A collection of awesome lipidomics tools, libraries, databases and resources.
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| Name | Workflow$ | Sample Handling | MS* | Identification# | Quantification | Input | Output | Last Release | Version | OpenSource | License | Programming Language | PMID | URL | Remarks |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ALEX & ALEX 123 | U | C, I, DI | MS1, MS2, MS3 | Manual | no | manual input of parameters | HTML | 2017 | NA | no | NA | NA (9) | 29161304 | https://pubmed.ncbi.nlm.nih.gov/29161304 | (9) Software is provided as a web application without further information. |
| Greazy (5) | U | C, DI | MS1, MS2 | Fragment / Spectral library + score | no | vendor, mzML | mzTab (via LipidLama) | 2022 | 3.0.22034 | yes | Apache v2 | C# | 27186799 | https://pubmed.ncbi.nlm.nih.gov/27186799 | (6) Supports phospholipids only. |
| LDA2 | U | C | MS1, MS2 | Rule based | yes | mzML, TXT | XLSX, mzTab-M | 2021 | 2.8.1 | yes | GPL v3 | Java | 29058722 | https://pubmed.ncbi.nlm.nih.gov/29058722 | |
| LIMSA | T | C, DI | MS1, MS2 | Compound / Fragment library | yes | NetCDF, XLSX, CSV, HTML | NA | 2006 | NA (7) | NA (7) | GPL v3 | C++, VBA, Excel | 17165823 | https://pubmed.ncbi.nlm.nih.gov/17165823 | (7) The software is no longer available. |
| Lipid-Pro | U | C | MSE / DIA | Compound / Fragment library | yes | CSV | XLSX, TXT | 2015 | 1.0.0 | no | Proprietary | C# | 25433698 | https://pubmed.ncbi.nlm.nih.gov/25433698 | |
| LipidBlast | U | C | MS1, MS2 | Spectral library + score | no | MSP, MGF, XLSX | MGF, XLSX | 2014 | 3 | yes | CC-BY 4 | VBA, Excel | 25340521 | https://pubmed.ncbi.nlm.nih.gov/25340521 | |
| LipidCreator & Skyline | T + U | C | MS1, MS2, MSE / DIA | Fragment / Spectral Library + score (1) | yes (1) | vendor, mzML (MS1 + MS2) | XLSX, CSV, BLIB | 2021 | 1.2.1.787 | yes | MIT | C# | 32345972 | https://pubmed.ncbi.nlm.nih.gov/32345972 | (1) Identification and quantification use other tools methods. |
| LipiDex | U | C | MS1, MS2 | Spectral library + rule based | yes | MGF, mzXML, CSV | CSV | 2018 | 1.1 | yes | MIT | Java | 30756325 | https://pubmed.ncbi.nlm.nih.gov/30756325 | |
| LipidFinder | U | C | MS1 | Rule based, LMSD | no | CSV, JSON (2) | PDF, XLSX | 2021 | v2.0.2 | yes | MIT | Python | 33027502 | https://pubmed.ncbi.nlm.nih.gov/33027502 | (2) XCMS input recommended, LIPID MAPS class assignment of suspect ions. |
| LipidHunter (5) | U | C, DI | MS1, MS2 | Rule based | yes | mzML, XLSX, TXT | XLSX, HTML, TXT | 2020 | RC3 | yes | GPL v2, Proprietary | Python | 28753264 | https://pubmed.ncbi.nlm.nih.gov/28753264 | (6) Supports phospholipids only. |
| LipidIMMS | U | C, IM | MS1+CCS, MS2 | CCS library + Spectral library + score | no | MSP, MGF | CSV, HTML | 2020 | 1.20 | no | NA | NA (9) | 31729667 | https://pubmed.ncbi.nlm.nih.gov/31729667 | (9) Software is provided as a web application without further information. |
| LipidMatch | U | C, I, DI | MS1, MS2, MSE / DIA | Compound / Fragment library + rule based | yes | CSV, MS2 (ProteoWizard) | CSV | 2020 | 3.0 (8) | yes | CC BY 4.0 | R | 28693421 | https://pubmed.ncbi.nlm.nih.gov/28693421 | (8) After release 3.0, LipidMatch is available as LipidMatch Flow (latest version 3.5, but without source code). |
| LipidMiner | U | C | MS1, MS2 | Compound / Fragment library + rule based | yes | raw | XLSX, CSV | 2014 | NA | no | NA | C#, Python | 24623704 | https://pubmed.ncbi.nlm.nih.gov/24623704 | |
| LipidMS | U | C | MS1, MS2, MSE / DIA | Compound / Fragment library + rule based | yes | mzXML, CSV | CSV | 2022 | 3.0.3 | yes | GPL v3 | R | 30500173 | https://pubmed.ncbi.nlm.nih.gov/30500173 | |
