HorIson 0.1.4

HorIson: tools for isotope simulation

HorIson

HorIson is a tool for vectorized isotope simulation, that applies Fast-fourier transform (FFT) or multinomial products.

How does HorIson work

HorIson provides 3 algorithms for different types of istope simulation.

1. FFT_Lowres, which computes convolved coarse isotopes (1 per 1 Da) at high speed.
2. FFT_Highres, which computes fine isotopes and profile spectra at variable resolution.
3. Multi_conv: which computes separate isotope combinstions at high speed.
   
   

To enable vectorization for FFT-based algorithms, isotope masses are placed on a uniform grid. For multinomial products, global isotope combinations and multnomial distribtuions are precomputed.

Usage:

HorIson can be imported as a module, or called from the command line. As input for each algorithm, a failepath to a tabular can be supplied, or an element string, or a DataFrame or array can be used when importing as a module. When no header information is present, the element order should be supplied with the element parameter.

Arguments.

General arguments

Parameter	Default value	Description
elements	[]	Specifies element column order if a headerless array is used as input
min_itensity	1e-6	Filters isotopes in output below a certain probability level
isotope_ranges	[-2,6]	Filters isotopes in output to a certain mass range
charge	1	charge of computed formulas, accepts either single value or array of different charges
normalize	False	Normalizes probabilies either total ("sum"), largest isotope ("max") or monoisotopic peak ("mono")
batch_size	1e4	How many formulas to simulate at once
add_mono	True	Add monoisotopic mass back to simluated isotope masses
peak_fwhm	0.01	Peak FWHM in Da, used for generating profile data (FFT_Highres, Multi_conv), accepts either single value or array of different FWHMs
divisor	4	Subsampling rate for convolution (FFT_Highres, Multi_conv)

FFT_Lowres specific arguments

Parameter	Default value	Description
bins	False	Set a fixed maximum grid size
mass_calc	True	Calculate exact isotope masses
return_borders	False	provide grid-sizes as output

FFT_Highres specific arguments

Parameter	Default value	Description
packing	True	Compress redundant grid sections
peak_picking	True	Output centroid data

Mutli_conv specific arguments

Parameter	Default value	Description
prune	1e-6	remove isotope combinations below a chance threshold or outside of isotope range
min_chance	1e-4	remove isotope combinations after pruning
convolve	"fast"	Output raw combinations (False) or profile (peak) data ("full") or centroid data ("fast")
add_borders	False	Compute peak borders
add_area	False	Compute peak area
Precomputed	[]	Re-use precomputed isotope combinations

Licensing:

The pipeline is licensed with standard MIT-license.
If you would like to use this pipeline in your research, please cite the following papers: