{ "_id": "6a1fe9e8b401979e7343e457", "Package": "msPurity", "Type": "Package", "Title": "Automated Evaluation of Precursor Ion Purity for Mass\nSpectrometry Based Fragmentation in Metabolomics", "Version": "1.39.0", "Date": "2025-03-10", "Authors@R": "c(\nperson(given = \"Thomas N.\", family = \"Lawson\",\nemail = \"thomas.nigel.lawson@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-5915-7980\")),\nperson(given = \"Ralf\", family = \"Weber\", role = \"ctb\"),\nperson(given = \"Martin\", family = \"Jones\", role = \"ctb\"),\nperson(given = \"Julien\", family = \"Saint-Vanne\", role = \"ctb\"),\nperson(given = \"Andris\", family = \"Jankevics\", role = \"ctb\"),\nperson(given = \"Ossama\", family = \"Edbali\",\nemail = \"o.edbali@bham.ac.uk\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-0132-8668\")),\nperson(given = \"Mark\", family = \"Viant\", role = \"ths\"),\nperson(given = \"Warwick\", family = \"Dunn\", role = \"ths\"))", "URL": "https://github.com/computational-metabolomics/msPurity/", "Description": "msPurity R package was developed to: 1) Assess the\nspectral quality of fragmentation spectra by evaluating the\n\"precursor ion purity\". 2) Process fragmentation spectra. 3)\nPerform spectral matching. What is precursor ion purity? -What\nwe call \"Precursor ion purity\" is a measure of the contribution\nof a selected precursor peak in an isolation window used for\nfragmentation. The simple calculation involves dividing the\nintensity of the selected precursor peak by the total intensity\nof the isolation window. When assessing MS/MS spectra this\ncalculation is done before and after the MS/MS scan of interest\nand the purity is interpolated at the recorded time of the\nMS/MS acquisition. Additionally, isotopic peaks can be removed,\nlow abundance peaks are removed that are thought to have\nlimited contribution to the resulting MS/MS spectra and the\nisolation efficiency of the mass spectrometer can be used to\nnormalise the intensities used for the calculation.", "Encoding": "UTF-8", "License": "GPL-3 + file LICENSE", "BugReports": "https://github.com/computational-metabolomics/msPurity/issues/new", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "biocViews": "MassSpectrometry, Metabolomics, Software", "Collate": "'all-generics.R' 'averaging.R' 'combineAnnotations.R'\n'create-database.R' 'createDatabase.R' 'flag-filter-remove.R'\n'iw-norm.R' 'matching-algs.R' 'meta_extract.R' 'msPurity.R'\n'pcalc.R' 'purityA-0-class.R' 'purityA-av-spectra.R'\n'purityA-constructor.R' 'purityA-create-msp.R'\n'purityA-filter-frag-spectra.R' 'purityA-frag4feature.R'\n'purityA-validate.R' 'purityD-class.R' 'purityD-constructor.R'\n'purityD-av-spectra.R' 'purityD-dims-purity.R'\n'purityD-fileList.R' 'purityD-filterp.R' 'purityD-subtract.R'\n'purityD-writeOut.R' 'purityX-class.R' 'purityX-constructor.R'\n'spectral-matching.R' 'spectralMatching.R' 'splinepurity.R'", "Config/pak/sysreqs": "libicu-dev libnetcdf-dev libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:43:35 UTC", "RemoteUrl": "https://github.com/bioc/msPurity", "RemoteRef": "HEAD", "RemoteSha": "977fbfa9e2f3a5f8f680c4061556eb1293471276", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 08:19:26 UTC", "User": "root" }, "Author": "Thomas N. Lawson [aut, cre] (ORCID:\n),\nRalf Weber [ctb],\nMartin Jones [ctb],\nJulien Saint-Vanne [ctb],\nAndris Jankevics [ctb],\nOssama Edbali [ctb] (ORCID: ),\nMark Viant [ths],\nWarwick Dunn [ths]", "Maintainer": "Thomas N. Lawson ", "MD5sum": "6a660f181c3de44ecd795bffb82245c1", "_user": "bioc", "_type": "src", "_file": "msPurity_1.39.0.tar.gz", "_fileid": "41dfc135ae9b671351397226e04dc7a23ba5796e51fa21445707d182b9ac00fb", "_filesize": 11415283, "_sha256": "41dfc135ae9b671351397226e04dc7a23ba5796e51fa21445707d182b9ac00fb", "_created": "2026-06-03T08:19:26.000Z", "_published": "2026-06-03T08:46:32.554Z", "_jobs": [ { "job": 79251557723, "time": 194, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7379355158" }, { "job": 79251557347, "time": 1052, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7379650210" }, { "job": 79251557279, "time": 836, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7379575819" }, { "job": 79251557350, "time": 579, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7379486538" }, { "job": 79251557283, "time": 996, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7379630759" }, { "job": 79247969963, "time": 1340, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7379287369" }, { "job": 79251557312, "time": 185, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7379351859" }, { "job": 79251557578, "time": 1531, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7379813627" }, { "job": 79251557310, "time": 951, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7379616343" }, { "job": 79251557569, "time": 1184, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7379694285" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26871563737", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/msPurity", "_commit": { "id": "977fbfa9e2f3a5f8f680c4061556eb1293471276", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380215 }, "_maintainer": { "name": "Thomas N. 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{ "page": "subtract-purityD-method", "title": "Using Subtract MZ values based on ppm tolerance and noise ratio", "topics": [ "subtract", "subtract,purityD-method" ] }, { "page": "subtractMZ", "title": "Subtract MZ values based on ppm tolerance and noise ratio", "topics": [ "subtractMZ" ] }, { "page": "validate-purityA-method", "title": "Validate precursor purity predictions using LC-MS and LC-MS/MS dataset", "topics": [ "validate", "validate,purityA-method" ] }, { "page": "writeOut-purityD-method", "title": "Using purityD object, save peaks as text files", "topics": [ "writeOut", "writeOut,purityD-method" ] } ], "_rundeps": [ "askpass", "Biobase", "BiocFileCache", "BiocGenerics", "biocmake", "bit", "bit64", "blob", "cachem", "cli", "codetools", "cpp11", "curl", "DBI", "dbplyr", "dir.expiry", "doSNOW", "dplyr", "farver", "fastcluster", "fastmap", "filelock", "foreach", "generics", "ggplot2", "glue", "gtable", "httr2", "isoband", "iterators", "labeling", "lifecycle", "magrittr", 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Lawson", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "purityA", "Assessing precursor purity of previously acquired MS/MS spectra", "Isolation efficiency", "frag4feature - mapping XCMS features to fragmentation spectra", "filterFragSpectra - filter the fragmentation spectra", "averageAllFragSpectra - average all fragmentation spectra", "averageIntraFragSpectra - average all fragmentation spectra", "averageInterFragSpectra - average all fragmentation spectra", "createMSP - create an MSP file of the fragmentation spectra", "createDatabase - create a spectral database", "spectralMatching - perfroming spectral matching to a spectral library", "purityX", "Assessing anticipated purity of XCMS features from an LC-MS run", "purityD", "Assessing anticipated purity from a DIMS run", "Calculating the anticipated (predicted) purity from a known m/z target list for DIMS", "References" ], "created": "2016-05-20 08:54:13", "modified": "2021-10-05 12:32:34", "commits": 9 }, { "source": "msPurity-spectral-database-vignette.Rmd", "filename": "msPurity-spectral-database-vignette.html", "title": "msPurity spectral database schema", "author": "Thomas N. 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