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| | =='''LipidXplorer Wiki'''== | | =='''LipidXplorer Wiki'''== |
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| − | <div style="width:49%; float:left; margin-top: 5px"> | + | <div style="width:100%; float:left; margin-top: 5px"> |
| | === Brought to you by === | | === Brought to you by === |
| | [[File:LIFS-signet-2017x03x13.jpg|228px|link=https://lifs.isas.de|LIFS Portal]] | | [[File:LIFS-signet-2017x03x13.jpg|228px|link=https://lifs.isas.de|LIFS Portal]] |
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| | Click on the link above | | Click on the link above |
| | for a quick overview and start to LipidXplorer | | for a quick overview and start to LipidXplorer |
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| − | === [[LipidXNews|News]] ===
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| − | ====2020-02-10 New LipidXplorer releases now tracked by Zenodo====
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| − | <p class="alert alert-info"><strong>Citing LipidXplorer</strong><br />
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| − | 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]
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| − | Please reference LipidXplorer in general by citing the following publications:<br />
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| − | <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 />
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| − | <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 />
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| − | ====2019-10-14 New release: LipidXplorer Version 1.2.8====
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| − | 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].
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| − | References:
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| − | # 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.
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| − | # Eggers, L.F. and D. Schwudke, Shotgun Lipidomics Approach for Clinical Samples. Methods Mol Biol, 2018. 1730: p. 163-174.
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| − | # Herzog, R., et al., LipidXplorer: a software for consensual cross-platform lipidomics. PLoS One, 2012. 7(1): p. e29851.
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| − | # 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.
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| − | # 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.
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| − | </div>
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| − | ====2019-02-12 LipidXplorer available as LIFS Web Application ====
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| − | <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>
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| − | ====2018-03-01 LipidXplorer Wiki now hosted by LIFS====
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| − | [[File:LIFS-signet-2017x03x13.jpg|228px|link=https://lifs.isas.de|LIFS Portal]]
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| − | </div>
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| − | <p>As of March 1st, 2018, the LipidXplorer Wiki has been relocated to the LIFS infrastructure.</p>
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| − | ====2016-05-09 New release: LipidXplorer Version 1.2.7====
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| − | 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.
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| | === [[LipidXplorer Documentation|LipidXplorer Documentation]] === | | === [[LipidXplorer Documentation|LipidXplorer Documentation]] === |
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| − | === [[MFQL library|MFQL library]] === | + | <!-- === [[MFQL library|MFQL library]] === --> |
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| | <!-- === [[FAQ|Frequently Asked Questions (FAQ)]] === --> | | <!-- === [[FAQ|Frequently Asked Questions (FAQ)]] === --> |
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| | ===Get LipidXplorer=== | | ===Get LipidXplorer=== |
| − | If you are on Windows you can try the [https://cld.isas.de/s/fDUKI4WJcdYpezQ Single file executable for Windows] | + | If you are on Windows you can try the [https://zenodo.org/records/15064195 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]
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| − | 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. | + | LipidXplorer is published under GPL and available here: [[https://github.com/lifs-tools/lipidxplorer LipidXplorer]]. Check out [[LipidXplorer Installation | the LipidXplorer installation instructions]] for help. |
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| | ===Citing LipidXplorer=== | | ===Citing LipidXplorer=== |
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| | ===Feature suggestions=== | | ===Feature suggestions=== |
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| − | 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: [[LipidXplorer wishlist| the LipidXplorer wishlist]]. | + | LipidXplorer will be further developed all the time. If you have suggestions for useful features, please write to the [[https://lifs-tools.org/support.html LIFS Contact Form]] and we will post them here. We also will post a status report on the suggested features: [[LipidXplorer wishlist| the LipidXplorer wishlist]]. |
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| − | ===[[Articles_Using_LipidXplorer | LipidXplorer MFQL Bibliography ]]===
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| − | [[LX Reference Yadav 2015 | 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'']]
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| − | [[LX Reference Khaliullina 2015 | Khaliullina H, Bilgin M, Sampaio JL, Shevchenko A, Eaton S:'''Endocannabinoids are conserved inhibitors of the Hedgehog pathway''' ''PNAS 2015 Feb 2'']]
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| − | [[LX Reference Hebbar 2014 | 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)'']]
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| − | [[LX Reference Papan 2014 | 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)'']]
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| − | [[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'']]
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| − | [[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'']]
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| | </div> | | </div> |
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| | ===Contact=== | | ===Contact=== |
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| − | For any '''questions''' and '''suggestions''' please put them on the [[http://groups.google.com/group/lipidxplorer-discussion-group LipidXplorer Google Group]] | + | For any '''questions''' and '''suggestions''' please put them on the [[https://lifs-tools.org/support.html LIFS Contact Form]] |
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| − | 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.
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| − | 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.
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| − | ===Known bugs===
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| − | Please check out the [[http://groups.google.com/group/lipidxplorer-discussion-group LipidXplorer Google Group]] to be up-to-date on found bugs.
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| − | ===Bug reports===
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| − | Please send Bug reports directly to mirandaa@mpi-cbg.de
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| − | ===Example spectra===
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| − | =====Example spectra for the LipidXplorer tutorial=====
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| − | * Spectra of E.coli acquired on the LTQ Orbitrap with different resolution settings:[[File:spectra_tutorial.zip]]
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| − | =====All spectra used in the LipidXplorer article=====
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| − | * 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]]
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| | </div> | | </div> |
| | </div> | | </div> |
