LipidMS v3.1

Lipid Annotation for LC-MS/MS DIA and DDA data analysis. New features:

• Batch processing: peak-picking, grouping and alignment wrapped in batchdataProcessing(). Lipid annotation for msbatch objects simplified with annotatemsbatch().
• New lipid classes: plasmanyl and plasmenyl PC and PE, acylceramides and ceramides phosphate.
• GUI through shiny app running LipidMSapp().
• Improved graphical outputs for lipid annotation.
• RT modelling to detect incorrect annotations and to propose new ones based on previous high confidence annotations identified by fragmentation rules.
  • Interactive shiny app to check the proposed annotations based on RT criteria through manualfilterapp().
  • Interactive shiny app to check new predicted annotations based on RT through manualpredictionapp().

Citation:

If you use this software in your research, please cite:

• Alcoriza-Balaguer MI., et al. (2019) LipidMS: An R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics. Anal Chem, 2019, 91(1), 836-845. doi:10.1021/acs.analchem.8b03409.
• LipidMS 3.0: an R-package and a web-based tool for LC-MS/MS data processing and lipid annotation. Bioinformatics, 2022. doi.org/10.1093/bioinformatics/btac581

References:

• Peak-picking algorithm has been imported from enviPick R-package (Martin Loos) (https://github.com/blosloos/enviPick)