Annotate-class: A list with functions usefull for annotating peptide...

In protViz/bibliospec: Reading and Analyzing Mass Spectrometric Search Results

Description

A list with functions usefull for annotating peptide sequences

Methods

addAA(letter1, Monoisotopic, formula = NULL, letter3 = NULL, Average = NULL)

add new amino acid

fragmentBYIonsUpTO(masses, charge = 1, wide = FALSE, genSeries = .self$fragmentIonBY)

generate fragment ions

fragmentIonBY(masses)

compute fragment ions

modifyMass(letter1, Monoisotopic, Average = NULL)

modify mass of existing amino acid

parentIonMass(masses, charge = 2)

get mass of parent ion

parentMassWithLoss(masses, charge, neutrallossMass = NULL, neutrallossName = NULL)

compute parent ion and neutral loss if any

Examples

masses <-c(  71.03711,  71.03711,  71.03711,  71.03711,  71.03711,
   71.03711,  71.03711,  57.02146,  71.03711,  71.03711, 57.02146,  57.02146, 156.10111)
ann <- Annotate()
ann$aaMasses
ann$atomMass
ann$fragmentIonBY(masses)
ann$parentMassWithLoss(masses, 2)
ann$parentMassWithLoss(masses, 2, neutrallossMass =-43.005814,
  neutrallossName = "Citrulline_Ornithine" )
sequence <- "AAADLMTYCDAHACEDPLITPVPTSENPFR"
ann$aa2mass(sequence)
ann$upIonsCharge(ann$fragmentIonBY(masses), charge=2) 
ann$fragmentIonBY(masses)
ann$fragmentBYIonsUpTO(masses)
ann$fragmentBYIonsUpTO(masses ,charge= 2)
res <- ann$fragmentBYIonsUpTO(masses ,charge= 3)
res <- ann$fragmentBYIonsUpTO(masses ,charge= 2, wide=TRUE)
ann$parentIonMass(masses)
ann$psmEasy(1:100,1:20)
ann$parentMassWithLoss(ann$aa2mass(sequence),
                      2,neutrallossMass =-43.005814, neutrallossName= "Citrulline_Ornithine")

protViz/bibliospec documentation built on May 26, 2019, 9:37 a.m.