Writing Polyglot Notebooks to quantify raw-data with MS-DIAL5 and then connect the output to SIRIUS

[kozo2]

Proposed mentors: @kozo2 @htsugawa

Lnaguage/skills: C# (Polyglot Notebooks), Peak picking of mass spectrometry raw data using MS-DIAL5, How to use SIRIUS CLI

Estimated Project Length: 90 hours

Difficulty: easy

Polyglot Notebooks is a VScode extension that enables the execution of C# in Jupyter Notebook. MS-DIAL5 is written in C# and mainly used through its GUI, which is only available on Windows. However, for Linux users, MS-DIAL provides a command-line tool. This idea involves calling the functionalities of MS-DIAL's command-line tool from Polyglot Notebooks and documenting the workflow to connect the analysis results to SIRIUS in a notebook. This will allow many people to learn about the workflow and reproduce it.

SIRIUS is a Java software for analyzing metabolites from tandem mass spectrometry data.
It combines the analysis of isotope patterns in MS spectra with the analysis of fragmentation patterns in MS/MS spectra.

SIRIUS expects processed peak lists (centroided spectra). It does not contain routines for peak picking from profiled spectra. In this idea, GSoC contributor will describe the workflow to obtain that peak list using Polyglot Notebooks and MS-DIAL's command-line tool. The steps for MS-DIAL5 would be documented in a C# notebook, while the steps for SIRIUS might be written with commands for SIRIUS CLI, or it might be written using pyOpenMS SiriusAdapterAlgorithm (in a Jupyter Notebook).