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Latest revision as of 16:27, 22 July 2020

LipidXplorer Wiki

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Quick Start

Click on the link above for a quick overview and start to LipidXplorer

Citing LipidXplorer
If you are using a particular version of LipidXplorer, from version 1.2.8 onwards, each release now has a citable DOI for LipidXplorer@Zenodo
Please reference LipidXplorer in general by citing the following publications:
Herzog R, Schuhmann K, Schwudke D, Sampaio JL, Bornstein SR, Schroeder M, et al. (2012) LipidXplorer: A Software for Consensual Cross-Platform Lipidomics. PLoS ONE 7(1): e29851. doi:19.1371/journal.pone
Herzog R, Schwudke D, Schuhmann K, Sampaio JL, Bornstein SR, Schroeder M, Shevchenko A (2011) A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol. 2011;12(1):R8. doi:10.1186/gb-2011-12-1-r8

2019-10-14 New release: LipidXplorer Version 1.2.8

This release is focused on improving the import module and implementing the recently introduced filtering approach based on counting reoccurrences of peaks in MS-scans and MS/MS-scans conceptually following Schuhmann et al. [1]. All other general functionalities of the former releases should not be affected [2-5]. Further changes were made for better documentation and simpler user guidance. Some experimental and/or unused options were deactivated (grouping samples, heuristic hierarchical alignment, dta/csv import). Details are available in the official release notes.

References:

Schuhmann, K., et al., Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics. Anal Chem, 2017. 89(13): p. 7046-7052.
Eggers, L.F. and D. Schwudke, Shotgun Lipidomics Approach for Clinical Samples. Methods Mol Biol, 2018. 1730: p. 163-174.
Herzog, R., et al., LipidXplorer: a software for consensual cross-platform lipidomics. PLoS One, 2012. 7(1): p. e29851.
Herzog, R., et al., A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol, 2011. 12(1): p. R8.
Herzog, R., D. Schwudke, and A. Shevchenko, LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms. Curr Protoc Bioinformatics, 2013. 43: p. 14 12 1-30.

2019-02-12 LipidXplorer available as LIFS Web Application

A web-based version of LipidXplorer is available via the LIFS web application portal. Please note that the application is not yet publicly available. If you want to test it, please request access.

2018-03-01 LipidXplorer Wiki now hosted by LIFS

As of March 1st, 2018, the LipidXplorer Wiki has been relocated to the LIFS infrastructure.

2016-05-09 New release: LipidXplorer Version 1.2.7

The new version Single file installer LipidXplorer v1.2.8 source code can now be downloaded. It includes some minor bug fixes and some speed improvements for MFQL lipid identification.

LipidXplorer Documentation

MFQL library

Troubleshooting

LXMerge: A tool for merging multiple results

Get LipidXplorer

If you are on Windows you can try the Single file executable for Windows If you are on Linux you can try the Single file executable for Linux

LipidXplorer is published under GPL and available here: [LipidXplorer GitLab@ISAS]. Check out the LipidXplorer installation instructions for help.

Citing LipidXplorer

If you use LipidXplorer, please cite the original LipidXplorer publications:

Herzog R, Schuhmann K, Schwudke D, Sampaio JL, Bornstein SR, Schroeder M, et al. (2012) LipidXplorer: A Software for Consensual Cross-Platform Lipidomics. PLoS ONE 7(1): e29851. https://doi.org/10.1371/journal.pone.0029851

Herzog R, Schwudke D, Schuhmann K, Sampaio JL, Bornstein SR, Schroeder M, Shevchenko A (2011) A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol. 2011;12(1):R8. https://doi.org/10.1186/gb-2011-12-1-r8

Additionally, if you are using a particular version of LipidXplorer, from version 1.2.8 onwards, each release has a citable DOI for LipidXplorer@Zenodo.

Feature suggestions

LipidXplorer will be further developed all the time. If you have suggestions for useful features, please write to the LipidXplorer mailing list and we will post them here. We also will post a status report on the suggested features: the LipidXplorer wishlist.

