Difference between revisions of "LipidXplorer Preface"
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| − | == | + | ==Aims and Scope== |
| − | + | In shotgun lipidomics lipids are extracted from cells, tissues or organisms and total extracts are directly infused into a tandem mass spectrometer (reviewed in [1]). Mass spectrometry characterizes lipid molecules in two major ways. First, in MS experiments it determines their intact masses. Second, in MS/MS experiments lipid precursors are dissociated into structure –specific fragments and individual molecular species can be recognized and quantified in total lipid extracts. | |
| − | total | ||
| − | |||
| − | |||
| − | + | Top-down lipidomics is a strategy that aims at the rapid quantitative characterization of global changes within the lipidome and is solely reliant on accurate masses of intact lipid precursors [2]. Bottom-up lipidomics quantifies individual molecular species by detecting characteristic structural fragment ions using tandem mass spectrometry [3]. | |
| − | |||
| − | |||
| − | + | LipidXplorer is a software that supports a variety of shotgun lipidomics experiments [4]. It is designed to support bottom-up and top-down shotgun lipidomics experimenters performed at all type of tandem mass spectrometers. Lipid identification does not rely on a database resource of reference or simulated mass spectra. | |
| − | |||
| − | + | ==Design and Operation Concept== | |
| − | |||
| − | + | LipidXplorer organizes MS and MS/MS spectra (all spectra acquired from all samples in the lipidomics experiments, including repeats) into a flat-file database termed MasterScan. Scans are merged and individual spectra aligned considering instrument specific peak attributes, such as mass resolution, mass accuracy, peak occupancy, among others. | |
| + | |||
| + | MasterScan is then interrogated by user-defined lipid class –specific and/or lipid species -specific queries written in a molecular fragmentation query language (MFQL). Identified and annotated lipid species, along with intensities of user-defined fragment or precursor ions, are reported. | ||
| − | + | Further details on the installation and all aspects of the lipid identification by LipidXplorer are provided in [4] and at this site. | |
| − | |||
| − | |||
| − | |||
| − | LipidX is written in Python 2.6. It uses wxPython 2.8 and Numpy 1.3.0 and | + | LipidX is written in Python 2.6. It also uses wxPython 2.8 and Numpy 1.3.0 or later versions; please see [4] for further details. |
| + | |||
| + | ==Disclaimer== | ||
| + | |||
| + | Despite a lot of effort has been put into the development and testing of each release of LipidXplorer, they might still contain some errors and bugs. Therefore we provide no warranty and assume no responsibility for any consequences caused by the program installation and use. Please use it on your own risk. | ||
==License== | ==License== | ||
| − | + | This program is a free software; you can redistribute it and/or modify it under | |
| − | |||
| − | This program is free software; you can redistribute it and/or modify it under | ||
the terms of the GNU General Public License as published by the Free Software | the terms of the GNU General Public License as published by the Free Software | ||
Foundation. See the file LICENSE.txt for details. | Foundation. See the file LICENSE.txt for details. | ||
| + | |||
| + | |||
| + | ==References== | ||
| + | |||
| + | [1] Han, X. and Gross, R.W. 2005. Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. Mass Spectrom Rev 24(3): 367-412. | ||
| + | |||
| + | [2] Schwudke, D., Hannich, J.T., Surendranath, V., Grimard, V., Moehring, T., Burton, L., Kurzchalia, T., and Shevchenko, A. 2007. Top-down lipidomic screens by multivariate analysis of high-resolution survey mass spectra. Anal Chem 79: 4083-4093. | ||
| + | |||
| + | [3] Schwudke, D., Oegema, J., Burton, L., Entchev, E., Hannich, J.T., Ejsing, C.S., Kurzchalia, T., and Shevchenko, A. 2006. Lipid profiling by multiple precursor and neutral loss scanning driven by the data-dependent acquisition. Anal Chem 78(2): 585-595. | ||
| + | |||
| + | [4] Herzog, R., Schwudke, D., Schuhmann, K., Sampaio, J.L., Bornstein, S.R., Schroeder, M., and Shevchenko, A. 2011. A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol 12(1): R8. | ||
Revision as of 00:19, 2 February 2011
Aims and Scope
In shotgun lipidomics lipids are extracted from cells, tissues or organisms and total extracts are directly infused into a tandem mass spectrometer (reviewed in [1]). Mass spectrometry characterizes lipid molecules in two major ways. First, in MS experiments it determines their intact masses. Second, in MS/MS experiments lipid precursors are dissociated into structure –specific fragments and individual molecular species can be recognized and quantified in total lipid extracts.
Top-down lipidomics is a strategy that aims at the rapid quantitative characterization of global changes within the lipidome and is solely reliant on accurate masses of intact lipid precursors [2]. Bottom-up lipidomics quantifies individual molecular species by detecting characteristic structural fragment ions using tandem mass spectrometry [3].
LipidXplorer is a software that supports a variety of shotgun lipidomics experiments [4]. It is designed to support bottom-up and top-down shotgun lipidomics experimenters performed at all type of tandem mass spectrometers. Lipid identification does not rely on a database resource of reference or simulated mass spectra.
Design and Operation Concept
LipidXplorer organizes MS and MS/MS spectra (all spectra acquired from all samples in the lipidomics experiments, including repeats) into a flat-file database termed MasterScan. Scans are merged and individual spectra aligned considering instrument specific peak attributes, such as mass resolution, mass accuracy, peak occupancy, among others.
MasterScan is then interrogated by user-defined lipid class –specific and/or lipid species -specific queries written in a molecular fragmentation query language (MFQL). Identified and annotated lipid species, along with intensities of user-defined fragment or precursor ions, are reported.
Further details on the installation and all aspects of the lipid identification by LipidXplorer are provided in [4] and at this site.
LipidX is written in Python 2.6. It also uses wxPython 2.8 and Numpy 1.3.0 or later versions; please see [4] for further details.
Disclaimer
Despite a lot of effort has been put into the development and testing of each release of LipidXplorer, they might still contain some errors and bugs. Therefore we provide no warranty and assume no responsibility for any consequences caused by the program installation and use. Please use it on your own risk.
License
This program is a free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. See the file LICENSE.txt for details.
References
[1] Han, X. and Gross, R.W. 2005. Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. Mass Spectrom Rev 24(3): 367-412.
[2] Schwudke, D., Hannich, J.T., Surendranath, V., Grimard, V., Moehring, T., Burton, L., Kurzchalia, T., and Shevchenko, A. 2007. Top-down lipidomic screens by multivariate analysis of high-resolution survey mass spectra. Anal Chem 79: 4083-4093.
[3] Schwudke, D., Oegema, J., Burton, L., Entchev, E., Hannich, J.T., Ejsing, C.S., Kurzchalia, T., and Shevchenko, A. 2006. Lipid profiling by multiple precursor and neutral loss scanning driven by the data-dependent acquisition. Anal Chem 78(2): 585-595.
[4] Herzog, R., Schwudke, D., Schuhmann, K., Sampaio, J.L., Bornstein, S.R., Schroeder, M., and Shevchenko, A. 2011. A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol 12(1): R8.
