Open source software libraries for reading, and for some writing, mzML

An important aspect is that metabolomics studies might comprise many raw data files, so the conversion from the vendor formats should not involve expensive manual intervention to add information beyond what is already stored in the instrument software. Furthermore, command line converters are easier to incorporate into local data processing pipelines. For bioinformaticians developing either software or databases, it is highly recommended to use existing I/O parsing software and libraries. Several such mzML libraries have been developed for different programming languages and software frameworks, summarised in Table below.

Language

Library/API

URL

License

Java

jmzML

https://​code.​google.​com/​p/​jmzml/​

Apache license 2.0

jmzreader

https://​code.​google.​com/​p/​jmzreader/​

Apache license 2.0

C++

OpenMS

http://​open-ms.​sourceforge.​net/​

BSD

Proteowizard

http://​proteowizard.​sourceforge.​net/​

Apache license 2.0

Python

pymzML

http://​pymzml.​github.​io/​

LGPL v3

R

mzR

http://​bioconductor.​org/​packages/​mzR/​ https://​github.​com/​sneumann/​mzR

Artistic-2.0

MatLab

MSiReader

http://​www4.​ncsu.​edu/​~dcmuddim/​msireader.​html

BSD 3-clause

Ruby

mspire

https://​github.​com/​princelab/​mspire

MIT

Perl

MzML::Parser (CPAN)

https://​github.​com/​Leprevost/​MzML-Parser http://​search.​cpan.​org/​dist/​MzML-Parser/​

Dual: GPL or artistic license

See also http://​www.​ms-utils.​org/​wiki/​pmwiki.​php/​Main/​SoftwareList for a growing link of MS related software