Lipidomic Tools

Oncología y Hematología
Unidad de Biomarcadores y Medicina de Precisión (UBYMP)

In the last years, lipidomics has emerged as a rapidly evolving tool in many fields of science. In our laboratory, we are particularly interested in unravelling the complex role of the wide range of lipids in the pathogenesis of disease (e.g. cancer). To this end, we are deeply committed in the development of workflows and tools focused on improving lipidome analysis and lipid annotation when liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) approaches are used. In this regard, we have developed the following tools:


LipidMS is an R-package aimed to confidentially identify complex lipids in untargeted LC-MS DIA and DDA data analysis. The lipid identification is based on a set of fragmentation and intensity rules which allow to annotate lipids at different levels of confidence. A recent update of LipidMS allowed batch data processing from a number of mass spectrometry vendors (i.e., Thermo, Agilent). Currently, the data analysis workflow is also available as a web-based tool with an user-friendly interface.

New features included in LipidMS v3.0:

  • Batch data processing: LipidMS covers the whole data processing workflow from peak-picking to alignment, grouping, peak filling and lipid annotation.
  • New lipid classes: plasmanyl and plasmenyl PC and PE, acylceramides and ceramides phosphate.
  • Lipid annotation for DIA and DDA data: from LipidMS 2.0 both acquisitions modes are implemented for annotation.
  • Improved graphical outputs for lipid annotation.

LipidMS is intended to be used for research purposes only, without any medical objective.

Click here to access LipidMS. 


  1. Alcoriza-Balaguer MI, García-Cañaveras JC, López A, Conde I, Juan O, Carretero J, Lahoz A. LipidMS: An R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics. Anal Chem. 2019 Jan 2;91(1):836-845. doi: 10.1021/acs.analchem.8b03409. Epub 2018 Dec 13. PMID: 30500173.
  2. LipidMS v3 R-package (


FAMetA is an R-based tool that relies on mass isotopologue distributions from GC-MS or LC-MS to estimate import (I), synthesis of FA(14:0)/FA(16:0) (S), fractional contribution of the 13C-tracer (D0, D1, D2, which represent the acetyl-CoA fraction with 0, 1 or 2 atoms of 13C, respectively), elongation (E) and desaturation (Δ) parameters for the expected network of FA synthesis reactions up to 26-carbons.

FAMetA is intended to be used for research purposes only, without any medical objective.

Click here to access FAMetA online.


  1. FAMetA v0.1 R-package (