{
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  "Package": "mspms",
  "Type": "Package",
  "Title": "Tools for the analysis of MSP-MS data",
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  "Authors@R": "person(\"Charlie\", \"Bayne\", email = \"baynec2@gmail.com\",\nrole = c(\"aut\", \"cre\"),comment=c(ORCID=\"0000-0003-1870-5298\"))",
  "Description": "This package provides functions for the analysis of data\ngenerated by the multiplex substrate profiling by mass\nspectrometry for proteases (MSP-MS) method. Data exported from\nupstream proteomics software is accepted as input and\nsubsequently processed for analysis. Tools for statistical\nanalysis, visualization, and interpretation of the data are\nprovided.",
  "License": "MIT + file LICENSE",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:02 UTC",
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  "Author": "Charlie Bayne [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-1870-5298>)",
  "Maintainer": "Charlie Bayne <baynec2@gmail.com>",
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    "plot_qc_check",
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    "plot_volcano",
    "prepare_diann",
    "prepare_fragpipe",
    "prepare_pd",
    "prepare_peaks",
    "prepare_sage",
    "process_qf"
  ],
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      "title": "all_possible_8mers_from_228_library All possible 8mers from the standard (as of 26April2024) 228 MSP-MS peptide library (This is equivalent to the result of mspms::calculate_all_cleavages(mspms::peptide_library$real_cleavage_seq,n=4)) vector of the 14 AA peptides used in the library.",
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      "rows": 4142,
      "table": true,
      "tojson": true
    },
    {
      "name": "mspms_tidy_data",
      "title": "mspms_tidy_data A tibble containing tidy data derived from QFeatures object",
      "object": "mspms_tidy_data",
      "class": [
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        "tbl",
        "data.frame"
      ],
      "fields": [
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        "cleavage_seq",
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        "peptide_type",
        "library_id",
        "library_match_sequence",
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      ],
      "rows": 24852,
      "table": true,
      "tojson": true
    },
    {
      "name": "peaks_prepared_data",
      "title": "peaks_prepared_data A QFeatures object prepared from PEAKS data of cathepsin data/.",
      "object": "peaks_prepared_data",
      "class": [
        "QFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "peptide_library",
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      "class": [
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        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "library_id",
        "library_match_sequence",
        "library_real_sequence"
      ],
      "rows": 228,
      "table": true,
      "tojson": true
    },
    {
      "name": "processed_qf",
      "title": "processed_qf A QFeatures object prepared from PEAKS data of Cathepsin data that has been processed (imputation/normalization)",
      "object": "processed_qf",
      "class": [
        "QFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "all_possible_8mers_from_228_library",
      "title": "all_possible_8mers_from_228_library All possible 8mers from the standard (as of 26April2024) 228 MSP-MS peptide library (This is equivalent to the result of mspms::calculate_all_cleavages(mspms::peptide_library$real_cleavage_seq,n=4)) vector of the 14 AA peptides used in the library.",
      "topics": [
        "all_possible_8mers_from_228_library"
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    },
    {
      "page": "calculate_all_cleavages",
      "title": "calculate_all_cleavages calculate all possible cleavages for a defined peptide library containing peptides of the same length.",
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        "calculate_all_cleavages"
      ]
    },
    {
      "page": "check_file_is_valid_diann",
      "title": "check_file_is_valid_diann Check to make sure the input data looks like the expected DIA-NN output file.",
      "topics": [
        "check_file_is_valid_diann"
      ]
    },
    {
      "page": "check_file_is_valid_fragpipe",
      "title": "check_file_is_valid_fragpipe Check to make sure the input data looks like the expected FragPipe file.",
      "topics": [
        "check_file_is_valid_fragpipe"
      ]
    },
    {
      "page": "check_file_is_valid_pd",
      "title": "check_file_is_valid_pd Check to make sure the input data looks like the expected ProteomeDiscoverer file.",
      "topics": [
        "check_file_is_valid_pd"
      ]
    },
    {
      "page": "colData",
      "title": "colData A tibble containing the colData associated with an experiment to proc",
      "topics": [
