MassKG

A Knowledge-based Mass Fragment Network Database to Identify Natural Products.

In this version (1.0), we have:
in-silico fragments of >400,000 known compounds and >200,000 generated compounds in both positive mode and negative mode. Refer to the picture below for overview of MassKG.

Getting Started!

Our website will undergo maintenance and updates during Beijing time 10:00 PM to 2:00 AM every day.

A Comprehensive Web Tool for Interpreting MS2 Data of Natural Products

In this website, we provide several strategies to query or browse in this database according to user's requirements. We hope to build a user friendly interface as well as a precise analysis method.

Spectrum Search

Spectral data provided to the forms following the given instructions. The system will return a ranked result by ranking all the possible candidates.

Batch Data Analysis

Batch data can be analyzed via this platform. Simply by uploading an integrated file to our system, and then retrieving your result after offline calculation.

Fragments Network Generation

Each candidate compound will get fragmentation through given cleavage rules using in silico method. Fragments can then generate a network of fragment tree.

Network exploration

The whole candidates were built to a network based on their structural similartiy, including the known nature products and generated molecules.

Dereplication&Exploration

Select different database for different task. Known natural product database for compound dereplication and generated database for novel structure exploration.

Chemical Information

To estabish the MassKG NP space, we collected the chemicals from COCONUT database, then a chemical language model was applied to generated compounds with novel structures.

Workflow of MassKG

All natural products were downloaded from COCONUT . Using an informatics tool RDKit to in silico cleavage all the known and the generated compounds to build the MassKG MS2 library. Users can upload a MS2 Spectrum to query its most similar candidates in MassKG.

Frequently Asked Questions

Here, we exhibited top three most frequently asked questions as a guidance for using this webtool.

Anim pariatur cliche reprehenderit, enim eiusmod high life accusamus terry richardson ad squid. 3 wolf moon officia aute, non cupidatat skateboard dolor brunch. Food truck quinoa nesciunt laborum eiusmod. Brunch 3 wolf moon tempor, sunt aliqua put a bird on it squid single-origin coffee nulla assumenda shoreditch et. Nihil anim keffiyeh helvetica, craft beer labore wes anderson cred nesciunt sapiente ea proident. Ad vegan excepteur butcher vice lomo. Leggings occaecat craft beer farm-to-table, raw denim aesthetic synth nesciunt you probably haven't heard of them accusamus labore sustainable VHS.
Anim pariatur cliche reprehenderit, enim eiusmod high life accusamus terry richardson ad squid. 3 wolf moon officia aute, non cupidatat skateboard dolor brunch. Food truck quinoa nesciunt laborum eiusmod. Brunch 3 wolf moon tempor, sunt aliqua put a bird on it squid single-origin coffee nulla assumenda shoreditch et. Nihil anim keffiyeh helvetica, craft beer labore wes anderson cred nesciunt sapiente ea proident. Ad vegan excepteur butcher vice lomo. Leggings occaecat craft beer farm-to-table, raw denim aesthetic synth nesciunt you probably haven't heard of them accusamus labore sustainable VHS.
Anim pariatur cliche reprehenderit, enim eiusmod high life accusamus terry richardson ad squid. 3 wolf moon officia aute, non cupidatat skateboard dolor brunch. Food truck quinoa nesciunt laborum eiusmod. Brunch 3 wolf moon tempor, sunt aliqua put a bird on it squid single-origin coffee nulla assumenda shoreditch et. Nihil anim keffiyeh helvetica, craft beer labore wes anderson cred nesciunt sapiente ea proident. Ad vegan excepteur butcher vice lomo. Leggings occaecat craft beer farm-to-table, raw denim aesthetic synth nesciunt you probably haven't heard of them accusamus labore sustainable VHS.

How to Cite Our Work and Contact Us

Should you have any questions or advices, please submit your voice to us using the feedback button. Also, you can send us emails anytime using the following contact information.

Corresponding Author
Jie Liao
Dr. Jie Liao
Pincipal Investigator

National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University

liaojie@zju.edu.cn
Corresponding Author
Prof. Xiaohui Fan
Prof. Xiaohui Fan
Director

National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University

fanxh@zju.edu.cn
First Author
Bingjie Zhu
Mr. Bingjie Zhu
Ph.D Student

National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University

zhubj@zju.edu.cn