Title:	Proteomics data acquistion QC: test phase
DNr:	NAISS 2025/22-1049
Project Type:	NAISS Small Compute
Principal Investigator:	Florian Rosenberger <florian.rosenberger@ki.se>
Affiliation:	Karolinska Institutet
Duration:	2025-08-15 – 2026-03-01
Classification:	10203
Keywords:

Abstract

This pilot project establishes an automated quality control pipeline for proteomics data from the Orbitrap Astral mass spectrometer at SciLifeLab Stockholm using AlphaKraken, developed by the Mann laboratory. Current manual QC approaches create processing bottlenecks for high-throughput proteomics workflows. AlphaKraken automatically monitors acquisitions, transfers raw data, processes samples using AlphaDIA, and provides comprehensive QC metrics through a web interface. We will process diverse datasets including human clinical samples, mouse tissues, Drosophila specimens, and HeLa QC standards. Raw files (~3GB each) will be transferred to Tetralith, analyzed, and then deleted to optimize storage. This project will process approximately 100 samples weekly at 2.5 CPU hours each, totaling 1000 CPU hours monthly. The pilot will validate computational requirements, optimize data transfer protocols, and establish automated workflows for scaling to medium allocations. Expected outcomes include optimized processing pipelines, QC metric databases, and automated reporting systems that will enhance proteomics data quality assessment for our group and others.