Automated Proteomics(DIA) Quant: Cloud Platform Engineering

This repository provides the dataset, workflow outputs, and supporting resources for a cloud-based quantitative proteomics analysis using DIA-NN and Nextflow. The input dataset consists of data-independent acquisition (DIA) mass-spectrometry data generated using a Thermo Fisher Orbitrap Exploris platform. Proteomics data processing and quantification were performed using the open-source `nf-diann` Nextflow workflow with DIA-NN as the primary analysis engine. The workflow was executed on Amazon Web Services (AWS), using Amazon S3 for persistent data storage and EC2 for computational processing. Containerized execution was used to provide a portable and reproducible analysis environment. Deposited materials include the analysis dataset, quantitative DIA-NN outputs, workflow execution logs, and relevant analysis metadata. The associated workflow demonstrates an end-to-end approach for transferring mass-spectrometry data to cloud infrastructure, performing reproducible proteomics analysis, and retrieving processed results. This resource is intended to support reproducibility, workflow development, and training in cloud-based computational proteomics.