msmu.read_fragpipe

Reads FragPipe output and returns a MuData object.

Parameters:

Name	Type	Description	Default
identification_file	str | Path | list	Path to the FragPipe PSM output file(s).	required
label	Literal['tmt', 'label_free']	Label type ('tmt' or 'label_free').	required
acquisition	Literal['dda', 'dia']	Acquisition method ('dda' or 'dia'). Note: 'dia' is not yet implemented.	required
quantification_file	str | Path | list | None	Path to combined_modified_peptide.tsv file(s) for LFQ intensities. Omit for an identification-only LFQ import. TMT intensities are read from the PSM file.	None

Returns:

Type	Description
MuData	A MuData object containing the FragPipe data.