MzJava: An open source library for mass spectrometry data processing.

摘要: Abstract Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need sharing reuse code among bioinformaticians working with MS data prompted design implementation MzJava, an open-source Java Application Programming Interface (API) related processing. MzJava provides structures algorithms representing processing mass spectra their associated molecules, such as metabolites, glycans peptides. includes functionality to perform calculation, peak (e.g. centroiding, filtering, transforming), spectrum alignment clustering, protein digestion, fragmentation peptides well scoring functions spectrum–spectrum peptide/glycan-spectrum matches. For import export implements readers writers commonly formats. many classes support Hadoop MapReduce (hadoop.apache.org) Apache Spark (spark.apache.org) frameworks cluster computing was implemented. library has been developed applying best practices software engineering. To ensure that contains correct easy use library's API carefully designed thoroughly tested. project distributed under AGPL v3.0 licence. requires 1.7 or higher. Binaries, source documentation can be downloaded from http://mzjava.expasy.org https://bitbucket.org/sib-pig/mzjava . This article part Special Issue entitled: Computational Proteomics.