Mass Spectrometry Analysis Tools

  • ALEX123 lipid calculator — An online lipid calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level.
  • Greazy — Open-source software for automated phospholipid tandem mass spectrometry identification
  • LION/web — bioinformatics tool for lipidomics that enables users to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations.
  • LIPEA — works with compound IDs for lipids found in the Kyoto Encyclopedia of Genes and Genomes (KEGG) Database and finds significantly perturbed pathways, applying statistical tests
  • LipidBlastin silico tandem mass spectrometry database for lipid identification
  • LipidCircos — tool for visualization of identified phospholipids via Circos plot
  • Lipidcreator — A new Skyline plugin for targeted LC-MS/MS-based lipidomics
  • LipiDex — unifies all stages of LC-MS/MS lipid identification, empowering intelligent data filtering to greatly reduce manual result curation and increase identification confidence
  • LipidIMMS Analyzer — integrates multi-dimensional information including m/z, retention time (RT), collision cross-section (CCS) and MS/MS spectra for lipid identification from ion mobility mass spectrometry
  • LipidXplorer — for Data Dependent Acquisition (DDA) using the Molecular Fragmentation Query Language (MFQL) in shotgun lipidomics
  • Lipid Calculator — draw and search lipid structures
  • Lipid Data Analyzer (LDA) — software for identifying novel lipid molecular species from mass spectrometry data
  • LipidHunter — tool for de novo identification of native phospholipids
  • LipidMS — Lipid annotation in untargeted liquid chromatography-data independent acquisition-mass spectrometry lipidomics based on fragmentation and intensity rules.
  • LPPtiger — tool for prediction and identification of oxidized phospholipids
  • LIQUID — an-open source software for identifying lipids in LC-MS/MS-based lipidomics data
  • MS-DIAL — software package for data-independent acquisition (DIA)-based identification and quantification of small molecules by mass spectral deconvolution for untargeted LC-MS/MS and GC-MS data, with graphical user interface. Reference: Tsugawa H et al. Nat Methods 2015; Tsugawa et al. Nat Methods 2019. DOI: 10.1038/nmeth.3393
  • massPix — an R package for processesing high resolution mass spectrometry imaging data; performs multivariate statistics (PCA, clustering) and lipid identification
  • Mass Spectrometry based Lipid(ome) Analyzer and Molecular Platform (MS-LAMP)MS-LAMP — standalone software capable of aiding in interpreting electrospray ionization (ESI) and/or matrix assisted laser desorption and ionization (MALDI) mass spectrometric data of lipids.
  • Skyline — open source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM - Targeted MS/MS), Data Independent Acquisition (DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data.