Calib-RT

Overview

Calib-RT is an open-source Python software package designed for RT (retention time) calibration. This package provides a flexible and robust solution for achieving accurate RT calibration across various data scales while handling a certain level of noise interference.

The workflow diagram is below, providing an overview of the process. For a comprehensive and in-depth explanation, please refer to the associated paper for detailed insights and analysis.

Installation

To use calib_rt, make sure you have the following dependencies installed:

• Python (>= 3.10)
• numpy (>= 1.26.0)
• pandas (>= 2.1.1)
• networkx (>= 3.1)
• statsmodels (>= 0.14.0)
• scipy (>= 1.11.3)

You can install the calib_rt package using pip:

pip install pycalib_rt 

Usage

Here is an example of how to use calib_rt for RT calibration:

import calib_rt

# basic information of all built-in datasets 
calib_rt.RTdatasets.get_datasets_list()  
         sample_type  datasets_num
   0   distort_left             2
   1  distort_right             2
   2            exp             2
   3         linear             2
   4              S             2

# use first of "S" type datasets
datasets = calib_rt.RTdatasets.get_pandas(sample_type="S",index_in_group=1)
x = datasets["Spectral library RT"]
y = datasets["Measured RT"]

# fit and predict
model = calib_rt.Calib_RT() 
model.fit(x,y)
y_pred = model.predict(x)         

Performance test

Code for performance test is available in the analysis. For a detailed analysis of the test conclusion, please refer to our paper.

References

Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data link of paper

License

This project is licensed under the MIT License. See the LICENSE file for details.