What is IDEOM?

[Darren]

IDEOM is a user-friendly application for analysis of LCMS metabolomics data.

The main functions of Ideom are noise filtering, metabolite identification and visualisation of results. 

Ideom has been designed and optimised for the application of high resolution LCMS data to untargeted or semi-targeted metabolomics studies. 

Default values are suitable for the HILIC-orbitrap platform, however the software may be used for any LCMS metabolomics dataset. 

The required input files are peak intensity tables (as txt or csv). Automated functions are included to obtain these peaklists from raw data using msconvert (Proteowizard), XCMS and mzMatch (through R). 

Ideom is a macro-enabled Excel template that runs in any recent version of Microsoft Excel (since 2007). More advanced functions require a current installation of the R statistical software. 

Noise filtering procedures include:

- Background noise filter - based on absolute peak intensity

- Contaminant noise filter - based on blank solvent samples

- Random noise filter - based on relative standard deviation of replicates and/or quality control samples

- Chromatographic noise filter - based on relative peak intensities and retention times

- MS artefact filter - based on common mass differences (isotopes, adducts, fragments) and peak intensities

- Annotation of possible MS artefacts - based on less-common mass differences (and mzMatch related-peaks annotation)

- Peak shape filter - (mzMatch codadw filter and XCMS Centwave algorithm recommended) Chromatograms can be viewed manually within Ideom (if imported from mzMatch) 

Identification algorithm:

- Chemical formula obtained by matching accurate mass to an extensive inbuilt (and adjustable) metabolite database

- (Charge state is determined by 13C natural isotope peak)

- Retention time is checked against authentic standards in database (if available) or against predicted retention time based on individual physicochemical properties and/or class-based properties. 

- Metabolites in database are given preference according to their predicted presence from biochemical databases (KEGG and BioCyc). Organism-specific annotations can be added to the database. 

- 13C isotope abundance and common isotopes, fragments and adducts are annotated to allow users to manually check metabolite identifications

- Putative metabolite identifications are given a confidence score based on retention time, predicted presence in organism of study and likelihood of being a MS artefact. 

Visualisation:

- Metabolites presented with colour-coded relative intensities for each sample group and links to numerous graphs and additional information

- Automatically generated graphs for individual metabolites or global analysis

- Automatically generated statistics for means, relative means, t-test, standard deviations and fisher ratios. 

- Simple export to R for automated multivariate statistics (PCA, HCA and heatmap) 

- Simple export to external websites for statistical (Metaboanalyst) or pathway focused analysis (Pathos or MetExplore)

- User-adjustable study groups to allow comparisons of different sample groups within the same study.

Ideom includes many additional functions for metabolomics data analysis including: 

- Targeted metabolite analysis

- Isotope search for stable isotope-labelling experiments

- Normalisation and quality control checking (by TIC or internal standards)

- Excel functions for calculating exact mass, mass error (ppm), natural isotope abundance and others

- Metabolite (or isomer) search function

- Visualisation of MSMS data and annotation of fragments and neutral losses

Further information, full documentation and free download available at the Ideom website:

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