MassCascade

Version: 1.1.0

Website

https://bitbucket.org/beisken/masscascade

Description

MassCascade is implemented in the KNIME workflow environment or alternatively can be accessed via the command line. It provides a modular pipeline for the analysis of LC-MS^n data. Data should be in the centroid format or they can be centroided with the implemented wavelet-based centroider. Firstly, a mass trace is built. The background is the subtracted and noise is reduced. At this stage the user can visualise the scans/ TIC. The data can then be normalised and filtered. Retention time alignment is performed using the obiwarp algorithm. For deconvolution Biemann and Savitzky Golay deconvolution are offered. Features can be compiled using Biemann or cosine compilers. A number of different filters are provided: Durbin, Feature and Mass. Two methods of smoothing are provided: Savitzky Golay smoother and Top Hat. For Putative Metabolite Annotation ChemSpider, MassBank and Metlin databases can be searched. Adducts can also be automatically annotated.

Functionality

• Workflow

Instrument Data Type

• MS/LC-MS/LC-MS/MS
• MS/LC-MS/LC-MS^n"

Approaches

Computer Skills

Medium

Software Type

Package

Interface

• Command line interface
• Graphical user interface

Operating System (OS)

• Unix/Linux
• Mac OS (not Mac OS for KNIME)
• Windows

Language

Java

Dependencies

N/A

Input Formats - Open

mzML

Input Formats - Proprietary

Thermo Scientific .raw

Published

2013

Last Updated

2017

License

GPL-3

Paper

https://www.ncbi.nlm.nih.gov/pubmed/26279687

PMID

26279687