LipidXplorer MFQL Bibliography

Yadav S, Garner K, Georgiev P, Li M, Gomez-Espinosa E, Panda A, Mathre S, Okkenhaug H, Cockcroft S and Raghu P: RDGBα, a PI-PA transfer protein regulates G-protein coupled PtdIns(4,5)P2 signalling during Drosophila phototransduction JCS 2015 July

Khaliullina H, Bilgin M, Sampaio JL, Shevchenko A, Eaton S:Endocannabinoids are conserved inhibitors of the Hedgehog pathway PNAS 2015 Feb 2

Hebbar S, Schulz W D, Sauer U and Schwudke D :Laser Capture Microdissection Coupled with On-Column Extraction LC-MSn Enables Lipidomics of Fluorescently Labeled Drosophila Neurons Anal. Chem. 2014 May 12, 86(11)

Papan C, Penkov S, Herzog R, Thiele C, Kurzchalia T, Shevchenko A:Systematic screening for novel lipids by shotgun lipidomics. Anal. Chem. 2014 Jan 28, 86(5)

Gaessler J, Bornstein T D, Goel D, Bhalla V P, Lohmann T, Wolf T, Koch M, Qin Y, Licinio J, Wong M-L, Chavakis T, Xu A, Shevchenko A, Schuhmann K, Schwarz P E H, Patel A, Bornstein S R:Lipidomic profiling before and after Roux-en-Y gastric bypass in obese patients with diabetes The Pharmacogenomics Journal 2013 Dec 24

Herzog R, Schwudke D, Shevchenko A:LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms Current Protocols in Bioinformatics 2013 Oct 15

Contact

For any questions and suggestions please put them on the [LipidXplorer Google Group]

If you do not want to join google, please write us (mirandaa@mpi-cbg.de or herzog@mpi-cbg.de) an email and I'll add you to the group.

If you want to contribute to the Wiki please write to mirandaa@mpi-cbg.de or herzog@mpi-cbg.de or also to the google group.

Known bugs

Please check out the [LipidXplorer Google Group] to be up-to-date on found bugs.

Bug reports

Please send Bug reports directly to mirandaa@mpi-cbg.de

Example spectra

Example spectra for the LipidXplorer tutorial

Spectra of E.coli acquired on the LTQ Orbitrap with different resolution settings:File:Spectra tutorial.zip

All spectra used in the LipidXplorer article

Spectra of E.coli and bovine heart acquired on LTQ Orbitrap XL, LTQ Orbitrap Velos and ABI QStar pulsar (in DDA and MPIS mode):File:Spectra article.zip

