MSbox
Mass Spectrometry Tools
Common mass spectrometry tools described in John Roboz (2013)
Common mass spectrometry tools for minimalist MS users.
Installation
## stable version v1.1.1install.packages('MSbox')Functions
- Check element isotopes
examples:
E_iso('C') # element symbol, case insensitiveE_iso('Carbon') # element full name, case insensitiveE_iso('carBon') # element full name, case insensitive- Get formula, structure and extra molecular information
examples:
formula('malic acid')formula(c('malic acid', 'citric acid', 'tartaric acid'))- Calculate monoisitopic mass
example:
mass('C7H6O1') # case insensitivemass(c('K1', 'C5H8', 'nA20')) # vector input- Calculate exact m/z values
example:
mz('C7H7O4', z = -1) # case insensitivemz(c('C7H7O4', 'c1'), z = -1) # vector input- Calculate the mass accuracy of measured m/z
examples:
ppm(155.03383, 155.03388) # with m/z valueppm(155.03383, .03388) # lazy input when the integer parts of m and t are the sameppm(155.03383, .03388, lazy = F) # lazy input disabledppm(155.03384, mz('C7H7O4', z = 1)) # with ion formula- Calculate isotope labelled molecular mass
example
Iso_mass(F = 'C7H6O4', iso = '[13]C2[2]H3') # Two 13C and three 2H are labled. Case insensitive.- Calculate isotope labelled m/z
example
Iso_mz(F = 'C7H6O4', iso = '[13]C2[2]H3', z = 1) # Two 13C and three 2H are labled. Case insensitive.- Check if an m/z value originates from possible contaminant
examples
contam(33.0335, ppm = 10, mode = '+')contam(44.998, ppm = 10, mode = '-')- Calculate common adduct ions in pos or neg ion mode
examples
adduct('C1H4',mode = '-') # case insensitiveadduct('C1H4',mode = '+') # case insensitive