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Add support for FlashLFQ #24

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MatthewThe opened this issue Dec 6, 2024 · 0 comments
Open

Add support for FlashLFQ #24

MatthewThe opened this issue Dec 6, 2024 · 0 comments

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@MatthewThe
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Currently, we cannot perform protein quantification on rescores results (see #23) because the quantification results are usually already filtered at 1% by the search engine, such as Sage's lfq.tsv file.

Mokapot (and packages using Mokapot such as Oktoberfest and MS2Rescore) can generate FlashLFQ input files to quantify the rescored peptides. It may be possible to use the QuantifiedPeptides.tsv output from FlashLFQ as input to Picked Group FDR in the same way Sage's lfq.tsv file is used.

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