Peptides SpecTra Annotations (PaSTA)

Background

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.

Challenges in the field

TBD

Workflow

Prerequisite

• Java
• CMake

Installation

Download the git repo

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

Download the dataset used

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

Download Human reference proteome database from UniProt

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

Install MSGFPlus

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

Install Percolator

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

Install Mimic

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

Run the whole pipeline

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.

Workflow availability on the NCI Cloud Resources

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.

Docker Instructions

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

Presentations

• Day 1
• Day 2
• Day 3

Resources

• 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.

Future development

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