lcicpms 0.0.1

A package for processing LC-ICPMS data

Overview

Purpose

The code is designed for handling and analyzing LC-ICP-MS (Liquid Chromatography-Inductively Coupled Plasma Mass Spectrometry) data. It includes functionality for loading raw data, performing calibration, applying internal standard corrections, and quantifying element concentrations.

Key Components

1. Data Handling and Loading

   • RawICPMSData Class:
     • Manages raw LC-ICP-MS data.
     • Loads data from .csv files.
     • Extracts and organizes information such as intensities, times, elements, and time labels.
     • Provides methods for visualizing raw data.

2. Integration

   • Integrate Class:
     • Calculates the area under the curve for signal traces within a specified time range.
     • Useful for quantifying the amount of analyte based on its signal intensity over time.

3. Calibration and Quantification

   • Dataset Class:
     • Manages the entire workflow from loading data to quantification.
     • Loading Raw Data:
       • Loads and organizes raw ICP-MS data files from a specified directory.
     • Calibration:
       • Performs calibration using standard concentration files.
       • Creates a Calibration object for further use in quantification.
     • Internal Standard Correction:
       • Applies correction based on an internal standard (e.g., "115In").
       • Computes the baseline for the internal standard to correct measurements.
     • Quantification:
       • Quantifies concentrations of specific elements using calibration data and internal standard corrections.
       • Integrates data over specified time ranges and produces a DataFrame of quantified concentrations.

Summary

The code provides a comprehensive toolkit for processing LC-ICP-MS data, including:

• Data Import: Load and process raw data files.
• Calibration: Set up and apply calibration curves based on known standards.
• Correction: Apply internal standard corrections to improve accuracy.
• Quantification: Calculate and report the concentrations of elements in samples.

It integrates various aspects of data handling and analysis into a coherent workflow, facilitating efficient and accurate analysis of LC-ICP-MS data.

---

Example Python Script

from lcicpms.dataset import Dataset

# Initialize Dataset object with the directory paths
raw_data_dir = 'path/to/raw_data'
cal_data_dir = 'path/to/calibration_data'
dataset = Dataset(raw_data_dir=raw_data_dir, cal_data_dir=cal_data_dir)

# Load raw data
dataset.load_raw_data(dir=raw_data_dir)

# Perform calibration
dataset.run_calibration(
    cal_std_concs=[0, 10, 25, 50, 100, 200],
    cal_keywords_by_conc=['std_0', 'std_1', 'std_2', 'std_3', 'std_4', 'std_5']
)


# Quantify elements (internal standard correction done automatically)
dataset.quantitate(
    time_range=(0, 1200),  # Specify your time range (seconds)
    cal_std_concs=[0, 10, 25, 50, 100, 200],
    cal_keywords_by_conc=['std_0', 'std_1', 'std_2', 'std_3', 'std_4', 'std_5']
)

# Print results
print(dataset.concentrations_df)

---

Documentation

Module: lcicpms

This module provides tools for handling LC-ICP-MS data, including integration, calibration, and quantification.

---

RawICPMSData Class

Overview

Handles raw LC-ICP-MS data, loading from files, and extracting relevant information for further processing.

Attributes

• raw_data_file (str): Path to the raw ICP-MS data file.
• data_type (str): Describes the raw file data type (set when data is loaded).
• min_time (float): Minimum time in the separation.
• max_time (float): Maximum time in the separation.
• intensities (dict): Dictionary of arrays containing intensities collected over time, with elements as keys.
• times (dict): Dictionary of arrays containing time points of intensity measurements, with elements as keys.
• elements (list): List of elements in the raw file.
• time_labels (dict): List of time labels.
• raw_data_df (DataFrame): DataFrame containing the raw data.

Methods

• __init__(self, raw_data_file: str = None)

  • Description: Initializes the RawICPMSData object and loads data from the specified file.
  • Args:
    • raw_data_file (str): Path to the raw ICP-MS data file.

• load_data(self)

  • Description: Determines the data type of the raw data file and loads the data. Currently supports only .csv files.

• get_elements_and_time_labels(self)

  • Description: Extracts elements and time labels from the raw data file.

