Ideom

Version: 19

Website

http://mzmatch.sourceforge.net/ideom.php

Description

IDEOM is an excel template which provides a GUI with implementations of mzMatch and xcms, along with macros for noise-filtering, metabolite identification and statistical analysis. msconvert can also be directly interfaced. Raw peaks can be extracted from within IDEOM or peak-picked data in the .txt or .csv format can be imported. Up to 10 internal/external standards can be entered and treatment/control groups can be entered for statistical analysis. Peaks are first picked with centWave and then mzMatch is used to convert them to .peakml. mzMatch can then be used to group peaks, filter peaks and annotate groups of related peaks. Normalisation can then be performed using TIC, median or used defined values (although this is not recommended for LC-MS). RT of authentic standards can be entered for metabolite identification. For metabolite identification, a metabolite library is also provided (consisting of KEGG, MetaCyc). To correct for mass calibration errors, a data-dependent polynomial mass recalibration step can be applied. There is then optionally tools for merging dual-polarity data, chemical formula determination for unidentified mass and stable isotope tracking. Specific metabolites can also be analysed in a targeted manner. Conditions can be statistically compared using univariate statistics: mean, relative intensity, SD, t-test and Fisher ratio.

Functionality

• Preprocessing

Instrument Data Type

• MS/LC-MS

Approaches

Computer Skills

Medium

Software Type

Excel Template

Interface

Graphical User Interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

Excel (≥ 2007), R

Input Formats - Open

csv, mzXML, txt

Input Formats - Proprietary

Agilent .d, Thermo Fisher Scientific .raw, Bruker Daltonics .d, waters .raw

Published

2012

Last Updated

2015

License

LGPL-2

Paper

http://www.ncbi.nlm.nih.gov/pubmed/22308147

PMID

22308147