nomspectra.diff module

class nomspectra.diff.Tmds(spec: Optional[nomspectra.spectrum.Spectrum] = None, table: Optional[pandas.core.frame.DataFrame] = None)

Bases: nomspectra.spectrum.Spectrum

A class for calculate TMDS (Total mass difference statistics) spectrum

Kunenkov, Erast V., et al. “Total mass difference statistics algorithm: a new approach to identification of high-mass building blocks in electrospray ionization Fourier transform ion cyclotron mass spectrometry data of natural organic matter.” Analytical chemistry 81.24 (2009): 10106-10115.

__init__(spec: Optional[nomspectra.spectrum.Spectrum] = None, table: Optional[pandas.core.frame.DataFrame] = None) → None

Parameters

• table (pandas Datarame) – tmds spectrum - mass, intensity and caclulatedd parameters

• metadata (MetaData) – Metadata object that consist dictonary of metadata

assign(generated_bruttos_table: Optional[pandas.core.frame.DataFrame] = None, error: float = 0.001, brutto_dict: Optional[dict] = None, max_num: Optional[int] = None) → nomspectra.diff.Tmds

Finding the nearest mass in generated_bruttos_table

Parameters

• generated_bruttos_table (pandas DataFrame) – Optional. with column ‘mass’ and elements, should be sorted by ‘mass’

• error (float) – Optional. Default 0.001. absolute error iin Da for assign formulas

• brutto_dict (dict) – Optional, default {‘C’:(-1,20),’H’:(-4,40), ‘O’:(-1,20),’N’:(-1,2)} generate brutto table if generated_bruttos_table is None.

• max_num (int) – Optional. Default 100

Return type

Tmds

calc(other: Optional[nomspectra.spectrum.Spectrum] = None, p: float = 0.2, wide: int = 10, C13_filter: bool = True) → nomspectra.diff.Tmds

Total mass difference statistic calculation

Parameters

• other (Spectrum object) – Optional. If None, TMDS will call by self.

• p (float) – Minimum relative intensity for taking mass-difference. Default 0.2.

• wide (int) – Minimum interval in 0.001*wide Da of peaks finding. Default 10.

• C13_filter (bool) – Use only peaks that have C13 isotope peak. Default True

Return type

Tmds

calc_by_brutto() → nomspectra.diff.Tmds

Calculate self difference by calculated mass from brutto

Return type

Tmds

nomspectra.diff.assign_by_tmds(spec: nomspectra.spectrum.Spectrum, tmds_spec: Optional[nomspectra.diff.Tmds] = None, tmds_brutto_dict: Optional[Dict] = None, rel_error: float = 3, p=0.2, max_num: Optional[int] = None, C13_filter: bool = True) → nomspectra.spectrum.Spectrum

Assigne brutto formulas by TMDS

Additianal assignment of masses that can’t be done with usual methods

Parameters

• spec (Spectrum object) – Mass spectrum for assign by tmds

• tmds_spec (Tmds object) – Optional. if None generate tmds spectr with default parameters Tmds object, include table with most intensity mass difference

• brutto_dict (dict) – Optional. Deafault None. Custom Dictonary for generate brutto table. Example: {‘C’:(-1,20),’H’:(-4,40), ‘O’:(-1,20),’N’:(-1,2)}

• abs_error (float) – Optional, default 1 ppm. Relative error for assign peaks by massdif

• p (float) – Optional. Default 0.2. Relative intensity coefficient for treshold tmds spectrum

• max_num (int) – Optional. Max mass diff numbers

• C13_filter (bool) – Use only peaks with C13 isotope peak for generate tmds. Default True.

Returns

• Spectrum – Assigned by tmds masses

• Reference

• ———

• Kunenkov, Erast V., et al. “Total mass difference

• statistics algorithm (a new approach to identification)

• of high-mass building blocks in electrospray ionization

• Fourier transform ion cyclotron mass spectrometry data

• of natural organic matter.”

• Analytical chemistry 81.24 (2009) (10106-10115.)