iPortal Ease of use and scale-up of Workflows for Proteomics Analysis

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Presentation transcript:

iPortal Ease of use and scale-up of Workflows for Proteomics Analysis Lorenz Blum SyBIT@ETHZ

Synopsis Web portal for simple submission of complex proteomics workflows Used by scientists at ETHZ and Lund University Developed as part of the SCI-BUS project

iPortal for developers Assembly of workflows Split, merge, join, embedding, conditional execution Workflow submission for many backends and supports "high-throughput"

iPortal for Users

New Functions Automated workflow testing Simplified reference FASTA upload

New Workflows Spectral reference library creation OpenSWATH analysis

SWATH MS/MS

[ [ SWATH MS/MS * MS/MS mode SWATH mode 25Da Collision Cell Isolation m/z * 200 400 600 800 1000 1200 Isolation Fragmentation Analysis Tandem mass spectrum SWATH mode Collision Cell Analyzer 1 Analyzer 2 [ m/z [ 25Da

SWATH MS/MS Data-Independent Acquisition Complete measurement of every sample Unbiased recording Quantitative MS/MS data for all peptides

SWATH MS/MS

OpenSWATH Workflow 1 sample: 20 GB spectral data Normalize Analyze Group features 1 sample: 20 GB spectral data few GB temporary files 5 h runtime

Scalability Yansheng Liu 246 samples 5 TB of spectra (mzXML) 1.5 TB temporary files 2000 job submissions 40'000 CPU hours 41 h runtime (23 h in alignment) analysis in progress…