| LipidomeDB | T | DI | MS1, MS2 | m/z library + Transitions + rule based | yes | XLSX | XLSX, HTML | 2019 | NA | no | NA | Java | 30575037 | https://pubmed.ncbi.nlm.nih.gov/30575037 | |
| LipidPioneer | T + U | C | MS1, MS2 | Compound / m/z Library (1) | yes (1) | XLSX | XLSX | 2017 | 1.0 | yes (4) | NA | VBA, Excel | 33119270 | https://pubmed.ncbi.nlm.nih.gov/33119270 | (1) Identification and quantification use other tools' methods. (4) The source code is provided for download, but no code license is defined. |
| LipidQA | T + U | DI | MS1, MS2 | Spectral library + score | yes | vendor (Thermo, Waters) | CSV | 2007 | NA (7) | NA (7) | NA | Visual C++ | 17720531 | https://pubmed.ncbi.nlm.nih.gov/17720531 | (7) The software is no longer available. |
| LipidQuant | T | C (5) | MS1 | m/z library + rule based | yes | TXT | XLSX | 2021 | 1.0 | yes | CC-BY 4 | VBA, Excel | 34498026 | https://pubmed.ncbi.nlm.nih.gov/34498026 | (5) Lipid class separation chromatography, e.g. HILIC, Supercritical Fluid Chromatography. |
| LipidXplorer | U | DI | MS1, MS2, MS3 | Rule based | no | mzML, mzXML (MS1 + MS2) | CSV, HTML | 2019 | 1.2.8.1 | yes | GPL v2 | Python | 26270171 | https://pubmed.ncbi.nlm.nih.gov/26270171 | |
| LipoStar | T + U | C, IM | MS1, MS2, MSE / DIA | Compound / Fragment library + rule based validation | yes | vendor | CSV | 2022 | 2.0.2 | no | Proprietary | C# | 28471643 | https://pubmed.ncbi.nlm.nih.gov/28471643 | |
| LipoStarMSI | T + U | DI, I | MS1, MS2 | Spectral library + rule based | yes | vendor (Bruker, Waters), imzML | CSV | 2020 | NA | no | Proprietary | C# | 32881505 | https://pubmed.ncbi.nlm.nih.gov/32881505 | |
| LiPydomics | U | C, IM | MS1 | CCS Library + m/z library + HILIC RT library + rule based | yes | CSV | XLSX | 2021 | 1.6.8 | yes | MIT | Python | 33119270 | https://pubmed.ncbi.nlm.nih.gov/33119270 | |
| LIQUID | U | C | MS1, MS2 | Spectral library + rule based | yes | RAW, mzML | TSV, mzTab, MSP | 2021 | 07.05.7860 | yes | Apache v2 | C# | 28158427 | https://pubmed.ncbi.nlm.nih.gov/28158427 | |
| LOBSTAHS | U | C | MS1 | Compound / m/z library + rule based | yes | mzML, mzXML, mzData, CSV | XLSX, CSV | 2021 | 1.20.0 | yes | GPL v3 | R | 27322848 | https://pubmed.ncbi.nlm.nih.gov/27322848 | |
| LPPTiger (3) | U | C | MS1, MS2 | Spectral library + score | yes | mzML, XLSX, TXT, MSP | XLSX, HTML | 2021 | v1.0 | yes | GPL v2, Proprietary | Python | 29123162 | https://pubmed.ncbi.nlm.nih.gov/29123162 | (3) Supports oxidized phospholipids only. |
| massPix | U | I | MS1 | m/z library + rule based | no | imzML | CSV | 2017 | 1.2 | yes | NA | R | 28989334 | https://pubmed.ncbi.nlm.nih.gov/28989334 | |
| MS-DIAL 4 | U | C, CE, IM | MS1, MS2, MSE / DIA | Spectral library + rule based | yes | vendor, mzML | CSV, mzTab-M, XLSX | 2022 | 4.80 | yes | GPL v3 | C# | 32541957 | https://pubmed.ncbi.nlm.nih.gov/32541957 | |
| MZmine 2 | U | C | MS1, MS2 | Spectral library + rule based | yes | vendor, mzML, mzXML, mzData, CSV, mzTab, XML | CSV, mzTab, XML | 2019 | 2.53 | yes | GPL v2 | Java | 29575335 | https://pubmed.ncbi.nlm.nih.gov/29575335 | |
| SmartPeak | T + U | C | MS1, MS2 | Transitions + rule based | yes | mzML, CSV | mzTab, XML, CSV | 2022 | v1.20.0 | yes | MIT | C++, Python | 33269929 | https://pubmed.ncbi.nlm.nih.gov/33269929 | |
| Smfinder | T + U | C | MS1, MS2 | Spectral library + score | yes | mzML, mzXML | XLSX, TXT | 2020 | 1.0 | yes (4) | NA | Python, R, C++ | 32501676 | https://pubmed.ncbi.nlm.nih.gov/32501676 | (4) The source code is provided for download, but no code license is defined. |
