Software LIQUID: an open-source software for identifying lipids in LC-MS/MS-based lipidomics data

LIQUID Software Overview

LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species. LIQUID is a software tool for identifying lipids in LC-MS/MS-based lipidomics data. It is described in publication LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data and can be found at the Pacific Northwest National Laboratory Developer Community at Zenodo.

Usage

• Instructions for use are described in LIQUID_installation_operation.pdf. Target libraries are available at https://github.com/PNNL-Comp-Mass-Spec/LIQUID/tree/master/TargetDatabase (and are also included in the .zip file attached to each Release). 

Dependencies

• .NET 4.6.2 (or newer)

Programming Language

• C# (100.0%)

License

LIQUID is licensed under the Apache License, Version 2.0; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/Apache-2.0.

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved

Acknowledgment of Federal Funding

The software described here was funded in whole or in part by the National Institute of Allergy and Infectious Diseases, of the National Institutes of Health under award number U19AI106772, and is a contribution of the "Modeling Host Responses to Understand Severe Human Virus Infections" Project at Pacific Northwest National Laboratory. Data generated by the Omics-LHV Core for proteomics, metabolomics, and lipidomics analyses for were performed at Pacific Northwest National Laboratory in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy’s (DOE) Office, operating under the Battelle Memorial Institute for the DOE under contract number DE-AC05-76RLO1830. 

Cite as

1. Matthew Monroe, Cameron Casey, Grant Fujimoto, Christopher Wilkins, Joon-Yong Lee, Cameron Giberson, & Michael Degan. PNNL-Comp-Mass-Spec/LIQUID: Release 7.5.8138 (v7.5.8138). Zenodo. https://doi.org/10.5281/zenodo.6459463.
2. Kyle JE, Crowell KL, Casey CP, Fujimoto GM, Kim S, Dautel SE, Smith RD, Payne SH, Metz TO. LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. Bioinformatics. 2017 Jun 1;33(11):1744-1746. doi: 10.1093/bioinformatics/btx046. PMID: 28158427; PMCID: PMC586005