OpenArm is an implementation of the Open Group's Application Response Measurement (ARM) standard. It provides a complete implementation of the ARM 4.0 Java interfaces, as well as ARM agent functionality that allows you to record your transaction events as log4J logging events, JMS messages, SNMP traps, JMX notifications, or as records in a relational database.
ProteomeCommons.org IO Framework is a proper Java framework for handling spectra and peak lists. The framework can read and write to a number of different spectra and peak list formats, and it provides a simple, intuitive Java object model for working with spectra or peak lists. All classes support two methods of handling peak list and spectrum data: in-memory or stream. The goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.
Luxor is an open-source XML User Interface Language (XUL) toolkit in Java that lets you build UIs using XML and also includes an ultra light-weight, multi-threaded Web server, a portal engine, and a template engine. It is also Web Start-ready, as everything fits in a jar and requires no loose files.