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The demo reference database and sample label file have been uploaded to the "demo" folder in the "code" module. The DDA and DIA raw data files have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD041360.
3.1 Part 1: run metaExpertPro for DDA-MS-based spectral library generation and DIA-MS-based peptide and protein quantification.
Run the analysis from the command line:
## Get help for DDA and DIA analysis
sudo docker run -it --rm -u $(id -u):$(id -g) guomics2017/metaexpertpro:v2.3 sh /metaEx/src/00.DDAspectrallib/00.DDA.DIA.sh --help
## Set dir
total_dir=/path/to/metaEx
## Run analysis
sudo docker run -it --rm \
-u $(id -u):$(id -g) \
-v $total_dir/DDAraw/:/metaEx/DDAraw/ \
-v $total_dir/DIAraw/:/metaEx/DIAraw/ \
-v $total_dir/fasta/:/metaEx/fasta/ \
-v $total_dir/Results/:/metaEx/Results/ \
-v /path/to/fragpipe20.0/:/metaEx/software/fragpipe20.0/ \
guomics2017/metaexpertpro:v2.3 sh /metaEx/src/00.DDAspectrallib/00.DDA.DIA.sh \
--total_dir /metaEx --project_name demo --fragpipe_switch on --diann_switch on --fasta_name IGC_unique.catalogue_modify_shuffle_humanswiss_contam_irt.fasta --dia_threads 40 \
--fragpipe_path /metaEx/software/fragpipe20.0 --db_split 20
3.2. Part 2: run metaExpertPro for functional and taxonomic annotation and quantitative matrix generation.
Run the analysis from the command line:
## Get help for annotation and quantitative matrix generation
docker run -it --rm -u $(id -u):$(id -g) guomics2017/metaexpertpro:v2.3 sh /metaEx/src/02.Annotation/01.annotation.sh --help
## Set dir
total_dir=/path/to/metaEx
## Run analysis
sudo docker run -it --rm \
-u $(id -u):$(id -g) \
-v $total_dir/sampleLabel/:/metaEx/sampleLabel/ \
-v $total_dir/Results/:/metaEx/Results/ \
-v $total_dir/software/eggnog-mapper/eggnog-mapper-data/:/metaEx/software/eggnog-mapper/eggnog-mapper-data/ \
guomics2017/metaexpertpro:v2.3 sh /metaEx/src/02.Annotation/01.annotation.sh --total_dir /metaEx --project_name demo --sample_label /metaEx/sampleLabel/demo_samples_file_sampleID_batchID.csv \
--database IGC_humanswiss_shuffle --input_pr_mat_name demo_DIAquant.pr_matrix.tsv --input_pg_mat_name demo_DIAquant.pg_matrix.tsv --anno_threads 40 --unipept_switch on --eggnog_switch on --kegg_switch on
The demo Result files have been uploaded to the "demo" folder in the "code" module.
