msanalyst 0.1.2

A tool for molecular networking and annotation

MSanalyst

This repository contains the original source code of MSanalyst

Installation

pip version

pip install msanalyst

docker version

docker pull

Quick start

Preprocess

Before applying MSanalyst, raw mass spectrometry (MS) data should be converted using MSconvert. It is recommended to use MZmine-based untargeted LC-MS workflow to generate the quant.csv and mgf files as inputs.

Module usage

Here we briefly introduce the command of MSanalyst quick start: Using -h for help messages in MSanalyst:

• main.py for Default analysis workflow of MSanalyst.

python main.py  -q ./example/example_quant.csv -m ./example/example.mgf -o ./example/

• re-networking.py for quick re-analysis of the results generated by main.py command.

python re-networking.py -m ./example/example.mgf -q ./example/example_quant.csv -scm neutral_loss -scs 0.5 -scp 4

• ms1search.py for single quick ms¹ searching

python ms1search.py -qms1 227.234

• ms2search.py for single ms² searching

python ms2search.py -m single.mgf

• customized_db.py for generating customized mass spectrometry database

python customized_db.py -m ./customed_db/Xiamenmycins.mgf -li ./customed_db/Xiamenmycins.xlsx 

• mn_merging.py for merging different molecular netowrks

python mn_merging.py -mn1 ./example/example_quant_result/example_modified_cosine_0.7_5.graphml -mn2 ./example/example_quant_result/example_modified_cosine_0.1_1.graphml -o ./example/

Documentation

Please see the following links for detailed instructions, parameter usage and more information.

• Online documentation
• Video tutorials
• MSanalyst library