IsoGen

Getting started

Installation

Install a published wheel:

python -m pip install isogen

IsoGen requires Python 3.9 or newer. Its native library uses ctypes and is independent of the CPython minor-version ABI.

IsoGen publishes precompiled native libraries for 64-bit Windows and Linux. Linux installations require the FFTW 3 runtime; released manylinux wheels bundle that dependency. Other platforms require a native build from source.

Generate distributions

Use a numeric neutral mass with any analyte model:

import isogen

protein_by_mass = isogen.isodist(10_000, type="PEPTIDE")
rna_by_mass = isogen.isodist(10_000, type="RNA")

For sequence input, IsoGen calculates the monoisotopic first mass:

protein = isogen.isodist("ACDEFGHIK", type="PEPTIDE", isolen=64)
rna = isogen.isodist("AUGCAGUACGUA", type="RNA", isolen=64)
dna = isogen.isodist("ATGCAGTACGTA", type="DNA", isolen=64)

For an elemental formula, select the FFT-only ATOM input type:

glucose = isogen.isodist("C6H12O6", type="ATOM", isolen=32)

The result has shape (isolen, 2). Column zero is neutral mass and column one is relative intensity:

masses = protein[:, 0]
intensities = protein[:, 1]

Supported type values are PEPTIDE, RNA, DNA, and ATOM; names are case-insensitive in the Python API. FFT, BRAIN, and NN are available for biopolymer inputs. ATOM supports FFT only.

Peptide ion types

Peptide sequence input represents an intact neutral peptide by default, using ion_type="H2O". For a fragment, pass only the residues present in that fragment and choose one of the supported ion types:

Ion type	Sequence to pass	Neutral terminal composition
H2O	Intact peptide	+H2O
a	N-terminal fragment	-CO
b	N-terminal fragment	No terminal shift
c	N-terminal fragment	+NH3
x	C-terminal fragment	+CO2
y	C-terminal fragment	+H2O
z	C-terminal fragment	+H2O-NH3

For example, split PEPTIDE into the appropriate N- or C-terminal sequence:

b6 = isogen.isodist(
    "PEPTID",
    type="PEPTIDE",
    ion_type="b",
)
y6 = isogen.isodist(
    "EPTIDE",
    type="PEPTIDE",
    ion_type="y",
)

IsoGen returns neutral masses. It does not add protons, assign charge, or convert these values to m/z.

RNA ions and terminal chemistry

ion_type is a peptide-only option. Named RNA fragmentation series such as a/b/c/d and w/x/y/z are not currently calculated automatically. To describe an intact or manually truncated RNA sequence, use the available terminal chemistry options:

Keyword	Supported values
threeend	OH (default), or no terminal adjustment
fiveend	OH, MP (default), or TP

rna_5_hydroxyl = isogen.isodist(
    "AUGC",
    type="RNA",
    threeend="OH",
    fiveend="OH",
)
rna_5_triphosphate = isogen.isodist(
    "AUGC",
    type="RNA",
    threeend="OH",
    fiveend="TP",
)

These options are terminal mass adjustments; they are not aliases for named RNA fragment-ion series.

!!! important ion_type, threeend, and fiveend are forwarded to the mass-axis calculation. They change the monoisotopic origin, but the FFT, BRAIN, or NN sequence-model intensity vector retains its standard terminal composition.

Choose the calculation engine

FFT is the default:

fft_result = isogen.isodist("PEPTIDE", method="FFT")
brain_result = isogen.isodist("PEPTIDE", method="BRAIN")
nn_result = isogen.isodist("PEPTIDE", method="NN")

FFT performs the direct isotope calculation, while BRAIN uses a polynomial recurrence. The neural-network engine uses the packaged pretrained model and can be useful for rapid approximation. Elemental formulas always use the direct FFT calculation.

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