Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing mass spectrometry data. The goals of the library are to provide a flexible data model with Java interfaces for mass-spectrometry related objects (including raw spectra, processed data sets, identification results etc.) and to integrate the existing algorithms that are currently scattered around various Java-based graphical tools.

MSDK requires Java runtime (JRE) version 1.7 or newer.

Please see the complete MSDK API.

MSDK jars are automatically deployed to Maven Central. In order to use MSDK, simply add the following dependency to your pom.xml:

 <dependency>
    <groupId>io.github.msdk</groupId>
    <artifactId>msdk-all</artifactId>
    <version>0.0.7</version>
 </dependency>

Please read our brief tutorial on how to contribute new code to MSDK.

Since this is a collaborative project, please adhere to the following code formatting conventions:

• All Java sources should be formatted according to the official Java Code Conventions with only one adjustment: use spaces for indentation instead of tabs
• You can use the msdk-eclipse-code-formater.xml file to automatically format your code in the Eclipse IDE
• Please write JavaDoc comments as full sentences, starting with a capital letter and ending with a period. Brevity is preferred (e.g., "Calculates standard deviation" is preferred over "This method calculates and returns a standard deviation of given set of numbers").

MSDK uses the SLF4J library for logging. This library can forward all logging calls to your favorite logging framework (java.util.logging, Apache log4j, or others). Please see SLF4J documentation for details.

See the BUILD.md file