msions.mzml

This module contains functions that are useful for interacting with mzML files in Python.

Module Contents

Functions

tic_df(→ pandas.DataFrame)

Find the TIC and injection time for each scan in an mzML file.

peak_df(→ pandas.DataFrame)

Create a pandas DataFrame containing the m/z,
msions.mzml.tic_df(input_mzml: str, level: str = '1', include_ms1_info: bool = False, faims: bool = False) → pandas.DataFrame[source]

Find the TIC and injection time for each scan in an mzML file.

Parameters:

  • input_mzml (str) – The input mzML file.

  • level (str) – Level of MS scan (1 or 2)

  • include_ms1_info (bool) – Returns MS1 scan number, m/z, and intensity associated with precursor analyzed in MS2 (requires level=”2”)

  • faims (bool) – Returns CV associated with each scan.

Returns:

A pandas DataFrame containing the retention time, TIC, and injection time for each scan.

Return type:

pd.DataFrame

Examples

>>> from msions.mzml import tic_df
>>> test_tic_df = tic_df("test.mzML")
msions.mzml.peak_df(input_mzml: str) → pandas.DataFrame[source]

Create a pandas DataFrame containing the m/z, ion current, and retention time for all MS1 peaks.

Parameters:

input_mzml (str) – The input mzML file.

Returns:

A pandas DataFrame containing the m/z, ion current, and retention time for all MS1 peaks.

Return type:

pd.DataFrame

Examples

>>> from msions.mzml import peak_df
>>> peak_df("test.mzML")