Learning Lipid Fragmentation from Individual Spectra
Library Forge accepts individual pairs of MS/MS spectra from a specific lipid class/adduct combination to learn lipid fragmentation and generate in silico spectra with minimal user input. Learned lipid fragmentation templates are seamlessly added to new spectral libraries which can be curated in Library Generator.
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Select the Starting Lipid Library
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Select the Library Forge icon.
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Select the pre-existing library which contains the lipid class, adduct, and fatty acid information for all potential lipid species in the sample and click "Choose Library". To learn more about creating a new library, please reference the Library Generator wiki article.
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Input Lipid Metadata
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To annotate lipid fragmentation from individual sets of spectra, the user must have two spectra of different lipids from the same lipid class/adduct combination (e.g. PC 16:0_18:1 [M+Ac-H]- and PC 18:1_24:1 [M+Ac-H]-).
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Select the "Spectrum Annotator Tab"
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Select the desired lipid class/adduct combination from the "Lipid Class" dropdown menu.
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Input the precursor m/z value and fatty acids for lipid 1 and lipid 2.
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Paste in MS/MS Spectra
- Paste the MS/MS spectra for each lipid into the Library Forge window. MS/MS spectra can either be pasted in as a tab-separated table of m/z values and intensities or pasted directly from Xcalibur Qual Browser.
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Analyze Spectra
- Once the MS/MS spectra have been pasted into the correct tables, select "Analyze" to learn the lipid fragmentation patterns from the spectra.
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Review Annotation Results
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For each lipid spectrum, the experimental fragments are rendered in gray and the matched in-silico fragments are rendered in the color corresponding to their fragment type.
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To save the learned fragmentation template to the spectral library selected earlier, click "Save to Library".
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