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Sage example (LFQ)

The integration of PickedGroupFDR with Sage is realized by taking PSM level identification information from results.sage.tsv and combining it with the quantification information in lfq.tsv.

The data consists of 9 RAW files with different pools of PrESTs spiked into an E. coli background. The dataset is described in this publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474350/

To run this example, follow these steps:

Option 1: reuse previous Sage results

Download Sage result files

  1. Download and unzip the sage.zip file from this folder. It contains the necessary Sage results files needed to run this example. For the settings used to generate these files, see step 3 in Option 2.

Running PickedGroupFDR

  1. Run the following command (for alternative options see run_picked_group_fdr.sh): 
    python3 -u -m picked_group_fdr \
   --fasta ./sage/iprg2016_with_labels.fasta \
   --sage_results ./sage/results.sage.tsv \
   --sage_lfq_tsv ./sage/lfq.tsv \
   --protein_groups_out ./results/combined_protein.tsv \
   --output_format fragpipe \
   --do_quant \
   --lfq_min_peptide_ratios 1 \
   --methods sage

A quantified protein group result in FragPipe format will be available at results/combined_protein.tsv. It is also possible to generate an output file in MaxQuant's proteinGroups.txt format using the --output_format maxquant flag.

Option 2: run Sage yourself

Download RAW files and convert

  1. Download the mixture{A,B,AB}rep{1,2,3}.raw files from the PRIDE repository PXD008425 into a new subfolder named RAW.
  2. Convert the raw files into mzML format into a new folder named mzML, e.g. with msconvert or ThermoRawFileParser

Running Sage

  1. Run sage using the config.json in this folder and the fasta file iprg2016_with_labels.fasta included in the sage.zip file. 
    sage --fasta iprg2016_with_labels.fasta --output_directory ./ config.json mzML/*

Running PickedGroupFDR

  1. Run the following command (for alternative options see run_picked_group_fdr.sh): 
    python3 -u -m picked_group_fdr \
   --fasta ./sage/iprg2016_with_labels.fasta \
   --sage_results ./sage/results.sage.tsv \
   --sage_lfq_tsv ./sage/lfq.tsv \
   --protein_groups_out ./results/combined_protein.tsv \
   --output_format fragpipe \
   --do_quant \
   --lfq_min_peptide_ratios 1 \
   --methods sage

A quantified protein group result in FragPipe format will be available at results/combined_protein.tsv. It is also possible to generate an output file in MaxQuant's proteinGroups.txt format using the --output_format maxquant flag.