ms2query 0.3.0

Tool to query MS/MS spectra against GNPS library data.

MS2Query - machine learning assisted library querying of MS/MS spectra.

MS2Query is a tool for fast library searching for both analogs and true matches.

Documentation for users

Prepare environmnent

We recommend to create an Anaconda environment with

conda create --name ms2query python=3.8
conda activate ms2query

Pip install MS2Query

MS2Query can simply be installed by running:

pip install ms2query

Run MS2Query

Below you can find an example script for running MS2Query. Before running the script, replace the variables ms2query_library_files_directory and ms2_spectra_directory with the correct directories.

This script will first download files for a default MS2Query library. This default library is trained on the GNPS library from 2021-04-09.

After downloading, a library search and an analog search is performed on the query spectra in your directory (ms2_spectra_directory). The results generated by MS2Query, are stored as csv files in a results directory within the same directory as your query spectra.

Note: When running, Tensorflow often raises a few warnings on most computers. These warnings are raised when no GPU is installed and can be ignored.

from ms2query.run_ms2query import download_default_models, default_library_file_base_names, run_complete_folder
from ms2query.ms2library import create_library_object_from_one_dir

# Set the location where all your downloaded model files are stored
ms2query_library_files_directory = "./ms2query_library_files"
# Define the folder in which your query spectra are stored.
# Accepted formats are: "mzML", "json", "mgf", "msp", "mzxml", "usi" or a pickled matchms object. 
ms2_spectra_directory = "specify_directory"

# Downloads pretrained models and files for MS2Query (>10GB download)
download_default_models(ms2query_library_files_directory, default_library_file_base_names())

# Create a MS2Library object
ms2library = create_library_object_from_one_dir(ms2query_library_files_directory, default_library_file_base_names())

# Run library search and analog search on your files.
run_complete_folder(ms2library, ms2_spectra_directory)

Documentation for developers

Prepare environmnent

We recommend to create an Anaconda environment with

conda create --name ms2query python=3.7
conda activate ms2query

Clone repository

Clone the present repository, e.g. by running

git clone https://github.com/iomega/ms2query.git

And then install the required dependencies, e.g. by running the following from within the cloned directory

pip install -e .

To run all unit tests, to check if everything was installed successfully run:

pytest

Contributing

If you want to contribute to the development of ms2query, have a look at the contribution guidelines.

License

Copyright (c) 2021, Netherlands eScience Center

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.