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annotation

annotation

Overview

This module is designed for annotating metabolites based on their m/z, retention time, and MS/MS spectra.

Functions

load_ms2_db

load_ms2_db(path)

Load MS2 database in pickle, msp, or json format.

Parameters:

  • path (str): The path to the MS2 database.

Returns:

  • entropy_search (FlashEntropySearch object): The MS2 database.

annotate_aligned_features

annotate_aligned_features(features, params, num=5)

Annotate feature’s MS2 using database.

Parameters:

  • features (list): A list of AlignedFeature objects.
  • params (Params object): The parameters for the workflow.
  • num (int): The number of top MS2 spectra to search.

Returns:

  • features (list): A list of AlignedFeature objects with MS2 annotation.

annotate_features

Annotate features from a single raw data file using MS2 database.

annotate_features(d, sim_tol=None, fuzzy_search=True, ms2_library_path=None)

Parameters:

  • d (MSData object): MS data file.
  • sim_tol (float): The similarity threshold for MS2 annotation. If not specified, the corresponding parameter from the MS data file will be used.
  • fuzzy_search (bool): Whether to further annotated the unmatched MS2 using fuzzy search.
  • ms2_library_path (str): The absolute path to the MS2 database. If not specified, the corresponding parameter from the MS data file will be used.

annotate_ms2

Annotate MS2 spectra using MS2 database.

annotate_ms2(ms2, ms2_library_path, sim_tol=0.7, fuzzy_search=True)

Parameters:

  • ms2 (Scan object): MS2 spectrum.
  • ms2_library_path (str): The absolute path to the MS2 database. If not specified, the corresponding parameter from the MS data file will be used.
  • sim_tol (float): The similarity threshold for MS2 annotation.
  • fuzzy_search (bool): Whether to further annotated the unmatched MS2 using fuzzy search.

Returns:

  • score (float): The similarity score.
  • matched (dict): The matched MS2 spectrum.
  • matched_peak_num (int): The number of matched peaks.
  • search_mode (str): The search mode, ‘identity_search’ or ‘fuzzy_search’.

feature_annotation_mzrt

feature_annotation_mzrt(features, path, mz_tol=0.01, rt_tol=0.3)

Annotate features based on a mzrt file (only .csv is supported now)

Parameters:

  • features (list): A list of features.
  • path (str): The path to the mzrt file in csv format.
  • mz_tol (float): The m/z tolerance for matching.
  • rt_tol (float): The RT tolerance for matching.

Returns:

  • features (list): A list of features with annotation.

feature_to_feature_search

feature_to_feature_search(feature_list)

Calculate the MS2 similarity between features using fuzzy search.

Parameters:

  • feature_list (list): A list of AlignedFeature objects.

Returns:

  • similarity_matrix (pandas.DataFrame): A DataFrame containing the similarity matrix between features.

index_feature_list

index_feature_list(feature_list)

A helper function to index a list of features for spectrum entropy search.

Parameters:

  • feature_list (list): A list of AlignedFeature objects.

Returns:

  • entropy_search (FlashEntropySearch object): The indexed feature list.

output_ms2_to_msp

output_ms2_to_msp(feature_table, output_path)

Output MS2 spectra to MSP format

Parameters:

  • feature_table (pandas.DataFrame): A DataFrame containing the MS2 spectra.
  • output_path (str): The path to the output MSP file.
alignmentclassifier_builder