Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments
Project description
Picked Protein Group FDR
Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments
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 the MaxQuant 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
- install Picked Protein Group FDR as explained below.
- make sure that you have run the MaxQuant search with 100% protein-level FDR.
- 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
- 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:
- make sure that you have
make
installed. - download the input files from zenodo: https://zenodo.org/record/7157677
- 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.
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