| XCMS | U | C | MS1, MS2 | Spectral library + score | yes | mzML, mzXML, netCDF | CSV | 2021 | 3.16.1 | yes | GPL v2 | R, C | 26673825 | https://pubmed.ncbi.nlm.nih.gov/26673825 |
Table 1: Overview of software for lipid identification from mass spectrometry. $: targeted includes Selected Ion and fragment monitoring (MRM), untargeted includes DDA and DIA approaches. *: Only the most important ones relevant to this review. All tools use some form of configuration file format, e.g. TXT or other formats for libraries or fragmentation rules. Workflow assignment designates the primary workflow a tool was designed for and stated by the authors, others may be available. We use direct infusion as a more generic synonym for what is usually referred to as ‘shotgun lipidomics’. #: rule based validation often includes spectral scores, ratios and thresholds, scores denote spectral similarity functions like the commonly used dot product / cosine variants. Abbreviations used in table: T: Targeted, U: Untargeted, C: Chromatography, CE: Capillary Electrophoresis, IM: Ion Mobility, DI: Direct Infusion, I: Imaging. Remarks: (1) Identification and quantification use other tools methods. (2) XCMS input recommended, LIPID MAPS class assignment of suspect ions. (3) Supports oxidized phospholipids only. (4) The source code is provided for download, but no code license is defined. (5) Lipid class separation chromatography, e.g. HILIC, Supercritical Fluid Chromatography. (6) Supports phospholipids only. (7) The software is no longer available. (8) After release 3.0, LipidMatch is available as LipidMatch Flow (latest version 3.5, but without source code). (9) Software is provided as a web application without further information.
| Name | Classification | Type | OpenSource | License | Programming Language | Last Release | Version | PMID | URL | Remarks |
|---|---|---|---|---|---|---|---|---|---|---|
| BioPAN | Ontology, Enrichment, Pathway Analysis | Web application | no | GPL v3 | PHP, R, HTML, JavaScript | 2020 | NA | 33564392 | https://pubmed.ncbi.nlm.nih.gov/33564392 | |
| Goslin | Post Processing | Web application, Library | yes | MIT, Apache v2 | C++, C#, Java, Python, R | 2022 | 2.0 | 32589019 | https://pubmed.ncbi.nlm.nih.gov/32589019 | (1) From molecular formulas, (2) Figshare id |
| Kendrick mass-defect plots | Visualization | Library (8) | yes | GPL v2 | Java | 2019 (9) | 2.53 | 29575335 | https://pubmed.ncbi.nlm.nih.gov/29575335 | (3) based on lipid structural features |
| LICAR | Post Processing | Web application | yes | MIT | R | 2021 | 1.0 | 33535740 | https://doi.org/10.1101/2020.04.09.033894 | |
| LION/web | Ontology, Enrichment | Web application | yes | GPL v3 | R | 2020 | NA | 31141612 | https://pubmed.ncbi.nlm.nih.gov/31141612 | |
| Lipid Classifier | Ontology, Classification (3) | Library | yes | A-GPL v3 | Ruby | 2014 | 0.0.0.1 | 25359887 | https://pubmed.ncbi.nlm.nih.gov/25359887 | (4) Library Rodin is used by the web application |
| Lipid Mini-On | Ontology, Enrichment | Web application, Library (4) | yes | BSD 2-Clause | R | 2019 | 0.1.43 | 30977807 | https://pubmed.ncbi.nlm.nih.gov/30977807 | |
| LipiDisease | Ontology, Enrichment | Web application | no | NA | R | 2021 | NA | 34358314 | https://pubmed.ncbi.nlm.nih.gov/34358314 | |
| LipidLynxX | Post Processing | Web application, Library | yes | GPL v3 | Python | 2020 | 0.9.24 | - | https://doi.org/10.1101/2020.04.09.033894 | |
