Internal Fragment Identification from Top-Down Mass Spectrometry

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Documentation for package ‘wrTopDownFrag’ version 1.0.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

.chargeCatchingAA	Cite Charge Catching Amino-Acids
.chColNa	Check Column Names from Matrix Or data.frame
.checkModTy	Check Modification Type
.countLET	Count Letters
.countModif	Count For All Proteins The Occurance Of Modification Types
.CtermPepCut	Make Named Character Vector Of Sequential C-Terminal Fragments
.evalIsoFra	Evaluate Selected Lines Of PepTab
.exNamesTyDeList	Reorganize List Of Peptide Fragments To Matrix
.multMatByColNa	Multiply Values Of Matrix By Its Colnames And Sum By Row
.NtermPepCut	Make Named Character Vector Of Sequential C-Terminal Fragments
.parCombinateAllAndSum	Multiprocessor Version For Full Combinatorial And Cumulative Values
.prefFragPattern	Return data.frame with pattern of perferential fragmentation sites
.singleSpecModif	Add Single Specific Modifications
.termPepCut	Make Named Character Vector Of Sequential Terminal Fragments
AAfragSettings	Settings For AA Fragmentation
addMassModif	Add Modifications To Peptide Mass
checkModTy	Check & complete mixed of variable and fixed modifications
combinateAllAndSum	Full Combinatorial And Cumulative Values
combinatIntTable	Planing For Making All Multiplicative Combinations
corInDelShift	Corrective Values For Random Sequences For In/Dels
corMutShift	Corrective Values For Random Sequences For Mutations
countChildrenParent	Identify Children/Parent Settings As a+b=c
countPotModifAAs	Make Table With Counts of Potential Modification Sites
evalIsoFragm	Evaluate Selected Lines Of PepTab (iso-mass) For Preferential Cutting Sites
fragmentSeq	Fragment Protein Or Peptide Sequence
identifFixedModif	Identify Fixed Modifications
identifVarModif	Idenitfy Variable Modifications
identifyPepFragments	Identify terminal and internal protein/peptide-fragments as matches to experimental MS-peaks
makeFragments	Make Terminal And Internal Fragments From Proteins
modifFragmTabOutput	Change fragment identification output format (for biologists)
plotFragmLoc	Plot Identified Fragments Relative To Their Location
plotMgfLike	Draw simplified (deconvoluted) spectrum of mgf type and highlight peaks with matches found to theoretical data
plotNTheor	Plot the number of theoretical random fragments
plotPrefFragPat	plot preferential fragmenation pattern Plot preferential fragmenation pattern equivalent to Fig 1b of Haverland et al 2017 (J Am Soc Mass Spectrom)
randMassByMut	Make decoy mass by full randomization
randMassByStochastic	Make Decoy Mass By Full Randomization
scoreChargeCatch	Scoring Of Charge Catching Potential For Peptides
scoreFragments	Scoring For Single Protein : Individual Components
scorePrefFrag	Identifcation and scoring of preferential cuting sites
scoreProteinFragments	Scoring Of Identifications (For Multi-Protein Queries)