Skip to content

Latest commit

 

History

History
72 lines (47 loc) · 4.97 KB

README.md

File metadata and controls

72 lines (47 loc) · 4.97 KB
Raw

IDSL.SUFA

Developed-by CRAN status Dependencies

A simplified version of the IDSL.UFA package to calculate isotopic profiles and adduct formulas from molecular formulas with no dependency on other R packages for online tools and educational mass spectrometry courses. The IDSL.SUFA package has functions to process user-defined adduct formulas.

Installation

install.packages("IDSL.SUFA")

Workflow

Main functions:

isotopic_profile_molecular_formula_feeder(molecular_formula,
					  peak_spacing = 0,
					  intensity_cutoff = 1,
					  IonPathway = "[M]",
					  UFA_IP_memeory_variables = c(1e30, 1e-12, 100),
					  plotProfile = TRUE,
					  allowedVerbose = TRUE)

formula_adduct_calculator(molecular_formula, IonPathway)

molecular_formula: A molecular formulas

peak_spacing: A maximum space between isotopologues in Da to merge neighboring isotopologues using the satellite clustering merging (SCM) method described in the reference[3].

intensity_cutoff: A minimum intensity threshold for isotopic profiles in percentage.

IonPathway: An ionization pathway (also known as adduct type). Pathways should be like [CoeffM+ADD1-DED1+...] where Coeff should be an integer between 1-9 and ADD1 and DED1 represent gain and loss formulas, respectively. ex: 'IonPathway <- c("[M]+", "[M+H]+", "[2M-Cl]-", "[3M+CO2-H2O+Na-KO2+HCl-NH4]-")'

UFA_IP_memeory_variables: A vector of three variables. Default values are c(1e30, 1e-12, 100) to manage memory usage. UFA_IP_memeory_variables[1] is used to control the overall size of isotopic combinations. UFA_IP_memeory_variables[2] indicates the minimum relative abundance (RA calculated by eq(1) in the reference [2]) of an isotopologue to include in the isotopic profile calculations. UFA_IP_memeory_variables[3] is the maximum elapsed time in seconds to calculate the isotopic profile on the setTimeLimit function of base R.

plotProfile: c(TRUE, FALSE). A TRUE plotProfile generates a spectra plot.

allowedVerbose: c(TRUE, FALSE). A TRUE allowedVerbose provides messages about the flow of the function.

Visit wiki for detailed documentations and tutorials for the list of consistent labeled isotopes, Standard Adduct Type, Definitions of Peak Spacing and Intensity Cutoff

example 1: Isotopic profile of selenomethionine (C5H11NO2Se)

library(IDSL.SUFA)
Isotopic_Profile <- isotopic_profile_molecular_formula_feeder(molecular_formula = "C5H11NO2Se")

Labeled molecular formulas

example 2: Isotopic profile of MBDD-2378 => 2,3,7,8-Tetrabromo(13C12)dibenzo-p-dioxin => 13C12H4Br4O2

library(IDSL.SUFA)
Isotopic_Profile <- isotopic_profile_molecular_formula_feeder(molecular_formula = "[13]C12H4Br4O2", IonPathway = "[M-Br+O]-")

example 3: PFOA (C8HF15O2) loosing carboxylic acid group

library(IDSL.SUFA)
Adduct_Formula <- formula_adduct_calculator(molecular_formula = "C8HF15O2", IonPathway = "[M-HCO2]-")

Visit https://ipc.idsl.me/ to see the isotopic profile calculation interface

Citation

[1] Fakouri Baygi, S., Banerjee S. K., Chakraborty P., Kumar, Y. Barupal, D.K. IDSL.UFA assigns high confidence molecular formula annotations for untargeted LC/HRMS datasets in metabolomics and exposomics. Analytical Chemistry, 2022, 94(39), 13315–13322.

[2] Fakouri Baygi, S., Crimmins, B.S., Hopke, P.K. Holsen, T.M. Comprehensive emerging chemical discovery: novel polyfluorinated compounds in Lake Michigan trout. Environmental Science and Technology, 2016, 50(17), 9460-9468.

[3] Fakouri Baygi, S., Fernando, S., Hopke, P.K., Holsen, T.M. and Crimmins, B.S. Automated Isotopic Profile Deconvolution for High Resolution Mass Spectrometric Data (APGC-QToF) from Biological Matrices. Analytical chemistry, 2019, 91(24), 15509-15517.