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Masskit is a Python package for easy-to-use, efficient and flexible computing on mass spectra. Masskit does this by taking advantage of modern software and hardware architectures. It features:

• Functions to filter, normalize, annotate, plot and compute on mass spectra.
• Searching and indexing of spectral libraries.
• Reading and writing of multiple file formats.
• Computational algorithms for small molecules, including reactions.
• Algorithms and encodings for peptides.
• Use of columnar memory for optimal efficiency in distributed, multicore computation.

Table of Contents

• Installation
• API Documentation
• The Team
• License

Installation

Requirements

• Masskit is installed using the package managers conda and mamba. If you do not have either installed we recommend installing mambaforge. Detailed installation instructions for macOS and Linux can be found here.

Windows

• If you intend to use Masskit AI, please use the Masskit AI instructions instructions instead.
• Download the latest Masskit Windows zip file from the Releases page.
• Extract the contents of the file to a directory on your computer by navigating explorer to the Downloads folder, right clicking on the zip file, and selecting Extract all....
• Run Miniforge Prompt or Anaconda Prompt from the Start menu depending on whether you installed mambaforge or a conda distribution.
• In the prompt window, use cd masskit* to change to the directory starting with masskit in the directory you extracted the downloads to.
• Run call init_masskit.bat to create the masskit package environment.
• Run pip install --find-links=. masskit.

Whenever using the programs in Masskit, please make sure you initialize the appropriate package environment:

• If you installed mambaforge run Miniforge Prompt from the Start menu otherwise run Anaconda Prompt from the Start menu.
• Run conda activate masskit.

Linux or macOS

• Our code is downloaded via git. If git is not installed, installers can be found at the Git website.
• Change to a directory that will hold the masskit directory.
• Run git clone https://github.com/usnistgov/masskit.git
• Run cd masskit.
• If you are going to use Masskit AI:
  • Run source environments/init_masskit.sh -m if you will be using GPUs.
  • Run source environments/init_masskit.sh -c if you will be using CPUs.
• If you are not using Masskit AI, run source environments/init_masskit.sh
• Run pip install .

Whenever using the programs in Masskit, please make sure you have initialized the appropriate package environment:

• If you installed using init_masskit.sh without options run conda activate masskit
• If you installed using init_masskit.sh -c run conda activate masskit_ai_cpu.
• If you installed using init_masskit.sh -m run conda activate masskit_ai