Mass Decomposition of Isotope Patterns — decomposeIsotopes • Rdisop

Calculate the elementary compositions from an exact mass or isotope pattern, obtained e.g. by FTICR or TOF mass spectrometers.

Usage

decomposeIsotopes(
  masses,
  intensities,
  ppm = 2,
  mzabs = 1e-04,
  elements = NULL,
  filter = NULL,
  z = 0,
  maxisotopes = 10,
  minElements = "C0",
  maxElements = "C999999"
)

decomposeMass(
  mass,
  ppm = 2,
  mzabs = 1e-04,
  elements = NULL,
  filter = NULL,
  z = 0,
  maxisotopes = 10,
  minElements = "C0",
  maxElements = "C999999"
)

isotopeScore(molecule, masses, intensities)

Arguments

masses: A vector of masses (or m/z values) of an isotope cluster.
intensities: Absolute or relative intensities of the masses peaks.
ppm: Allowed deviation of hypotheses from given mass.
mzabs: Absolute deviation in Dalton (mzabs and ppm will be added).
elements: List of allowed chemical elements, defaults to CHNOPS. See initializeElements.
filter: NYI, will be a selection of DU, DBE and Nitrogen rules.
z: Charge z of m/z peaks for calculation of real mass, keep z=0 for auto-detection.
maxisotopes: Maximum number of isotopes shown in the resulting molecules.
minElements: Molecular formula, defining lower boundaries of allowed elements.
maxElements: Molecular formula, defining upper boundaries of allowed elements.
mass: A single mass (or m/z value).
molecule: An initialized molecule as returned by getMolecule() or the decomposeMass() and decomposeIsotopes() functions.

Value

A list of molecules, which contain the sub-lists `formulas` potential formulas, `exactmass` exact mass of each hypothesis (not monoisotopic), `score` calculated score, `isotopes` a list of isotopes.

Details

Sum formulas are calculated which explain the given mass or isotope pattern.

References

For a description of the underlying IMS see citation("Rdisop")

Author

Steffen Neumann <sneumann@IPB-Halle.DE>

Examples

# query some measurement values from a Glutamate peak which will return two
# suggested/potential sum formulas
m <- c(147.0529, 148.0563, 149.0612)
i <- c(0.91, 0.06, 0.01)
mol <- decomposeIsotopes(m, i, maxisotopes = 3)
getFormula(mol)
#> [1] "C5H9NO4"  "C3H17P2S"

# Rdisop returns the scores (how well does the exact data match the measured 
# data) in a normalized fashion, but you can calculate the raw scores
getScore(mol)
#> [1] 1.000000e+00 1.911174e-73
isotopeScore(mol, m, i)
#> [[1]]
#> [1] 3.799128e-10
#> 

# using a 5 mDa window, the number of potential candidates is increased to 26
getFormula(decomposeIsotopes(m, i, mzabs = 0.005))
#>  [1] "C5H9NO4"    "C3H7N4O3"   "C6H5N5"     "C3H17P2S"   "C8H7N2O"   
#>  [6] "CH12N2O4P"  "C2H11O7"    "C3H15O2S2"  "C4H10N3OP"  "C6H13P2"   
#> [11] "C2H8N6P"    "C6H12O2P"   "C2H13NO4S"  "CH5N7O2"    "C2H16NP3"  
#> [16] "H19O2S3"    "CH13N3OS2"  "C2H15NO2P2" "C6H11O2S"   "C2H14NO2PS"
#> [21] "CH134"      "H21P2S2"    "C3H9N5S"    "H9N3O6"     "H11N4O3S"  
#> [26] "H13N4OP2"  

# elemental ranges can be specified to affect the result
# use maxElements to exclude all of the above suggestions containing more 
# than one S and/or one P.
getFormula(decomposeIsotopes(m, i, mzabs = 0.005, maxElements = "S1P1"))
#>  [1] "C5H9NO4"    "C3H7N4O3"   "C6H5N5"     "C8H7N2O"    "CH12N2O4P" 
#>  [6] "C2H11O7"    "C4H10N3OP"  "C2H8N6P"    "C6H12O2P"   "C2H13NO4S" 
#> [11] "CH5N7O2"    "C6H11O2S"   "C2H14NO2PS" "CH134"      "C3H9N5S"   
#> [16] "H9N3O6"     "H11N4O3S"