Welcome to Picked Group FDR’s documentation!

Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments.

Different search engine outputs are supported:

• MaxQuant (LFQ, TMT, SILAC)

• Percolator (no quantification)

• FragPipe (LFQ)

• Sage (LFQ)

Examples on how to run Picked Protein Group FDR with these different search engine outputs can be found under Basic usage and in the data/ folder.

Contents:

• Installation
• Basic usage
• Manuscript figures
• How to cite