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Table 1 Software for the three basic steps of molecular formula identification using isotope patterns

From: Computational mass spectrometry for small molecules

Decomposing monoisotopic peaks
Decomp[100, 101] for arbitrary alphabets of elements
  requires only little memory
  swift in practice
SIRIUS[102], [103] implementing Decomp approach for MS
  decomposing real-valued masses
“Seven GoldenRules” [104] to filter molecular formulas
Simulating isotope patterns
IsoPro[105] multinomial expansion to predict “center masses”
  memory- and time-consuming
Mercury[106] pruning by probability thresholds and/ormass range
  reduced memory and time consumption
  reduced accuracy of the predictions
Emass[107] &SIRIUS[102] iterative (stepwise) computation of isotopepattern
  probability-weighted center masses
  probabilities and masses are updated as atomsare added
IsoDalton[108] models the folding procedure as a Markovprocess
BRAIN[109] Newton-Girard theorem and Vietes formulae to calculate intensities and masses
Fourier[110] 2D Fast Fourier Transform that splits up thecalculation in a coarse and a fine structure
  running time improvement for large compounds
Scoring candidate compounds
SigmaFit commercial software by Bruker Daltonics
SIRIUS[102] Bayesian statistics for scoring intensities andmasses of the isotope pattern
MZmine[111] simple scoring based only on intensities
  1. *Recommended tools.