Opentargets - OTAR3091

Proteomics Data Processing Pipeline

This repository contains the workflow used for selecting, processing, and post-processing public proteomics datasets from the PRIDE database for integration into the Open Targets Platform.

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Step 1. Dataset Selection

The complete list of datasets in the PRIDE database was obtained using the PRIDE API.

Run:

Download_PRIDE_Datasets.py

The resulting TSV file was manually filtered according to the dataset selection criteria:

• https://github.com/PRIDE-Archive/opentargets/blob/main/guidelines/Dataset_Selection.md

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Step 2. SDRF (Sample and Data Relationship Format)

Annotate sample metadata according to the SDRF guidelines.

SDRF specification

• https://github.com/bigbio/proteomics-sample-metadata/blob/master/sdrf-proteomics/README.adoc

Annotated SDRF files

• https://github.com/PRIDE-Archive/opentargets/tree/main/sdrf

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Step 3. Process Datasets

DDA (MaxQuant)

Process raw files using MaxQuant.

Important: The assay name field in the SDRF file must exactly match the Experiment field in MaxQuant.

DIA (DIA-NN)

Process raw files using DIA-NN.

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Step 4. Post-process Results

DDA (MaxQuant)

Run:

OpenTargets_dataset_Summary_reportfile.py

Required input files

• proteinGroups.txt
• SDRF file

DIA (DIA-NN)

Run:

OpenTargets_DIA_Summary_report.py

Required input files

• report.tsv
• SDRF file

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Summary of Post-processing Scripts

Data Type	Script
DDA / TMT / iTRAQ	OpenTargets_dataset_Summary_reportfile.py
DIA	OpenTargets_DIA_Summary_report.py

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Processed Data

Raw and post-processed results are available from the PRIDE FTP server:

https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/otargets/