| lipidr | Statistical Analysis, Visualization | Library | yes | MIT | R | 2021 | 2.8.1 (5) | 32168452 | https://pubmed.ncbi.nlm.nih.gov/32168452 | |
| LipidSuite | Statistical Analysis, Visualization | Web application | no | NA | R | 2021 | 1 | 33950258 | https://pubmed.ncbi.nlm.nih.gov/33950258 | |
| liputils | Post Processing | Library | yes | GPL v3 | Python | 2021 | 0.16.2 | 32770020 | https://pubmed.ncbi.nlm.nih.gov/32770020 | (5) Part of Bioconductor release 3.14 |
| LUX Score | Statistical Analysis, Visualization | Web application, application | yes | Apache v2 | Perl, R, Python | 2018 | 1.0.1 | 26393792 | https://pubmed.ncbi.nlm.nih.gov/26393792 | |
| MetaboAnalyst | Statistical Analysis, Visualization | Web application, Library | no (6) | GPL v2 | Java, R (7) | 2021 | 5.0 | 34019663 | https://pubmed.ncbi.nlm.nih.gov/34019663 | (6) Only the R package is OpenSource, (7) R package MetaboAnalystR 3.2 (2021) |
| RefMet | Post Processing | Web application | no | NA | PHP, R | 2021 | NA | 33199890 | https://pubmed.ncbi.nlm.nih.gov/33199890 | (8) Part of MZmine 2, (9) MZmine 3 release is planned for 2022 |
| SMIRFE | Ontology, Classification (1) | Library | yes | NA | Python | 2020 | 187eb261983b6d0aca1c (2) | 32214009 | https://pubmed.ncbi.nlm.nih.gov/32214009 |
Table 2. Libraries and web applications for Pathway analysis, ontology mapping / classification, enrichment analysis, post-processing, visualization and statistical analysis. Remarks: (1) From molecular formulas. (2) Figshare id. (3) Based on lipid structural features. (4) Library Rodin is used by the web application. (5) Part of Bioconductor release 3.14. (6) Only the R package is OpenSource. (7) R package MetaboAnalystR 3.2 (2021). (8) Part of MZmine 2. (9) MZmine 3 release is planned for 2022.
| Name | Classification | Main Purpose | Lipid specific | Lipid Structures | Structural levels | Ontology | Spectral Data | Biochemical Reaction Data | Curation | PMID | URL | Remarks | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CCS-Compendium | Database | Compendium of experimentally acquired Collisional Cross Section (Ion Mobility) data from molecular standards acquired on drift tube instruments | yes | yes | yes (1) | ClassyFire/ChemOnt | no | no | manual | 30816114 | https://pubmed.ncbi.nlm.nih.gov/30816114 | (1) kingdom, superclass, class, subclass | ||||||
| GNPS | Database | Knowledge base for raw, processed or annotated fragmentation mass spectrometry data | no | yes | no | - | yes (2) | yes (3) | no (4) | 27504778 | https://pubmed.ncbi.nlm.nih.gov/27504778 | (2) internal and through MassIVE, (3) via integration with multiple tools, (4) via MassIVE and other public repositories | ||||||
| HMDB | Database | Curated database of small molecule metabolites found in the human body | no | yes | yes (5) | ClassyFire/ChemOnt | yes (6) | yes | manual | 29140435 | https://pubmed.ncbi.nlm.nih.gov/29140435 | (5) via search, (6) local and linked via SPLASH to MONA, MassBank | ||||||
| LimeMap | Resource | Curated CellDesigner XML and Vanted GML graph of lipid mediator pathways | yes | no | no (15) | - | no | yes (16) | manual | 33504811 | https://pubmed.ncbi.nlm.nih.gov/33504811 | (16) metabolic pathways of lipid mediators | ||||||
| LIPID MAPS | Database | Curated portal for LIPID MAPS lipid classification, experimentally determined structures, in-silico combinatorial structures and other lipid resources | yes | yes | yes (7) | LIPID MAPS (8) | yes (9) | yes | manual | 17098933 | https://pubmed.ncbi.nlm.nih.gov/17098933 | (7) via search and shorthand abbreviation, (8) Original and Liebisch 2020, (9) via Metabolomics Workbench | ||||||
