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MassSpecChemicals

Build Status Coverage

A package for representing molecules or ions formed in mass spectrometers.

Basic type

  1. Chemical: unstructured chemicals, storing name, formula, and other information; Chemical(name::String, formula::String, info::Vector{Pair{Symbol, Any}}).
  2. Ion: charged Chemical with specific adduct or molecule loss; Ion(core::AbstractChemical, adduct::AbstractAdduct).
  3. IonCluster: multiple Ions with similar m/z; IonCluster(ions::Vector{<: AbstractIon}, abundance::Vector{Float64}).

Formula

Currently supported elements:

C, H, O, N, P, S, Li, Na, K, F, Cl, Ag, [13C], [2H] (D), [3H] (T), [17O], [18O], [15N], [33S], [34S], [35S], [6Li], [40K], [41K], [37Cl], [109Ag]

Adduct

Prefefined adducts:

  • LossElectron: [M]+
  • Protonation: [M+H]+
  • ProtonationNLH2O: [M+H-H2O]+
  • ProtonationNL2H2O: [M+H-2H2O]+
  • ProtonationNL3H2O: [M+H-3H2O]+
  • DiProtonation: [M+2H]2+
  • TriProtonation: [M+3H]3+
  • AddNH4: [M+NH4]+
  • AddHNH4: [M+H+NH4]2+
  • Add2NH4: [M+2NH4]2+
  • Sodization: [M+Na]+
  • SodizationProtonation: [M+Na+H]2+
  • DiSodization: [M+2Na]2+
  • AddElectron: [M]-
  • Deprotonation: [M-H]-
  • DeprotonationNLH2O: [M-H-H2O]-
  • DiDeprotonation: [M-2H]2-
  • TriDeprotonation: [M-3H]3-
  • AddOAc: [M+CH3COO]-
  • AddHCOO: [M+HCOO]-
  • LossCH2O: [M-CH2O]-
  • AddO: [M+O]-
  • AddC2H2O: [M+C2H2O]-
  • LossCH8NO: [M-CH8NO]-
  • LossC2H8NO: [M-C2H8NO]-
  • AddC3H5NO: [M+C3H5NO]-
  • AddC2H5NO: [M+C2H5NO]-
  • LossCH3: [M-CH3]-
  • DeprotonationLossSerineAddH2O: [M-H-Serine+H2O]-

User can custumize adduct by PosAdduct and NegAdduct.

For example, [2M+H]+, and [M-2H-2H2O]2- can be created by PosAdduct(2, "+H", 1), and NegAdduct(1, "-2H-2H2O", 2) respectively.

Interface

  • chemicalname: name of a chemical (AbstractChemical).
  • chemicalformula: formula of a chemical.
  • ischemicalequal: whether two chemicals equal.
  • ioncore: core of an ion.
  • ionadduct: adduct of an ion.
  • kmer: number of "M" of an adduct or ion.
  • charge: number of charges of an adduct or ion.
  • adductelement: changes of elements of an adduct or ion.
  • adductformula: formula of an adduct.
  • abundantion: most abundant ion of an IonCluster.
  • isionequal: whether two ions equal.
  • isionequal: whether two adducts equal.
  • rt: retention time.

Other function

  • mw: molecular weight of a chemical.
  • mz: m/z of an ion.
  • abundance: abundance of a chemical among natural isotopes.
  • isotopic_abundance: formula and abundance of possible natural isotopes of a chemical.
  • getisotopes: formula of possible natural isotopes of a chemical.
  • isobar_rt_mz1: coeluting isobars as a table.
  • getisobars: coeluting isobars as a vector.
  • acrit: create absolute criterion.
  • rcrit: create relative criterion.
  • crit: create both absolute and relative criterion.
  • @ri_str: real number interval.

BioChemicals

This submodule defines multiple biology related molecules, including aminoacids, lipids, glycans, etc. (still in active development)