Technion
Rappaport Faculty of Medicine
Resources

Resources

The list below includes either freely accessible tools or tools that are available through collaboration with us

Data Conversion:

msConvert (Proteowizzard) – A tool for converting vendor specific files to open-source formats such as mzML, mzXML and more

Data Analysis and Visualization Tools:

MetaboAnalyst – a comprehensive, Web-based tool designed for processing, analyzing, and interpreting metabolomic data. It handles most of the common metabolomic data types including compound concentration lists, spectral bin lists, peak lists, and raw MS spectra.

Metabolite AutoPlotter – Web-based tool designed to conveniently read, process and plot metabolite data sets analyzed elsewhere (e.g. with manufacture’s software). It converts and cleans-up the data, allows data normalization while automatically generates a single plot for every metabolite in the data-set. Different plot-types can be used which can be further adapted to personal preferences. It also allows to perform multivariate data analysis, e.g. run a PCA, a correlation analysis or to generate Volcano Plots.

Skyline – freely-available, open-source data analysis software for mass spectrometry data, including selected reaction monitoring (SRM), HRMS datasets, and calibrated quantification.

MS-DIAL – universal program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters).

MZmine – toolbox for processing and visualization of mass spectrometry based molecular profile data. It is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data

Metabolites Databases:

KEGG – An important database of metabolites and metabolic pathways, containing a large amount of metabolite, reaction, enzyme, and gene information for all species.

MetaCyc Database – curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes

Human Metabolome Database (HMDB) – freely available electronic database containing detailed information about small molecule metabolites found in the human body. Under the HMDB umbrella, other databases include more focused specific databases:

  • The Urine Metabolome Database – freely available electronic database containing detailed information about ~3100 small molecule metabolites found in human urine along with ~3900 concentration values.
  • The Serum Metabolome Database – freely available electronic database containing detailed information about 4651 small molecule metabolites found in human serum along with 10895 concentration values
  • The CSF Metabolome Database – freely available electronic database containing detailed information about 468 small molecule metabolites found in human CSF along with 1650 concentration values
  • The Saliva Metabolome Database – freely available electronic database containing detailed information about many small molecule metabolites found in human saliva and many concentration values
  • The Fecal Metabolome Database – freely available electronic database containing detailed information about many small molecule metabolites found in human feces and many concentration values
  • The Sweat Metabolome database – freely available electronic database containing detailed information about many small molecule metabolites found in human sweat and concentration values
  • FooDB – the world’s largest and most comprehensive resource on food constituents, chemistry and biology. It provides information on both macronutrients and micronutrients, including many of the constituents that give foods their flavor, color, taste, texture and aroma. It currently has data on over 26,500 food compounds and food associations
  • Yeast Metabolome Database (YMDB) – freely available electronic database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast)
  • E. Coli Metabolome Database(ECMDB) – freely available electronic database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655)
  • mzCloud – comprises curated databases of high and low resolution MSn spectra acquired under a number of experimental conditions which address the spectra reproducibility problem. It is a freely searchable collection of spectra, spectral trees, structures, fragments, precursor ions, chromatographic data and compound related reference

MassBank Database – an open source mass spectral library for the identification of small chemical molecules of metabolomics, exposomics and environmental relevance. The vast majority of MassBank contents now features high-resolution mass spectrometry data, although all kinds of mass spectral data are accepted. A range of search options are available for browsing the data. The MassBank library is based on text file records containing the record metadata and the mass spectral information in the MassBank record format. All data is archived on GitHub and Zenodo; the code is also on GitHub. The MassBank library can be downloaded in different formats such as text records, database files (sql) and MSP files.

Lipid Maps – LIPID Metabolites And Pathways Strategy (LIPID MAPS®) is a multi-institutional supported website and database that provides access to a large number of globally used lipidomics resources including the structure, spectrum and classification information of more than 40,000 kinds of lipids

Lipidblast Database – a computer-generated (in-silico) tandem mass spectral (MS/MS) database that can be used to annotate and identify hundreds of lipids in plants, bacteria, algae, animals, humans, viruses. LipidBlast library works with low-resolution and high-resolution instruments.

Vendor’s Software:

Compound Discoverer – Contains tutorial and updates about compound discoverer software. It also allows for submitting specific questions and request feature for upcoming versions.

TraceFinder – Contains tutorial and updates about TraceFinder software. It also allows for submitting specific questions and request feature for upcoming versions

Accessibility by WAH