Unlike the genomics field, currently most tools/workflows for analyzing proteomics data are either tied to a specific platform, such as Galaxy, or an operating system (OS), such as Microsoft Windows or Linux. This lack of publicly available, non-platform/OS-dependent and reusable proteomics tools and workflows is preventing valuable public proteomic datasets, such as those in NCI’s Proteomic Data Commons, to be analyzed. This proposal is to create an analysis workflow to generate annotated peptide sequence from proteomic spectra using containerized tools.

TBD

• Java
• CMake

git clone https://github.com/NCBI-Hackathons/Peptides-SpecTra-Annotations-PaSTA
cd Peptides-SpecTra-Annotations-PaSTA

wget --recursive --no-parent --reject="index.html*" -e robots=off https://cptc-xfer.uis.georgetown.edu/publicData/Phase_II_Data/TCGA_Colorectal_Cancer_S_022/TCGA-A6-3807-01A-22_Proteome_VU_20121019/TCGA-A6-3807-01A-22_Proteome_VU_20121019_mzML/
gzip -d cptc-xfer.uis.georgetown.edu/publicData/Phase_II_Data/TCGA_Colorectal_Cancer_S_022/TCGA-A6-3807-01A-22_Proteome_VU_20121019/TCGA-A6-3807-01A-22_Proteome_VU_20121019_mzML/TCGA-A6-3807-01A-22_W_VU_201210*.mzML.gz

wget -O AUP000005640_sp.fasta "https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+proteome:UP000005640&format=fasta"

wget https://github.com/MSGFPlus/msgfplus/releases/download/v2018.07.17/v2018.07.17.zip
mkdir -p software/MSGFPlus
unzip -d software/MSGFPlus v2018.07.17.zip
rm v2018.07.17.zip

wget https://github.com/percolator/percolator/releases/download/rel-3-02-01/ubuntu64.tar.gz
tar -xvzf ubuntu64.tar.gz
sudo dpkg -i *.deb
sudo apt-get install -f

wget https://github.com/percolator/mimic/archive/rel-1-00.zip
unzip rel-1-00.zip
cd mimic-rel-1-00
cmake -DCMAKE_INSTALL_PREFIX=$(pwd)/../software/ src/ && make && make install
cd ..
rm -rf mimic-rel-1-00 rel-1-00.zip

bash examples/workflow_mimic_msgf_percolator.sh
bash examples/run_one_example.sh

Default Mods.txt can be found in: software/MSGFPlus/doc/examples Instruction for adding custom modifications is also available in Mods.txt.

A proof-of-concept of this workflow has been created on the Seven Bridges Cancer Genomics Cloud using Rabix Composer in Common Workflow Language Version 1.

A Docker image for the tools in the workflow is avialable here. The image includes all the prerequisites and dependencies.
To run the Docker image -

docker run -v `pwd`:`pwd` -w `pwd` -i -t stevetsa/proteomics:latest

This mounts the current working directory to the same directory structure inside the container. You will be able to access all files and folders downstream of the current working directory.
All the executibles are in /usr/bin, /usr/local/bin, MS-GF+ JAR file is /opt/MSGFPlusv2018.07.17.jar

• Day 1
• Day 2
• Day 3

• Information of dastset used in the example https://cptac-data-portal.georgetown.edu/cptac/s/S022.
• MS-GF+: GitHub repo HTML help pages
• Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets.
• Mimic: Mimic shuffles peptides in a manner that conserves homolog peptides.

• Downstream analysis: like meme-suite
• Run the whole pipeline in a Docker image