Google Summer of Code 2025

Mass spectrometry is an exciting and versatile tool that can be used to answer many questions in biology and chemistry. To help you get started with the project, you can take a look at the following resources below:

Community Building Phase (February 27th - March 24th)

• During the community building phase of Google Summer of Code (GSoC), we expect those interested to introduce themselves, submit their application to OpenMS and to Google and to get familiar with the codebase. See GSoC Contributors
• Remember the GSOC 2025 timeline
• Join the OpenMS discord server and introduce yourself. Be sure to tag @singjc and @LLYX!

Literature / Reading

• An Introduction to Mass Spectrometry-Based Proteomics (2023)
• Dinosaur: A Refined Open-Source Peptide MS Feature Detector (2016)
• DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics
• diaTracer enables spectrum-centric analysis of diaPASEF proteomics data
• Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics
• The Deconvolution Method for Obtaining Correspondence in Data-Independent Acquisition Mass Spectrometry Data
• Correlation-Based Deconvolution (CorrDec) To Generate High-Quality MS2 Spectra from Data-Independent Acquisition in Multisample Studies
• Dear-DIAXMBD: Deep Autoencoder Enables Deconvolution of Data-Independent Acquisition Proteomics
• DiffMS: Diffusion Generation of Molecules Conditioned on Mass Spectra

Courses and Video Lectures

• SWATH / DIA lecture: http://dia-swath-course.ethz.ch/videos.html -- specifically the following lectures:
  • Christina Ludwig - Targeted Proteomics Primer
  • Ben Collins - Introduction to DIA/SWATH acquisition and concepts