Targeted Transition List Generation

targeted-transition-list-generation

Summary

Generate user-defined precursor-to-fragment transition lists and spectral libraries from lipid definitions for targeted proteomics experiments (PRM/MRM). This skill automates the conversion of lipid species, chain compositions, and adduct specifications into Skyline-compatible transition metadata (m/z values, collision energies, retention time windows).

When to use

Use this skill when you have a set of lipid targets defined by species name, acyl chain composition, and expected adducts, and you need to configure a targeted mass spectrometry workflow (PRM or MRM) in Skyline. Typical triggers: designing a lipidomics assay, transitioning from discovery to targeted analysis, or scaling a lipid panel to new instrument platforms (Thermo QExactive HF, Agilent QTOF).

When NOT to use

• Your lipid targets are already in a Skyline project file (.sky) or a pre-formatted transition list — use direct import instead of re-generating.
• You have only nominal mass data or insufficient chain-level annotation — the tool requires explicit acyl chain composition to calculate fragment m/z accurately.
• Your workflow is untargeted (discovery mode) and does not require predefined transition lists — use data-dependent acquisition workflows instead.

Inputs

• lipid definitions (species name, chain composition, adduct type)
• input specification file (text or structured format listing target lipids)
• instrument configuration (ionization polarity, m/z range, collision energy normalization)

Outputs

• tab-delimited or CSV transition list (precursor m/z, fragment m/z, collision energy, polarity, retention time window per row)
• Skyline-compatible target list file
• spectral library file (.blib or .msp format) for fragment matching

How to apply

Parse the lipid definitions (species, chain composition, adducts) from an input specification file. For each lipid target, calculate precursor m/z values and apply retention time prediction models. Using lipid-class-specific fragmentation rules and chain cleavage patterns, compute expected fragment m/z values for each transition. Assemble a target list table containing precursor m/z, fragment m/z, collision energy, polarity, and retention time windows. Export as tab-delimited or CSV format compatible with Skyline import, or generate a standalone fragment library file (.blib or .msp) for spectral matching. Validate that all transitions fall within the instrument's m/z range and that collision energies match the instrument's normalization scheme.

Related tools

• Skyline (Primary interface for importing and managing transition lists; host environment for LipidCreator plugin; visualization and curation of precursor-fragment pairs and collision energies) — https://skyline.ms/project/home/software/Skyline/begin.view
• LipidCreator (Standalone and command-line tool that generates target lists and fragment libraries from lipid definitions; can run as Skyline plugin or as independent executable) — https://github.com/lifs-tools/lipidcreator
• Thermo QExactive HF (Tested target instrument platform; collision energy and m/z calibration reference for transition validation)
• Agilent QTOF (Tested target instrument platform; collision energy and m/z calibration reference for transition validation)

Evaluation signals

• All precursor m/z values fall within the instrument's specified m/z range and match theoretical values for the lipid species and adduct type (±5 ppm for high-resolution instruments).
• Fragment m/z values match predicted cleavage patterns for the acyl chain composition (fatty acid chain losses, headgroup fragments) with no impossible or duplicate transitions.
• Collision energy values are assigned appropriately for the instrument's normalization scheme and match expected ranges for the lipid class and precursor charge.
• Retention time windows are assigned and are consistent with the lipid class or user-provided predictions (e.g., 2–3 min windows for reversed-phase separation).
• Output file format is correctly parsed by Skyline with no import errors; precursor and fragment m/z columns are numeric and polarity is correctly encoded.

Limitations

• Retention time prediction accuracy depends on the availability and quality of calibration standards; predictions may diverge significantly across different LC methods or lipid standards not represented in the training set.
• Fragmentation rule coverage is limited to common lipid classes and chain compositions; unusual or oxidized lipids may not generate accurate fragment m/z predictions.
• Collision energy recommendations are approximate and may require manual tuning for new instrument platforms or LC–MS configurations not in the tested set (Thermo QExactive HF, Agilent QTOF).
• The tool does not account for isotopic variants or in-source rearrangements; practitioners must manually filter or annotate such variants.
• Linux/Ubuntu and macOS builds rely on Mono framework, which has partial UI compatibility issues affecting window repainting in scrollable areas; command-line mode is recommended for non-Windows platforms.

Evidence

• [readme] LipidCreator is a plugin for Skyline supporting targeted workflow development in lipidomics.: "LipidCreator is a plugin for Skyline supporting targeted workflow development in lipidomics."
• [readme] It can be used to create user-defined target lists and fragment libraries for PRM and MRM experiments in Skyline.: "It can be used to create user-defined target lists and fragment libraries for PRM and MRM experiments in Skyline."
• [other] Parse lipid definitions, generate precursor m/z and retention time predictions, calculate fragment m/z from fragmentation rules, and assemble a Skyline-compatible output.: "Parse lipid definitions (species, chain composition, adducts) from input specification. 2. Generate precursor m/z values and retention time predictions for each lipid target. 3. Calculate expected"
• [other] Output formatted as tab-delimited or CSV compatible with Skyline import or as standalone spectral library.: "Format output as tab-delimited or CSV target list file compatible with Skyline import (precursor m/z, fragment m/z, collision energy, polarity, retention time window). 6. Optionally generate"
• [readme] Tested with Thermo QExactive HF and Agilent QTOF instruments.: "It has been tested with Thermo QExactive HF and Agilent QTOF instruments."
• [readme] Supports standalone and command-line operation in addition to Skyline plugin mode.: "It also supports standalone and command-line operation."
• [readme] On Linux, locate the directory containing LipidCreator.exe, open a terminal and run with Mono framework.: "To run LipidCreator, locate the directory containing LipidCreator.exe, open a terminal and type mono LipidCreator.exe"