Metadata-Version: 2.1
Name: protmaster
Version: 0.0.3
Summary: A powerful proteomic analysis tool
Home-page: UNKNOWN
Author: Tang Ting
Author-email: ttang1900@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6

protmaster: Tools For working with proteomics
=====================================================================================================

protmaster is a Python package designed to process high-resolution mass spectrometry data that is coupled with liquid chromatography (LC). Its primary objective is to provide scientists with a user-friendly tool that can be used to read, process, and visualize proteomics data acquired using LC/GC-HRMS .

By utilizing protmaster, users can more easily analyze complex data sets, resulting in a more efficient and streamlined research process. Whether working with LC coupled HRMS data, protmaster is a reliable and effective solution that can help researchers to achieve their scientific goals.

Contributer: Ting Tang
======================
First release date: Sep.17.2024

Update
======
Sep.18.2024: protmaster update Log 0.0.3::

    * update the extract_tic method


protmaster can be installed and import as following:

.. code-block:: python

    pip install protmaster


If you just want to update a new version, please update as following:

.. code-block:: python

    pip install protmaster -U



pyhrms requires major dependencies:
===================================

* numpy>=1.19.2

* pandas>1.3.3

* matplotlib>=3.3.2

* pymzml>=2.4.7

* scipy>=1.6.2

* molmass==2021.6.18

* tqdm>=4.62.3

* openpyxl>=3.0.9

* networkx>=2.6.3

* scikit-learn>=1.0.2

* pyopenms >= 3.0.0


Features
========
protmaster provides following functions:

* Read raw LC/GC-HRMS data in mzML format;
* Powerful and accurate peak picking function for LC/GC HRMS;
* retention time (rt) and mass over Z stands for charge number of ions (m/z) will be aligned based on user defined error range.
* Covert profile data to centroid
* Parallel computing to improve efficiency;
* Interactive visualizations of raw mzML data;
* Supporting searching for Local database and massbank;
* MS quality evaluation for ms data in profile.
* Can process SWATH data.




Licensing
=========

The package is open source and can be utilized under MIT license. Please find the detail in licence file.


Table of Content
~~~~~~~~~~~~~~~~~~~

1. Quick start

* **Feature prioritization :** multi_process()

* **Database matching :** multi_process_database_matching()

* **Result filtering :** post_filter()

* **Result summarizing :** summarize_results()

Note
*********************************************
Please note that the documentation is currently a work in progress, and there is more content that is being written. I apologize for any inconvenience this may cause, but rest assured that I am continually updating the documentation to provide you with the most comprehensive guide to using protmaster.




