Description: Purpose of All Tools

State of the art technology in instrumentation and data-acquisition provide a wealth of information in metabolomics and lipidomics studies. Unlike in proteomics and genomics, lipidomics and metabolomics are emerging fields, with software and methodologies in identification and statistical analysis only recently emerging. Open source tools which can be improved by the larger community can serve to provide the information researchers need through novel and user friendly data processing and data analysis strategies. On this page you will find free open source software tools that can aid in lipidomics and metabolomics research. These tools can be edited to meet your needs, and video tutorials and manuals are included. We ask that you please cite the tools appropriately and maintain the authors on additional edits. Links to download software tools are provided below.


  • LipidMatch can be used to annotate lipids detected using LC-HRMS/MS targeted, data-dependent and data-independent experiments using various vendor formats. LipidMatch can also be employed for direct infusion HRMS/MS experiments. LipidMatch in-silico fragmentation libraries contain over 250,000 lipid species across more than 50 lipid types.


  • LipidPioneer, an interactive excel template, can be used to generate exact masses and molecular formulas of various lipid adducts. Over 60 lipid classes are present in the LipidPioneer template, and include several unique lipid species, such as ether-linked lipids and lipid oxidation products.


  • IE-Omics is a R script that automates “iterative exclusion” (IE) experiments. In IE, previously selected ions for fragmentation using ddMS2-topN are excluded from selection in sequential injections. IE significantly increases the number of lipid identifications obtained in data-dependent analysis.


  • is an extensive and user-friendly genome informatics portal containing 7,600 microbial genomes and associated metabolic pathways. This four hour tutorial will cover many aspects of BioCyc, with a focus on metabolomics data analysis.

SECIM Galaxy Tools

  • SECIMTools project aims to develop a suite of tools for processing of metabolomics data, which can be run in a standalone mode or via Galaxy Genomics Framework.

Future Tools

Future tools include automation of univariate and multivariate statistical analysis of lipidomics and metabolomics datasets using excel and R; also quality control and statistical tool boxes in Galaxy will be added.