The MassTRIX webserver is written in Perl using CGI for dynamic content representation and runs on an Apache2 web server (version 2.2.11).
A calibrated mass list, consisting of tab separated masses, intensity values and an additional unique identifier, like an ID or a retention time, serves as main input for MassTRIX. These masses are compared within a certain error range against the theoretical adducts of compounds from different metabolic databases. The default database is a combination of KEGG [4] (link), [5] (link), HMDB [6] (link) and LipidMaps [7] (link) with isotopic peaks. As alternatives the same combination without isotopic peaks, KEGG expanded lipids (where all residues R in formulas, are exchanged by hydrocarbon chains of different lengths), LipidMaps alone for lipidomics and MetaCyc [8] (link) as other databases or a separate m/z list are possible. For the analysis of gene expression data from Affymetrix arrays, R (version 2.10) with the gcrma package are used. Affymetrix identifiers are mapped to the respective KEGG ontology (KO) numbers for visualization on metabolic pathway maps. Correctly annotated KEGG metabolites and KO’s are colored on the respective pathways of a chosen organism by calling the KEGG API. Additionally, enzymes of interest, submitted either as EC-numbers or KEGG identifiers can be highlighted. The obtained maps are fully clickable and cross-linked between the different result pages. Different jobs can be compared on pathway or compound level and all results are downloadable.
A calibrated mass list, consisting of tab separated masses, intensity values and an additional unique identifier, like an ID or a retention time, serves as main input for MassTRIX. These masses are compared within a certain error range against the theoretical adducts of compounds from different metabolic databases. The default database is a combination of KEGG [4] (link), [5] (link), HMDB [6] (link) and LipidMaps [7] (link) with isotopic peaks. As alternatives the same combination without isotopic peaks, KEGG expanded lipids (where all residues R in formulas, are exchanged by hydrocarbon chains of different lengths), LipidMaps alone for lipidomics and MetaCyc [8] (link) as other databases or a separate m/z list are possible. For the analysis of gene expression data from Affymetrix arrays, R (version 2.10) with the gcrma package are used. Affymetrix identifiers are mapped to the respective KEGG ontology (KO) numbers for visualization on metabolic pathway maps. Correctly annotated KEGG metabolites and KO’s are colored on the respective pathways of a chosen organism by calling the KEGG API. Additionally, enzymes of interest, submitted either as EC-numbers or KEGG identifiers can be highlighted. The obtained maps are fully clickable and cross-linked between the different result pages. Different jobs can be compared on pathway or compound level and all results are downloadable.
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