77
Table 4.5 Software tools for lipidomic data analysis
Software tools URL
Data type Details
ALEX
http://mslipidomics.info/contents/
MS/MS
A software-based platform for streamlined data processing,
management, and visualization of shotgun lipidomic data acquired using
high mass accuracy or high- resolution mass spectrometers
AMDMS-SL
https://pharmacometabolomics.duhs.duke.edu/
resources-tools/
sanfordburnham-medical-research-institute
MS/MS
This tool has been developed to identify and quantify individual lipid
species from the data obtained from the MDMS-SL approach
LIMSA
http://www.helsinki.fi/science/lipids/software.html MS/MS
It serves as an interface to process data from individual full MS and
tandem mass spectra. It searches and integrates peaks in a mass
spectrum, matches the peaks with a user- supplied list of expected lipids,
corrects for overlap in their isotopic patterns, and quantifies the
identified lipid species according to internal standards
LipidBlast
http://fiehnlab.ucdavis.edu/projects/LipidBlast
MS/MS
It is in silico tandem mass spectral library, maintained by Fiehn Lab
(University of California-Davis) and freely available for commercial and
noncommercial uses. It contains 212, 516 tandem mass spectra for 119,
200 different lipids in 26 lipid classes. It can be successfully applied to
analyze MS/MS data from over 40 different types of mass spectrometers
LipidomeDB
DCE
https://www.k-state.edu/lipid/analytical_laboratory/
analysis_components/lipidomedb_dce/index.html
MS/MS
A tool to process mass spectrometry data acquired after direct infusion
of a lipid- containing biological extract containing a cocktail of internal
standards into an electrospray source. It has been developed as a joint
project of the Kansas Lipidomics Research Center and the K-INBRE
Bioinformatics Core Facility
Lipid Data
Analyzer (LDA)
http://genome.tugraz.at/lda/lda_description.shtml
LC-MS
A tool for the quantitation of lipids in LC-MS data which is empowered
with a 3D algorithm that confines the peak borders in m/z and time
direction and the use of theoretical isotopic distribution of an analyte as
selection/exclusion criterion. It also provides standardization, a
statistical module for results analysis, a batch mode for unattended
analysis of several runs, and a 3D viewer for the manual verification
(continued)
4 Seaweed Lipidomics in the Era of ‘Omics’ Biology: A Contemporary Perspective
Table 4.5 Software tools for lipidomic data analysis
Software tools URL
Data type Details
ALEX
http://mslipidomics.info/contents/
MS/MS
A software-based platform for streamlined data processing,
management, and visualization of shotgun lipidomic data acquired using
high mass accuracy or high- resolution mass spectrometers
AMDMS-SL
https://pharmacometabolomics.duhs.duke.edu/
resources-tools/
sanfordburnham-medical-research-institute
MS/MS
This tool has been developed to identify and quantify individual lipid
species from the data obtained from the MDMS-SL approach
LIMSA
http://www.helsinki.fi/science/lipids/software.html MS/MS
It serves as an interface to process data from individual full MS and
tandem mass spectra. It searches and integrates peaks in a mass
spectrum, matches the peaks with a user- supplied list of expected lipids,
corrects for overlap in their isotopic patterns, and quantifies the
identified lipid species according to internal standards
LipidBlast
http://fiehnlab.ucdavis.edu/projects/LipidBlast
MS/MS
It is in silico tandem mass spectral library, maintained by Fiehn Lab
(University of California-Davis) and freely available for commercial and
noncommercial uses. It contains 212, 516 tandem mass spectra for 119,
200 different lipids in 26 lipid classes. It can be successfully applied to
analyze MS/MS data from over 40 different types of mass spectrometers
LipidomeDB
DCE
https://www.k-state.edu/lipid/analytical_laboratory/
analysis_components/lipidomedb_dce/index.html
MS/MS
A tool to process mass spectrometry data acquired after direct infusion
of a lipid- containing biological extract containing a cocktail of internal
standards into an electrospray source. It has been developed as a joint
project of the Kansas Lipidomics Research Center and the K-INBRE
Bioinformatics Core Facility
Lipid Data
Analyzer (LDA)
http://genome.tugraz.at/lda/lda_description.shtml
LC-MS
A tool for the quantitation of lipids in LC-MS data which is empowered
with a 3D algorithm that confines the peak borders in m/z and time
direction and the use of theoretical isotopic distribution of an analyte as
selection/exclusion criterion. It also provides standardization, a
statistical module for results analysis, a batch mode for unattended
analysis of several runs, and a 3D viewer for the manual verification
(continued)
4 Seaweed Lipidomics in the Era of ‘Omics’ Biology: A Contemporary Perspective