        "colData"
      ]
    },
    {
      "page": "generate_report",
      "title": "generate_report",
      "topics": [
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      ]
    },
    {
      "page": "limma_stats",
      "title": "limma_stats",
      "topics": [
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    },
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      "title": "log2fc_t_test",
      "topics": [
        "log2fc_t_test"
      ]
    },
    {
      "page": "log2fc_t_test_data",
      "title": "log2fc_t_test_data A tibble containing the results of t-tests and log2fc compared to time 0 14,497 × 19",
      "topics": [
        "log2fc_t_test_data"
      ]
    },
    {
      "page": "mspms_tidy",
      "title": "mspms_tidy Convert a SummarizedExperiment object within a QFeatures object into a tidy tibble.",
      "topics": [
        "mspms_tidy"
      ]
    },
    {
      "page": "mspms_tidy_data",
      "title": "mspms_tidy_data A tibble containing tidy data derived from QFeatures object",
      "topics": [
        "mspms_tidy_data"
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    },
    {
      "page": "peaks_prepared_data",
      "title": "peaks_prepared_data A QFeatures object prepared from PEAKS data of cathepsin data/.",
      "topics": [
        "peaks_prepared_data"
      ]
    },
    {
      "page": "peptide_library",
      "title": "peptide_library",
      "topics": [
        "peptide_library"
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    },
    {
      "page": "plot_all_icelogos",
      "title": "plot_all_icelogos",
      "topics": [
        "plot_all_icelogos"
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    },
    {
      "page": "plot_cleavages_per_pos",
      "title": "plot_cleavages_per_pos",
      "topics": [
        "plot_cleavages_per_pos"
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    {
      "page": "plot_heatmap",
      "title": "plot_heatmap",
      "topics": [
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      "page": "plot_icelogo",
      "title": "plot_icelogo",
      "topics": [
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    {
      "page": "plot_nd_peptides",
      "title": "plot_nd_peptides",
      "topics": [
        "plot_nd_peptides"
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    },
    {
      "page": "plot_pca",
      "title": "plot_pca",
      "topics": [
        "plot_pca"
      ]
    },
    {
      "page": "plot_qc_check",
      "title": "plot_qc_check plot the the percentage of the peptide library undetected in each sample per each sample group.",
      "topics": [
        "plot_qc_check"
      ]
    },
    {
      "page": "plot_time_course",
      "title": "plot_time_course",
      "topics": [
        "plot_time_course"
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    },
    {
      "page": "plot_volcano",
      "title": "plot_volcano",
      "topics": [
        "plot_volcano"
      ]
    },
    {
      "page": "prepare_diann",
      "title": "prepare_diann",
      "topics": [
        "prepare_diann"
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    },
    {
      "page": "prepare_fragpipe",
      "title": "prepare_fragpipe",
      "topics": [
        "prepare_fragpipe"
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    },
    {
      "page": "prepare_pd",
      "title": "prepare_pd Prepare a label free quantification file exported from Proteome Discoverer for subsequent mspms analysis.",
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        "prepare_pd"
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    },
    {
      "page": "prepare_peaks",
      "title": "Prepare PEAKS label-free quantification data for MSP-MS analysis",
      "topics": [
        "prepare_peaks"
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    },
    {
      "page": "prepare_sage",
      "title": "prepare_sage Prepare a label free quantification file exported from Sage for subsequent mspms analysis.",
      "topics": [
        "prepare_sage"
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    },
    {
      "page": "process_qf",
      "title": "process_qf",
      "topics": [
        "process_qf"
      ]
    },
    {
      "page": "processed_qf",
      "title": "processed_qf A QFeatures object prepared from PEAKS data of Cathepsin data that has been processed (imputation/normalization)",
      "topics": [
        "processed_qf"
      ]
    }
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      "filename": "mspms_vignette.html",
      "title": "mspms_vignette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "r BiocStyle::Biocpkg(\"mspms\")",
        "Introduction",
        "Quickstart",
        "Overview",
        "Pre-processing data",
        "A note on colData",
        "PEAKS",
        "Fragpipe",
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        "Data Processing",
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