCMS recover many more metabolites, and, also important, with more extracted ion chromatograms per metabolite, yielding a more accurate mass spectrum. At the same time, I notice that profiles are not as clean as before, but that’s where the peak fitting with (Modified) Gaussians come into play.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/map6.png",
      "date_published": "2008-06-05T00:00:00+00:00",
      "date_modified": "2025-10-11T00:00:00+00:00",
      "tags": ["metabolomics","rstats"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}