@@ Line 18: / Line 18: @@
 <div id="grey">
+=== [[Quick Start]] ===
+Click on the link above
+for a quick overview and start to LipidXplorer
 === [[LipidXNews|News]] ===
+====2020-02-10 New LipidXplorer releases now tracked by Zenodo====
+<p class="alert alert-info"><strong>Citing LipidXplorer</strong><br />
+If you are using a particular version of LipidXplorer, from version 1.2.8 onwards, each release now has a citable [https://doi.org/10.5281/zenodo.3483976 DOI for LipidXplorer@Zenodo]
+<br />
+Please reference LipidXplorer in general by citing the following publications:<br />
+<em>Herzog R, Schuhmann K, Schwudke D, Sampaio JL, Bornstein SR, Schroeder M, et al. (2012) LipidXplorer: A Software for Consensual Cross-Platform Lipidomics. PLoS ONE 7(1): e29851.</em> [https://doi.org/10.1371/journal.pone.0029851 doi:19.1371/journal.pone]<br />
+<em>Herzog R, Schwudke D, Schuhmann K, Sampaio JL, Bornstein SR, Schroeder M, Shevchenko A (2011) A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol. 2011;12(1):R8.</em> [https://doi.org/10.1186/gb-2011-12-1-r8 doi:10.1186/gb-2011-12-1-r8]<br />
+<br />
+</p>
 <div id="small">
+====2019-10-14 New release: LipidXplorer Version 1.2.8====
+This release is focused on improving the import module and implementing the recently introduced filtering approach based on counting reoccurrences of peaks in MS-scans and MS/MS-scans conceptually following Schuhmann et al. [1]. All other general functionalities of the former releases should not be affected [2-5]. Further changes were made for better documentation and simpler user guidance. Some experimental and/or unused options were deactivated (grouping samples, heuristic hierarchical alignment, dta/csv import). Details are available [https://lifs.isas.de/tools/68-lipidxplorer-1-2-8-release.html in the official release notes].
+References:
+# Schuhmann, K., et al., Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics. Anal Chem, 2017. 89(13): p. 7046-7052.
+# Eggers, L.F. and D. Schwudke, Shotgun Lipidomics Approach for Clinical Samples. Methods Mol Biol, 2018. 1730: p. 163-174.
+# Herzog, R., et al., LipidXplorer: a software for consensual cross-platform lipidomics. PLoS One, 2012. 7(1): p. e29851.
+# Herzog, R., et al., A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol, 2011. 12(1): p. R8.
+# Herzog, R., D. Schwudke, and A. Shevchenko, LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms. Curr Protoc Bioinformatics, 2013. 43: p. 14 12 1-30.
+</div>
+<div id="small">
 ====2019-02-12 LipidXplorer available as LIFS Web Application ====
-<p>A web-based version of LipidXplorer is available via the [https://apps.lifs.isas.de/lipidxplorer| LIFS web application portal]. Please note that the application is not yet publically available. If you want to test it, please [https://lifs.isas.de/support.html| request access].</p>
+<p>A web-based version of LipidXplorer is available via the [https://apps.lifs.isas.de/lipidxplorer LIFS web application portal]. Please note that the application is not yet publicly available. If you want to test it, please [https://lifs.isas.de/support.html request access].</p>
 </div>
@@ Line 35: / Line 68: @@
 ====2016-05-09 New release: LipidXplorer Version 1.2.7====
-The new version [http://sourceforge.net/projects/lipidxplorer/files/LipidXplorer-1.2.7.zip/download LipidXplorer v1.2.7] can now be downloaded. It includes some minor bug fixes and some speed improvements for MFQL lipid identification.
+The new version [https://cloud.mpi-cbg.de/index.php/s/Z5slSEynLpiO8LC Single file installer][https://gitlab.isas.de/lifs-public/lipidxplorer LipidXplorer v1.2.8 source code] can now be downloaded. It includes some minor bug fixes and some speed improvements for MFQL lipid identification.
@@ Line 58: / Line 91: @@
 ===Get LipidXplorer===
-If you are on Windows you can try the [https://git.mpi-cbg.de/labShevchenko/LipidXplorer/wikis/Single_file_installer Single file installer for Windows]
+If you are on Windows you can try the [https://cld.isas.de/s/fDUKI4WJcdYpezQ Single file executable for Windows]
+If you are on Linux you can try the [https://cld.isas.de/s/V8CtK3lfT21Qub0 Single file executable for Linux]
+LipidXplorer is published under GPL and available here: [[https://gitlab.isas.de/lifs-public/lipidxplorer LipidXplorer GitLab@ISAS]]. Check out [[LipidXplorer Installation | the LipidXplorer installation instructions]] for help.
+===Citing LipidXplorer===
+If you use LipidXplorer, please cite the original LipidXplorer publications:
-LipidXplorer is published under GPL and available here: [[http://sourceforge.net/projects/lipidxplorer/files/ LipidXplorer on Sourceforge]]. Check out [[LipidXplorer Installation | the LipidXplorer installation instructions]] for help.
+Herzog R, Schuhmann K, Schwudke D, Sampaio JL, Bornstein SR, Schroeder M, ''et al.'' (2012) '''LipidXplorer: A Software for Consensual Cross-Platform Lipidomics'''. PLoS ONE 7(1): e29851. https://doi.org/10.1371/journal.pone.0029851
+Herzog R, Schwudke D, Schuhmann K, Sampaio JL, Bornstein SR, Schroeder M, Shevchenko A (2011) '''A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language'''. Genome Biol. 2011;12(1):R8. https://doi.org/10.1186/gb-2011-12-1-r8
+Additionally, if you are using a particular version of LipidXplorer, from version 1.2.8 onwards, each release has a citable DOI for [https://zenodo.org/search?page=1&size=20&q=LipidXplorer LipidXplorer@Zenodo].
 </div>
@@ Line 94: / Line 135: @@
 [[LX Reference Graessler 2013 | Gaessler J, Bornstein T D, Goel D, Bhalla V P, Lohmann T, Wolf T, Koch M, Qin Y, Licinio J, Wong M-L, Chavakis T, Xu A, Shevchenko A, Schuhmann K, Schwarz P E H, Patel A, Bornstein S R:'''Lipidomic profiling before and after Roux-en-Y gastric bypass in obese patients with diabetes''' ''The Pharmacogenomics Journal 2013 Dec 24'']]
-[[LX Reference Herzog 2013 | Herzog R, Schwudke D, Shevchenko A:'''UNIT 14.12 LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms''' ''Current Protocols in Bioinformatics 2013 Oct 15'']]
+[[LX Reference Herzog 2013 | Herzog R, Schwudke D, Shevchenko A:'''LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms''' ''Current Protocols in Bioinformatics 2013 Oct 15'']]
 </div>