MassCascade: A Mass Spectrometry Library

Copyright (C) 2013 EMBL - European Bioinformatics Institute

Contributors:

• Stephan Beisken - initial API and implementation

It is released under the General Public License (GPL), version 3.

The MassCascade library provides functionality for tandem mass spectrometry data processing and visualisation. It provides a plug-in for the workflow platform KNIME and has been tested with metabolomics LC-MS data.

Description

The following input formats are supported:

• Thermo RAW file format
• PSI mzML file format

Functionality includes:

• input (mzML, raw)
• raw data- or profile-based sample alignment
• background subtraction and noise reduction
• data binning for the m/z and time domain
• data and profile filters for the m/z and time domain
• gap filling for chromatographic profiles using natural cubic splines
• isotope and list-based adduct detection
• ion chromatogram extraction and manipulation
• data smoothing in the m/z and time domain
• visualisation of spectra and chromatograms

The core classes are representations of essential mass spectrometry objects. These core objects are manipulated by task classes, each carrying out a single task on the core object. To reduce memory load and ensure persistence within a workflow environment, every task can serialize the core object to a specified directory if required.

Installation

The library can be freely used as backend for mass spectrometry data processing. All task classes implement the 'Callable<?>' interface and can be configured via the 'setParameters()' method or constructed fully parameterized.

Currently, the library is used in the KNIME MassCascade feature. "KNIME is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform." (http://knime.org/)

For the API see the JavaDoc pages.

Changelog

1.0.0

• Initial release.