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HPLC data analysis in Python

Code style: black

Python 3.10

Testing (CI)

Publishing (CI)

The hplc_data_analysis tool automates the typical analysis of HPLC data, saving time, avoiding human error, and increasing comparability of results from different groups.

Some key features:

  • handle multiple HPLC semi-quantitative data tables (obtained with different methods)
  • duild a database of all identified compounds and their relevant properties using PubChemPy
  • split each compound into its functional groups using a published fragmentation algorithm
  • produce single file report, single replicate (intended as the sum of more methods applied to one vial), comprehensive multi-sample (average and deviation of replicates) reports and aggregated reports based on functional group mass fractions in the samples
  • provides plotting capabilities

Framework

File

A .txt or .csv file located in the project folder that contains time, area, and concentration information for many compunds for a measure.

Depending on the instrument export parameter, the structure of Files can differ slightly. Project-Parameters ensure that the loading process can lead to the same data structure to allow to perform all downstream computations.

A good naming convention for Files ensures the code handles replicates of the same sample correctly. Filenames have to follow the convention: method_name-of-sample-with-dashes-only_replicatenumber

Examples that are correctly handled:

  • 210_Bio-oil-foodwaste-250C_1
  • 254_Bio-oil-foodwaste-250C_1
  • 210_FW_2
  • 254_FW_2

Examples of NON-ACCEPTABLE names are

  • 210-bio_oil_1
  • 254-FW1

Replicate

If more Files belong to the same material (Sample, see below) but represent different methods that see different compounds (for example, different wavelengths are used in the detector), they can be merged into the same Replicate.

A Replicate is the union of files with different methods that are complementary in the analysis of a material.

Sample

A collection of Replicates that replicate the same measure and allow to assess reproducibility.

Project

The folder path indicates where the Files are located and where the output folder will be created.

The Project-Parameters are valid for each Sample.

The Project can generate Reports and Plots for all Files, Replicates, or Sample or only for some of them.

Reports

Reports contain the results for one parameter (abbreviated as param) for all Files, Replicates, or Sample.

There are two types of reports:

Reports (simple-reports or compound-reports)

These report report the param value for each compound in each Files, Replicates, or Sample.

Example: the values of conc_vial_mg_L for each compound in each File are collected in a single pandas dataframe (and saved as excel worksheet) for an easy comparison.

Aggrreps (aggregated reports)

These report report the param value for each aggregated functional group in each Files, Replicates, or Sample.

The results of componds are aggregated by functional group (see this paper for details).

Plots

Each report can be plotted using the plot_report method of the Project class.

Documentation

Check out the documentation.

Installation

You can install the package from PyPI:

Examples

Each example is available as a folder in the examples folder and contains the code and the necessary input data. To run examples:

  1. Install hplc_data_analysis in your Python environment
  2. Download the folder that contains the example
  3. Run the code
  4. If you run the scripts as Jupyter Notebooks, replace the relative path at the beginning of each example with the absolute path to the folder where the code is located

Plotting with myfigure

Plots rely on the package myfigure, a package to simplify scientific plotting in data analysis packages. Check out its documentation and GitHub.