• get_intensities(self)

  • Description: Extracts and stores the intensities of each element from the DataFrame.

• get_times(self)

  • Description: Extracts and stores the time points for each element from the DataFrame.

• plot_raw_data(self, elements: list = None)

  • Description: Plots raw data for specified elements or all elements if none are specified.
  • Args:
    • elements (list): List of elements to plot.

---

Integrate Class

Overview

Provides functionality to integrate signal traces to calculate the area under the curve.

Methods

• integrate(intensities, times, time_range: tuple = None)

  • Description: Computes the area under the signal trace curve within a specified time range.
  • Args:
    • intensities: Array of intensity values.
    • times: Array of time points corresponding to the intensities.
    • time_range (tuple): Tuple specifying the start and end times for integration. If None, integrates over the entire range.
  • Returns:
    • float: Calculated peak area under the curve.

• other()

  • Description: Placeholder method for additional processing (currently commented out).

---

Dataset Class

Overview

Manages raw LC-ICP-MS data, performs calibration, applies internal standard corrections, and quantifies element concentrations.

Attributes

• raw_data_dir (str): Directory containing raw ICP-MS data files.
• cal_data_dir (str): Directory containing calibration files.
• skip_keywords (list): List of keywords to exclude certain files.
• raw_data_dict (dict): Dictionary of loaded raw data files.
• cal_icpms_obj_dict (dict): Dictionary of calibration files for each concentration.
• _cal_has_run (bool): Flag indicating whether calibration has been performed.
• cal (Calibration): Calibration object with standard concentrations and elements.
• concentrations_df (DataFrame): DataFrame of quantified concentrations.

Methods

• __init__(self, raw_data_dir: str = None, cal_data_dir: str = None, skip_keywords: list = ['results'])

  • Description: Initializes the Dataset object with directories for raw and calibration data.
  • Args:
    • raw_data_dir (str): Directory for raw data files.
    • cal_data_dir (str): Directory for calibration files.
    • skip_keywords (list): Keywords to filter out certain files (default: ['results']).

• load_raw_data(self, dir: str)

  • Description: Loads raw ICP-MS data files from the specified directory.
  • Args:
    • dir (str): Directory from which to load raw data.
  • Returns:
    • dict: Dictionary of file paths and RawICPMSData objects.

• run_calibration(self, cal_std_concs: list = [0, 10, 25, 50, 100, 200], cal_keywords_by_conc: list = ['std_0', 'std_1', 'std_2', 'std_3', 'std_4', 'std_5'])

  • Description: Performs calibration using standard concentrations and associated files.
  • Args:
    • cal_std_concs (list): List of standard concentrations (default: [0, 10, 25, 50, 100, 200]).
    • cal_keywords_by_conc (list): Keywords to identify files for each concentration (default: ['std_0', 'std_1', 'std_2', 'std_3', 'std_4', 'std_5']).

• internal_std_correction(self)

  • Description: Applies internal standard correction using the element "115In". Computes baseline for correction.
  • Returns:
    • float: Baseline value for "115In".
  • Raises:
    • Exception: If calibration hasn't been run or "115In" is not found.

• quantitate(self, time_range: tuple = (-1, -1), elements: list = ['Fe', 'Co', 'Mn', 'Ni', 'Cu'], cal_std_concs: list = [0, 10, 25, 50, 100, 200], cal_keywords_by_conc: list = ['std_0', 'std_1', 'std_2', 'std_3', 'std_4', 'std_5'])

  • Description: Quantifies concentrations of specified elements using calibration data and internal standard correction.
  • Args:
    • time_range (tuple): Tuple indicating time range for integration (default: (-1, -1)).
    • elements (list): List of elements to quantify (default: ['Fe', 'Co', 'Mn', 'Ni', 'Cu']).
    • cal_std_concs (list): List of standard concentrations (default: [0, 10, 25, 50, 100, 200]).
    • cal_keywords_by_conc (list): Keywords to identify calibration files (default: ['std_0', 'std_1', 'std_2', 'std_3', 'std_4', 'std_5']).
  • Returns:
    • DataFrame: DataFrame with quantified concentrations for each element.

---