Picked Protein Group FDR

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 in the data/ folder.

Running Picked Protein Group FDR using the GUI

On Windows, you can download the PickedGroupFDR_GUI_windows.zip from the latest release, unzip it and open PickedGroupFDR.exe to start the GUI (no installation necessary).

Make sure that you have run your database search with 100% protein-level FDR.

Alternatively, on all platforms, first install Picked Protein Group FDR as explained below. Then install PyQt5 (pip install PyQt5) and run:

python gui.py

Running Picked Protein Group FDR from the command line (MaxQuant results)

1. install Picked Protein Group FDR as explained below.
2. make sure that you have run the MaxQuant search with 100% protein-level FDR.
3. the posterior error probabilities (PEP) of MaxQuant are not well-calibrated. Therefore, we first recalculate these with Mokapot (=Percolator for Python):

   python3 -u -m picked_group_fdr.pipeline.andromeda2pin </path/to/mq_evidence_txt> --outputTab andromeda.tab --databases </path/to/fasta_file>
   python3 -u -m picked_group_fdr.pipeline.run_mokapot 0.01 0.01 percolator <num_threads>
   python3 -u -m picked_group_fdr.pipeline.update_evidence_from_pout --mq_evidence </path/to/mq_evidence_txt> --perc_results percolator/andromeda.mokapot.psms.txt percolator/andromeda.mokapot.decoys.psms.txt --mq_evidence_out percolator/evidence.txt

   Alternatively, you can use Prosit's Percolator results files directly:

   python3 -u -m picked_group_fdr.pipeline.update_evidence_from_pout --mq_evidence </path/to/mq_evidence_txt> --perc_results prosit_target.psms prosit_decoy.psms --mq_evidence_out percolator/evidence.txt --pout_input_type prosit

4. to obtain protein group level FDRs, run:

   python -m picked_group_fdr --mq_evidence percolator/evidence.txt --fasta </path/to/fasta_file>

Installation

Picked Protein Group FDR is available on PyPI and can be installed with pip:

pip install picked_group_fdr

Alternatively, you can install directly from this repository:

git clone https://github.com/kusterlab/picked_group_fdr.git
pip install .

Manuscript figures

To reproduce the figures from the manuscript:

1. make sure that you have make installed.
2. download the input files from zenodo: https://zenodo.org/record/7157677
3. specify the location of the input files and run the make command with the figure you want to reproduce, e.g.:

   export DATA_DIR=</path/to/zenodo/files>
   make Figure3a

Check the file MakefileFigures to see which figures are available.