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  "Title": "Protein Quantification in Mass Spectrometry-Based Proteomics",
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  "Description": "An implementation of the MaxLFQ algorithm by Cox et al.\n(2014) <doi:10.1074/mcp.M113.031591> in a comprehensive\npipeline for processing proteomics data in data-independent\nacquisition mode (Pham et al. 2020\n<doi:10.1093/bioinformatics/btz961>; Pham et al. 2026\n<doi:10.1021/acs.jproteome.5c01038>). It offers additional\noptions for protein quantification using the N most intense\nfragment ions, using all fragment ions, the median polish\nalgorithm by Tukey (1977, ISBN:0201076160), and a robust linear\nmodel. In general, the tool can be used to integrate multiple\nproportional observations into a single quantitative value.",
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        "PG.Genes",
        "PG.ProteinNames"
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      "title": "Creating a list of matrices of fragment ion intensities for all proteins",
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        "create_protein_list"
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    },
    {
      "page": "create_protein_table",
      "title": "Protein quantification for a list of proteins",
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    },
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      "title": "Protein annotation extraction",
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      "title": "The MaxLFQ algorithm",
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      "topics": [
        "long_format_to_iq_format"
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      "title": "The MaxLFQ algorithm for protein quantification",
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        "maxLFQ"
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      "page": "meanInt",
      "title": "The meanInt algorithm for protein quantification",
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      "title": "A wrapper for the R implementation of the median polish algorithm",
      "topics": [
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    },
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