LipidCreator_skyline

LipidCreator_skyline generates Skyline-ready target lists and fragment libraries for targeted lipidomics, supporting PRM and MRM mass spectrometry experiments to enable MS/MS-based lipid identification and quantification.

Key Features:

• Skyline integration: Produces custom target lists and fragment libraries compatible with Skyline for PRM and MRM experiments.
• MS/MS fragment mass computation: Computes MS/MS fragment masses for over 60 lipid classes.
• Fragment definition and isotope management: Allows users to define fragments and manage stable isotope labeling for targeted assays.
• Collision energy optimization: Supports optimization of collision energy settings for targeted MS experiments.
• In silico spectral library generation: Generates in silico spectral libraries for use in targeted lipidomics workflows.
• Execution modes: Supports standalone and command-line operation.
• Validation and scale: Has been validated computationally and analytically for the generation of large-scale targeted experiments.

Scientific Applications:

• Targeted lipidomics assay development: Enables development and optimization of targeted assays for lipid quantification using PRM and MRM.
• Quantification across biological conditions: Supports robust quantification of selected lipids under diverse biological conditions.
• Large-scale targeted studies of complex samples: Facilitates generation of large-scale targeted experiments for analysis of complex biological samples such as blood.
• Lipid-signaling pathway analysis: Aids investigation of lipid-signaling pathways, exemplified by studies in human platelets.

Methodology:

Computes MS/MS fragment masses for >60 lipid classes, allows defining fragments and managing stable isotope labeling, optimizes collision energy settings, and generates in silico spectral libraries and Skyline-compatible target lists for PRM and MRM; supports standalone and command-line execution.