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.
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.tsvoutput from FlashLFQ as input to Picked Group FDR in the same way Sage'slfq.tsvfile is used.