TY - JOUR
T1 - Algorithms for automatic processing of data from mass spectrometric analyses of lipids
AU - Song, Haowei
AU - Ladenson, Jack
AU - Turk, John
N1 - Funding Information:
Work in the authors’ laboratories was supported by United States Public Health Service Grants R37-DK34388, P41-RR00954, P60-DK20579, and P30-DK56341. The authors thank Dr. Fong-Fu Hsu for many helpful discussions and Alan Bohrer for excellent technical assistance.
PY - 2009/9/15
Y1 - 2009/9/15
N2 - Lipidomics comprises large-scale studies of the structures, quantities, and functions of lipid molecular species. Recently developed mass spectrometric methods for lipid analyses, especially electrospray ionization (ESI) tandem mass spectrometry, permit identification and quantitation of an enormous variety of distinct lipid molecular species from small amounts of biological samples but generate a huge amount of experimental data within a brief interval. Processing such data sets so that comprehensible information is derived from them requires bioinformatics tools, and algorithms developed for proteomics and genomics have provided some strategies that can be directly adapted to lipidomics. The structural diversity and complexity of lipids, however, also requires the development and application of new algorithms and software tools that are specifically directed at processing data from lipid analyses. Several such tools are reviewed here, including LipidQA. This program employs searches of a fragment ion database constructed from acquired and theoretical spectra of a wide variety of lipid molecular species, and raw mass spectrometric data can be processed by the program to achieve identification and quantification of many distinct lipids in mixtures. Other approaches that are reviewed here include LIMSA (Lipid Mass Spectrum Analysis), SECD (Spectrum Extraction from Chromatographic Data), MPIS (Multiple Precursor Ion Scanning), FIDS (Fragment Ion Database Searching), LipidInspector, Lipid Profiler, FAAT (Fatty Acid Analysis Tool), and LIPID Arrays. Internet resources for lipid analyses are also summarized.
AB - Lipidomics comprises large-scale studies of the structures, quantities, and functions of lipid molecular species. Recently developed mass spectrometric methods for lipid analyses, especially electrospray ionization (ESI) tandem mass spectrometry, permit identification and quantitation of an enormous variety of distinct lipid molecular species from small amounts of biological samples but generate a huge amount of experimental data within a brief interval. Processing such data sets so that comprehensible information is derived from them requires bioinformatics tools, and algorithms developed for proteomics and genomics have provided some strategies that can be directly adapted to lipidomics. The structural diversity and complexity of lipids, however, also requires the development and application of new algorithms and software tools that are specifically directed at processing data from lipid analyses. Several such tools are reviewed here, including LipidQA. This program employs searches of a fragment ion database constructed from acquired and theoretical spectra of a wide variety of lipid molecular species, and raw mass spectrometric data can be processed by the program to achieve identification and quantification of many distinct lipids in mixtures. Other approaches that are reviewed here include LIMSA (Lipid Mass Spectrum Analysis), SECD (Spectrum Extraction from Chromatographic Data), MPIS (Multiple Precursor Ion Scanning), FIDS (Fragment Ion Database Searching), LipidInspector, Lipid Profiler, FAAT (Fatty Acid Analysis Tool), and LIPID Arrays. Internet resources for lipid analyses are also summarized.
KW - Algorithms and software tools
KW - Electrospray ionization (ESI)
KW - Lipidomics
KW - Tandem mass spectrometry
UR - http://www.scopus.com/inward/record.url?scp=67949103796&partnerID=8YFLogxK
U2 - 10.1016/j.jchromb.2008.12.043
DO - 10.1016/j.jchromb.2008.12.043
M3 - Review article
C2 - 19131280
AN - SCOPUS:67949103796
SN - 1570-0232
VL - 877
SP - 2847
EP - 2854
JO - Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences
JF - Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences
IS - 26
ER -