Mass Spectrometry Tools

Common mass spectrometry tools described in John Roboz (2013) . It allows checking element isotopes, calculating (isotope labelled) exact monoisitopic mass, m/z values and mass accuracy, and inspecting possible contaminant mass peaks, examining possible adducts in electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) ion sources.


CRAN status CRAN downloads

Common mass spectrometry tools for minimalist MS users.

Installation

## stable version v1.1.1
install.packages('MSbox')

Functions

  1. Check element isotopes

examples:

E_iso('C') # element symbol, case insensitive
E_iso('Carbon') # element full name, case insensitive
E_iso('carBon') # element full name, case insensitive
  1. Get formula, structure and extra molecular information

examples:

formula('malic acid')
formula(c('malic acid', 'citric acid', 'tartaric acid'))
  1. Calculate monoisitopic mass

example:

mass('C7H6O1') # case insensitive
mass(c('K1', 'C5H8', 'nA20')) # vector input
  1. Calculate exact m/z values

example:

mz('C7H7O4', z = -1) # case insensitive
mz(c('C7H7O4', 'c1'), z = -1) # vector input
  1. Calculate the mass accuracy of measured m/z

examples:

ppm(155.03383, 155.03388) # with m/z value
ppm(155.03383, .03388) # lazy input when the integer parts of m and t are the same
ppm(155.03383, .03388, lazy = F) # lazy input disabled
ppm(155.03384, mz('C7H7O4', z = 1)) # with ion formula
  1. Calculate isotope labelled molecular mass

example

Iso_mass(F = 'C7H6O4', iso = '[13]C2[2]H3') # Two 13C and three 2H are labled. Case insensitive.
  1. 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.
  1. Check if an m/z value originates from possible contaminant

examples

contam(33.0335, ppm = 10, mode = '+')
contam(44.998, ppm = 10, mode = '-')
  1. Calculate common adduct ions in pos or neg ion mode

examples

adduct('C1H4',mode = '-') # case insensitive
adduct('C1H4',mode = '+') # case insensitive

News

Reference manual

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install.packages("MSbox")

1.4.0 by Yonghui Dong, 4 months ago


https://github.com/YonghuiDong/MSbox


Report a bug at https://github.com/YonghuiDong/MSbox/issues/new


Browse source code at https://github.com/cran/MSbox


Authors: Yonghui Dong


Documentation:   PDF Manual  


GPL-2 license


Imports stringr, crayon, xml2, stats, reshape2, ggplot2, ggfortify, plotly


See at CRAN