PeakAnalyzer is implemented as a Java program encompassing two software components, PeakSplitter and PeakAnnotator. These subprograms are also implemented separately in C++ and Java so that users can choose a distribution suited to their requirements. Core facilities needing to process numerous datasets have the option to incorporate the faster C++ versions into a production workflow, whereas the Java implementations can be run either as individual command-line utilities or as a single cross-platform desktop application with an intuitive graphical interface.