protmaster 0.0.3

A powerful proteomic analysis tool

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:

pip install protmaster

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

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.