R/fragments-utils.R

In rformassspectrometry/PSM: Handling and Managing Peptide Spectrum Matches

##' Returns a `data.frame` of amino acid properties: `AA`,
##' `ResidueMass`, `Abbrev3`, `ImmoniumIonMass`, `Name`,
##' `Hydrophobicity`, `Hydrophilicity`, `SideChainMass`, `pK1`, `pK2`
##' and `pI`.
##'
##' @title Amino acids
##'
##' @return `data.frame`
##'
##' @author Laurent Gatto
##'
##' @export
##'
##' @examples
##'
##' getAminoAcids()
getAminoAcids <- function()
    data.frame(AA = c("peg","A","R","N","D","C","E",
                      "Q","G","H","I","L", "K","M","F",
                      "P","S","T","W","Y","V"),
               ResidueMass = c(44.00000,
                               71.03711,  156.10111, 114.04293, 115.02694,
                               103.00919, 129.04259, 128.05858, 57.02146,
                               137.05891, 113.08406, 113.08406, 128.09496,
                               131.04049, 147.06841, 97.05276,  87.03203,
                               101.04768, 186.07931, 163.06333, 99.06841),
               Abbrev3 = c(NA,
                           "Ala", "Arg", "Asn", "Asp", "Cys",
                           "Glu", "Gln", "Gly", "His", "Ile",
                           "Leu", "Lys", "Met", "Phe", "Pro",
                           "Ser", "Thr", "Trp", "Tyr", "Val"),
               ImmoniumIonMass = c(NA,
                                   44.05003,  129.11400, 87.05584,  88.03986,  76.02210,
                                   102.05550, 101.07150, 30.03438,  110.07180, 86.09698,
                                   86.09698,  101.10790, 104.05340, 120.08130, 70.06568,
                                   60.04494,  74.06059,  159.09220, 136.07620, 72.08133),
               Name = c("Polyethylene glycol",
                        "Alanine",    "Arginine",      "Asparagine", "Aspartic acid",
                        "Cysteine",   "Glutamic acid", "Glutamine",  "Glycine",
                        "Histidine",  "Isoleucine",    "Leucine",    "Lysine",
                        "Methionine", "Phenylalanine", "Proline",    "Serine",
                        "Threonine",  "Tryptophan",    "Tyrosine",   "Valine"),
               ## The hydrophobicity values are from JACS, 1962, 84: 4240-4246. (C. Tanford)
               Hydrophobicity = c(NA, 0.62, -2.53, -0.78, -0.9, 0.29,
                                  -0.74, -0.85, 0.48, -0.4, 1.38, 1.06, -1.5, 0.64, 1.19,
                                  0.12, -0.18, -0.05, 0.81, 0.26, 1.08),
               ## The hydrophilicity values are from PNAS, 1981, 78:3824-3828 (T.P.Hopp & K.R.Woods)
               Hydrophilicity = c(NA, -0.5, 3, 0.2, 3, -1, 3, 0.2, 0,
                                  -0.5, -1.8, -1.8, 3, -1.3, -2.5, 0, 0.3, -0.4, -3.4,
                                  -2.3, -1.5),
               SideChainMass = c(NA, 15, 101, 58, 59, 47, 73, 72,
                                 1, 82, 57, 57, 73, 75, 91, 42, 31, 45, 130, 107, 43),
               ## CRC Handbook of Chemistry and Physics, 66th ed., CRC Press, Boca Raton, Florida (1985).
               ## R.M.C. Dawson, D.C. Elliott, W.H. Elliott, K.M. Jones, Data for Biochemical Research 3rd ed., Clarendon Press Oxford
               pK1 = c(NA, 2.35, 2.18, 2.18, 1.88, 1.71, 2.19,
                       2.17, 2.34, 1.78, 2.32, 2.36, 2.2, 2.28, 2.58,
                       1.99, 2.21, 2.15, 2.38, 2.2, 2.29),
               pK2 = c(NA, 9.87, 9.09, 9.09, 9.6, 10.78, 9.67, 9.13,
                       9.6, 8.97, 9.76, 9.6, 8.9, 9.21, 9.24, 10.6, 9.15,
                       9.12, 9.39, 9.11, 9.74),
               pI = c(NA, 6.11, 10.76, 10.76, 2.98, 5.02, 3.08,
                      5.65, 6.06, 7.64, 6.04, 6.04, 9.47, 5.74, 5.91,
                      6.3, 5.68, 5.6, 5.88, 5.63, 6.02))


##' Returns a `double` of used atomic mass.
##'
##' @title Atomic mass.
##'
##' @return A named `double`.
##'
##' @author Sebastian Gibb
##'
##' @export
##'
##' @examples
##' getAtomicMass()
getAtomicMass <- function() {
    ## taken from:
    ## http://www.chem.ualberta.ca/~massspec/atomic_mass_abund.pdf
    c(H = 1.007825,
      C = 12,
      N = 14.003074,
      O = 15.994915,
      p = 1.007276)
}