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  <title>Computational Proteomics | Lund University</title>
  <meta name="description" content="Software and resources from the Computational Proteomics Group at the Department of Immunotechnology, Lund University (Faculty of Engineering, LTH).">
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      <p class="eyebrow"><a class="eyebrow-link" href="https://www.immun.lth.se/" target="_blank" rel="noopener noreferrer">Department of Immunotechnology · Lund University</a></p>
      <h1>Computational Proteomics Group</h1>
      <p class="lead">
        We develop computational methods for mass spectrometry-based proteomics, enabling high-resolution and comprehensive protein measurements for translational and molecular research.
      </p>
      <p class="summary">
        Our work transforms complex proteomics data into robust biological insight. Building on large-scale protein profiling, we design and apply analytical methods in collaborative projects across clinical and life-science domains.
      </p>
    </header>

    <section class="panel">
      <h2>Software</h2>
      <ul class="software-grid">
        <li class="software-card">
          <article class="software-card-inner">
            <p class="software-title">proteoDeconv <span class="software-year">(2025)</span></p>
            <p class="software-desc">R package for deconvolution of bulk proteomics data to estimate cell-type proportions.</p>
            <p class="software-links">
              <a class="software-link" href="/proteoDeconv/" target="_blank" rel="noopener noreferrer">Docs</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://github.com/ComputationalProteomics/proteoDeconv" target="_blank" rel="noopener noreferrer">GitHub</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://doi.org/10.1021/acs.jproteome.4c00868" target="_blank" rel="noopener noreferrer">Paper</a>
            </p>
          </article>
        </li>
        <li class="software-card">
          <article class="software-card-inner">
            <p class="software-title">OmicLoupe <span class="software-year">(2021)</span></p>
            <p class="software-desc">Interactive exploration of omics datasets for quality assessment and biological trend discovery.</p>
            <p class="software-links">
              <a class="software-link" href="omicloupe/index.html" target="_blank" rel="noopener noreferrer">Info</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://omicloupe.serve.scilifelab.se/" target="_blank" rel="noopener noreferrer">Live app</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://github.com/ComputationalProteomics/OmicLoupe" target="_blank" rel="noopener noreferrer">GitHub</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://doi.org/10.1186/s12859-021-04043-5" target="_blank" rel="noopener noreferrer">Paper</a>
            </p>
          </article>
        </li>
        <li class="software-card">
          <article class="software-card-inner">
            <p class="software-title">NormalyzerDE <span class="software-year">(2019)</span></p>
            <p class="software-desc">Normalization-method evaluation and differential-expression analysis for omics expression data.</p>
            <p class="software-links">
              <a class="software-link" href="https://normalyzerde.serve.scilifelab.se/" target="_blank" rel="noopener noreferrer">Live server</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="/NormalyzerDE/" target="_blank" rel="noopener noreferrer">Docs</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://github.com/ComputationalProteomics/NormalyzerDE" target="_blank" rel="noopener noreferrer">GitHub</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://doi.org/10.1021/acs.jproteome.8b00523" target="_blank" rel="noopener noreferrer">Paper</a>
            </p>
          </article>
        </li>
        <li class="software-card">
          <article class="software-card-inner">
            <p class="software-title">Dinosaur <span class="software-year">(2016)</span></p>
            <p class="software-desc">Open-source MS1 peptide feature detector for isotope patterns in LC-MS/HPLC-MS data.</p>
            <p class="software-links">
              <a class="software-link" href="https://github.com/fickludd/dinosaur/" target="_blank" rel="noopener noreferrer">GitHub</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://doi.org/10.1021/acs.jproteome.6b00016" target="_blank" rel="noopener noreferrer">Paper</a>
            </p>
          </article>
        </li>
        <li class="software-card">
          <article class="software-card-inner">
            <p class="software-title">DIANA <span class="software-year">(2014)</span></p>
            <p class="software-desc">Algorithm and software tools for DIA-MS (data-independent acquisition) analysis.</p>
            <p class="software-links">
              <a class="software-link" href="diana/index.html" target="_blank" rel="noopener noreferrer">Info</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://github.com/flevander/diana" target="_blank" rel="noopener noreferrer">GitHub</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://doi.org/10.1093/bioinformatics/btu686" target="_blank" rel="noopener noreferrer">Paper</a>
            </p>
          </article>
        </li>
        <li class="software-card">
          <article class="software-card-inner">
            <p class="software-title">Normalyzer <span class="software-year">(2014)</span></p>
            <p class="software-desc">Deprecated predecessor of NormalyzerDE.</p>
            <p class="software-links">
              <a class="software-link" href="https://normalyzerde.serve.scilifelab.se/" target="_blank" rel="noopener noreferrer">NormalyzerDE server</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://doi.org/10.1021/pr401264n" target="_blank" rel="noopener noreferrer">Paper</a>
            </p>
          </article>
        </li>
        <li class="software-card">
          <article class="software-card-inner">
            <p class="software-title">SRM QC <span class="software-year">(2013)</span></p>
            <p class="software-desc">Tool for tracking SRM instrument performance and generating QC reports.</p>
            <p class="software-links">
              <a class="software-link" href="srmqc/index.html" target="_blank" rel="noopener noreferrer">Info</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://doi.org/10.1016/j.jprot.2013.03.029" target="_blank" rel="noopener noreferrer">Paper</a>
            </p>
          </article>
        </li>
        <li class="software-card">
          <article class="software-card-inner">
            <p class="software-title">FEvER <span class="software-year">(2012)</span></p>
            <p class="software-desc">Method and software for functional interpretation of differential quantitative proteomics data.</p>
            <p class="software-links">
              <a class="software-link" href="fever/index.html" target="_blank" rel="noopener noreferrer">Info</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://doi.org/10.1021/pr300038b" target="_blank" rel="noopener noreferrer">Paper</a>
            </p>
          </article>
        </li>
        <li class="software-card">
          <article class="software-card-inner">
            <p class="software-title">Anubis <span class="software-year">(2012)</span></p>
            <p class="software-desc">Automated peptide detection and quantification in SRM data.</p>
            <p class="software-links">
              <a class="software-link" href="anubis/index.html" target="_blank" rel="noopener noreferrer">Info</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://github.com/fickludd/anubis/" target="_blank" rel="noopener noreferrer">GitHub</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://doi.org/10.1021/pr300256x" target="_blank" rel="noopener noreferrer">Paper</a>
            </p>
          </article>
        </li>
        <li class="software-card">
          <article class="software-card-inner">
            <p class="software-title">Proteios Software Environment <span class="software-year">(2009)</span></p>
            <p class="software-desc">Multi-user platform for analysis and management of proteomics data.</p>
            <p class="software-links">
              <a class="software-link" href="https://www.proteios.org/" target="_blank" rel="noopener noreferrer">proteios.org</a>
              <span aria-hidden="true">•</span>
              <a class="software-link" href="https://doi.org/10.1021/pr900189c" target="_blank" rel="noopener noreferrer">Paper</a>
            </p>
          </article>
        </li>
      </ul>
    </section>

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        Computational Proteomics Group
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        <a href="https://www.immun.lth.se/" target="_blank" rel="noopener noreferrer">Department of Immunotechnology</a>
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