Matrisome Project tools

The following are tools used by the Matrisome project (http://matrisome.org) to process proteomic data to add Matrisome annotations to proteins and generate a summary report.

process_ecm.sh

Tool will process mzML and idXML/pepXML file to obtain PSM counts and EIC intensities for each peptide then annotate proteins using ECM database

usage: process_ecm.sh [mzML file] [idXML/pepXML file] [ECM DB file] [output peptide table] [output protein table]

ecm_report.R

Script will generate a summary report of output protein tables from the process_ecm.sh script. The multiple protein tables from different samples can be provided to create an overall report of a given sample set. The script will generate the following...

• Summary report - Summary of number of proteins, number of peptides, number of PSMs/spectra, and EIC sum for each sample broken down for each Matrisome division as well as collagens. This output file is specified with the -o/--output option.
• Combined sample report - Report of each protein with Matrisome annotations and summed counts of peptides, PSMs/spectra and EIC area for each sample.
• Plots - Pie or barcharts of summariezed protein, peptide, PSM/spectra counts and EIC area colored by Matrisome division.

Usage: /export/home/clustcrilab/internal_tools/george_tools/matrisome_qc/ecm_report.R [options]
Generate report for ECM data.

Options:
	-o OUTPUT, --output=OUTPUT
		Output summary report (text). Default is STDOUT.

	-d DETAILS, --details=DETAILS
		Output combined protein report (text).

	--gene_details=GENE_DETAILS
		Output combined protein report summarized by gene (text).

	-i MANIFEST, --manifest=MANIFEST
		Manifest of input files. Assumes a header row. If just a list of files, will assume there is NOT a header. If this is not specified then provide files as arguments.

	-m MIN_PEPTIDES, --min_peptides=MIN_PEPTIDES
		Minimum number of peptides required to include a protein. Default is 2

	-u, --unique_peptides
		Minimum peptides must be unique.

	-p PLOT, --plot=PLOT
		Output plot file(s).

	-t TYPE, --type=TYPE
		Plot format, either png or pdf. Default is pdf.

	-s STYLE, --style=STYLE
		Plot style, either bar or pie. Default is bar.

	-h NUMBER, --height=NUMBER
		Height of plots (600px if PNG, 7in if PDF).

	-w NUMBER, --width=NUMBER
		Width of plots (600px if PNG, 7in if PDF).

	-r, --rotate
		Rotate plots (x on the vertical).

	--help
		Display this help message and exit.

Galaxy tools

Building Docker images

The current Galaxy tool XML files are written to use Docker containers. The following Dockerfiles are provided for each of the Galaxy tools

• Dockerfile.process_ecm
• Dockerfile.ecm_report

To build the Docker images execute the following, where tool is process_ecm or ecm_report.

docker build -f Dockerfile.<tool> -t <tool> ./

Note: The process_ecm.py script fetches protein information from Uniprot (https://uniprot.org). When running a process_ecm Docker container, the container needs to have Internet access. If you are using the local_docker job runner be sure to set the docker_net parameter for the local_docker destination. The following is an example enabling network access via a bridge interface.

<destination id="local_docker" runner="local">
   ...
   <param id="docker_net">bridge</param>
   ...
</destination>