SkyLine @ HiLIFE
Open-Source MS Data Analysis Training for Viikki & Meilahti Researchers
SkyLine for HiLIFE training initiative was launched to equip Master's, PhD students, and postdoctoral researchers with hands-on skills in open-source mass spectrometry data analysis. Recognizing the limitations of proprietary software, this program promotes SkyLine, an open-source, vendor-neutral and user-friendly tool for proteomics and metabolomics analysis.
The first iteration of this training was offered in Autumn 2024 to users within Najumudeen Lab and MetaStem Centre of Excellence, where users explored Skyline’s capabilities for targeted and untargeted metabolomics, quantification, and high-resolution mass spectrometry data analysis. Feedback from this initial cohort demonstrated the ease of use, reproducibility, and enhanced data transparency facilitated by Skyline compared to closed-source alternatives.
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Following the success of the pilot program, we are now expanding Skyline for HiLIFE to a broader audience across the Viikki and Meilahti campuses, ensuring accessibility for researchers in biochemistry, molecular biology, systems biology, and bioinformatics. This initiative aims to:
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Provide structured training on Skyline workflows for quantitative proteomics and metabolomics.
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Offer hands-on sessions where participants analyze their own mass spectrometry datasets, transitioning from proprietary software to open-source, flexible solutions.
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Facilitate knowledge-sharing between research groups at HiLIFE (BI, FIMM) and Biomedicum, and other metabolomics facilities, fostering a community of Skyline users.
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Training Structure
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Introductory Module: Basics of mass spectrometry data processing, Skyline installation, and software navigation.
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Hands-on Data Analysis: Working with Skyline for targeted and untargeted metabolomics/proteomics.
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Case Studies and Real Data: Analyzing participant datasets using Skyline’s quantification and calibration tools.
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Advanced Workflows: Integrating Skyline with other bioinformatics tools (e.g., R, Python, MetaboAnalyst, and Proteome Discoverer).
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Open Discussion and User Forum: Encouraging problem-solving and collaborative troubleshooting among researchers.
Future Prospects
The long-term goal is to establish Skyline as a core analytical tool across HiLIFE’s research community, giving students and researchers greater autonomy, cost-effective solutions, and reproducible data analysis workflows. We also aim to explore collaborations with Skyline developers to refine methodologies relevant to our research needs.
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Call for Participants
We invite students, postdocs, and researchers working in proteomics and metabolomics to participate in this training program. The next sessions will be announced soon, with priority given to researchers in the Viikki and Meilahti campuses in Helsinki.
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For further details and registration, please contact: Rafa Najumudeen or Shima Naddafi in Najumudeen Lab