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Spectrum Clustering
Provides an implementation of clustering and merging methods for MS/MS data. Spectrum Clustering is a user-friendly software that supports various methods for spectrum similarity scoring, clustering, and merging. This application presents a graphical user interface to the user, which is divided into sections that correspond with the different tasks that can be performed: “input”, “similarity options”, “clustering options”, “merging options”, and “output”.
MzJava
An open-source Java library for the analysis of mass spectrometry data from large scale proteomics and glycomics experiments. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce and Apache Spark frameworks for cluster computing was implemented.
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