{ "_id": "6a102467acfb0bcc41c8dbef", "Package": "wrTopDownFrag", "Title": "Internal Fragment Identification from Top-Down Mass Spectrometry", "Version": "1.0.4", "Authors@R": "person(\"Wolfgang\", \"Raffelsberger\", email = \"w.raffelsberger@unistra.fr\", role = c(\"aut\", \"cre\"))", "Author": "Wolfgang Raffelsberger [aut, cre]", "Maintainer": "Wolfgang Raffelsberger ", "Description": "Top-Down mass spectrometry aims to identify entire\nproteins as well as their (post-translational) modifications or\nions bound (eg Chen et al (2018)\n). The pattern of internal\nfragments (Haverland et al (2017)\n) may reveal important\ninformation about the original structure of the proteins\nstudied (Skinner et al (2018) and\nLi et al (2018) ). However, the number\nof possible internal fragments gets huge with longer proteins\nand subsequent identification of internal fragments remains\nchallenging, in particular since the the accuracy of\nmeasurements with current mass spectrometers represents a\nlimiting factor. This package attempts to deal with the\ncomplexity of internal fragments and allows identification of\nterminal and internal fragments from deconvoluted\nmass-spectrometry data.", "License": "GPL-3", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 09:35:31 UTC", "User": "root" }, "Repository": "https://wraff.r-universe.dev", "Date/Publication": "2025-04-21 08:10:02 UTC", "RemoteUrl": "https://github.com/cran/wrTopDownFrag", "RemoteRef": "HEAD", "RemoteSha": "fe1e8354e5111adcda66ac407f88577764e95850", "MD5sum": "c4364ef6fce1703fecd92453565d8b89", "_user": "wraff", "_type": "src", "_file": "wrTopDownFrag_1.0.4.tar.gz", "_fileid": "cf4687d039434b8cef6e00f4926dacaf752c39bd66c94ea14a6b3983afd4e224", "_filesize": 473878, "_sha256": "cf4687d039434b8cef6e00f4926dacaf752c39bd66c94ea14a6b3983afd4e224", "_created": "2026-05-22T09:35:31.000Z", "_published": "2026-05-22T09:39:51.342Z", "_distro": "noble", "_jobs": 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"topics": [ ".chColNa" ] }, { "page": "dot-checkModTy", "title": "Check Modification Type", "topics": [ ".checkModTy" ] }, { "page": "dot-countLET", "title": "Count Letters", "topics": [ ".countLET" ] }, { "page": "dot-countModif", "title": "Count For All Proteins The Occurance Of Modification Types", "topics": [ ".countModif" ] }, { "page": "dot-CtermPepCut", "title": "Make Named Character Vector Of Sequential C-Terminal Fragments", "topics": [ ".CtermPepCut" ] }, { "page": "dot-evalIsoFra", "title": "Evaluate Selected Lines Of PepTab", "topics": [ ".evalIsoFra" ] }, { "page": "dot-exNamesTyDeList", "title": "Reorganize List Of Peptide Fragments To Matrix", "topics": [ ".exNamesTyDeList" ] }, { "page": "dot-multMatByColNa", "title": "Multiply Values Of Matrix By Its Colnames And Sum By Row", "topics": [ ".multMatByColNa" ] }, { "page": "dot-NtermPepCut", "title": "Make Named Character Vector Of Sequential C-Terminal Fragments", "topics": [ ".NtermPepCut" ] }, { "page": 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}, { "page": "combinatIntTable", "title": "Planing For Making All Multiplicative Combinations", "topics": [ "combinatIntTable" ] }, { "page": "corInDelShift", "title": "Corrective Values For Random Sequences For In/Dels", "topics": [ "corInDelShift" ] }, { "page": "corMutShift", "title": "Corrective Values For Random Sequences For Mutations", "topics": [ "corMutShift" ] }, { "page": "countChildrenParent", "title": "Identify Children/Parent Settings As a+b=c", "topics": [ "countChildrenParent" ] }, { "page": "countPotModifAAs", "title": "Make Table With Counts of Potential Modification Sites", "topics": [ "countPotModifAAs" ] }, { "page": "evalIsoFragm", "title": "Evaluate Selected Lines Of PepTab (iso-mass) For Preferential Cutting Sites", "topics": [ "evalIsoFragm" ] }, { "page": "fragmentSeq", "title": "Fragment Protein Or Peptide Sequence", "topics": [ "fragmentSeq" ] }, { "page": "identifFixedModif", "title": "Identify Fixed Modifications", "topics": [ "identifFixedModif" ] }, { "page": "identifVarModif", "title": "Idenitfy Variable Modifications", "topics": [ "identifVarModif" ] }, { "page": "identifyPepFragments", "title": "Identify terminal and internal protein/peptide-fragments as matches to experimental MS-peaks", "topics": [ "identifyPepFragments" ] }, { "page": "makeFragments", "title": "Make Terminal And Internal Fragments From Proteins", "topics": [ "makeFragments" ] }, { "page": "modifFragmTabOutput", "title": "Change fragment identification output format (for biologists)", "topics": [ "modifFragmTabOutput" ] }, { "page": "plotFragmLoc", "title": "Plot Identified Fragments Relative To Their Location", "topics": [ "plotFragmLoc" ] }, { "page": "plotMgfLike", "title": "Draw simplified (deconvoluted) spectrum of mgf type and highlight peaks with matches found to theoretical data", "topics": [ "plotMgfLike" ] }, { "page": "plotNTheor", "title": "Plot the number of theoretical random fragments", "topics": [ "plotNTheor" ] }, { "page": "plotPrefFragPat", 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