| LipidHome | Database | In-silico generated theoretical lipid structures | yes | yes (10) | no | Liebisch 2013 | no | no | manual | 23667450 | https://pubmed.ncbi.nlm.nih.gov/23667450 | (10) GP and GL only | ||||||
| LipidWeb | Resource | Literature review and biochemistry of lipids | yes | yes (17) | no | - | yes (17) | yes (17) | manual | - | https://www.lipidmaps.org/resources/lipidweb/index.php?page=index.html | (17) not necessarily machine readable | ||||||
| MassBank | Repository | Curated database of mass spectrometry reference spectra | no | no | no | - | yes | no | manual (11) | 20623627 | https://pubmed.ncbi.nlm.nih.gov/20623627 | (11) based on Mass Bank submission format | ||||||
| MetaboLights | Repository | Repository for metabolomics experiments (MS and NMR) and derived information | no | yes | no | ChEBI | yes (12) | no | manual (13) | 31691833 | https://pubmed.ncbi.nlm.nih.gov/31691833 | (12) via reference to spectral data, (13) based on submission format ISA-Tab | ||||||
| Metabolomics Workbench | Repository | Repository metabolomics data and metadata | no | yes | yes | RefMet | yes | no | manual (14) | 26467476 | https://pubmed.ncbi.nlm.nih.gov/26467476 | (14) based on submission format mwTab | ||||||
| Metabolonote | Repository | Wiki-based repository for metabolomics metadata | no | no | no | - | yes (12) | no | manual | 25905099 | https://pubmed.ncbi.nlm.nih.gov/25905099 | |||||||
| MetabolomXchange | Repository | Aggregator of metabolomics metadata from MetaboLights, Metabolomics Workbench, Metabolonote and Metabolomic Repository Bordeaux | no | no | no | - | no | no | no | 28092796 | https://pubmed.ncbi.nlm.nih.gov/28092796 | |||||||
| METASPACE | Repository | Repository for imaging mass spectrometry for metabolomics | no | yes | no | HMDB/ClassyFire/ChemOnt (15) | yes | no | manual | 27842059 | https://pubmed.ncbi.nlm.nih.gov/27842059 | (15) others are available, e.g. LIPID MAPS, SwissLipids | ||||||
| Panomics CCS | Database | Collisional Cross Section (Ion Mobility) Database for Metabolites and Xenobiotics acquired on drift tube instruments | no | yes | no | no | no | yes | manual | 29568436 | https://pubmed.ncbi.nlm.nih.gov/29568436 | |||||||
| SwissLipids | Database | Curated database of lipid structures with experimental evidence and integration with biological knowledge and models | yes | yes | yes | Liebisch 2013 | no | yes | manual | 25943471 | https://pubmed.ncbi.nlm.nih.gov/25943471 |
Table 3. Overview of databases and resources for lipidomics grouped by classification, specific support for lipids, general availability of lipid structures, support for different levels of structural resolution (shorthand notation), main type of lipid ontology supported, availability of mass spectral data, availability and cross-linking of biochemical reaction data and curation model. Remarks: (1) kingdom, superclass, class, subclass. (2) internal and through MassIVE. (3) via integration with multiple tools. (4) via MassIVE and other public repositories. (5) via search. (6) local and linked via SPLASH to MONA, MassBank. (7) via search and shorthand abbreviation. (8) Original and Liebisch 2020. (9) via Metabolomics Workbench. (10) GP and GL only. (11) based on Mass Bank submission format. (12) via reference to spectral data. (13) based on submission format ISA-Tab. (14) based on submission format mwTab. (15) others are available, e.g. LIPID MAPS, SwissLipids. (16) metabolic pathways of lipid mediators. (17) not necessarily machine readable.
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