An overview of the tutorial

1 Installation

We start the tutorial by installing everything required here.

2 The example of the ATP 2019

Next, we explain step by step how to run the pipeline on a real dataset, the ATP 2019 dataset (Sridharan et al. 2019), from loading the data (here) to running the unique Nextflow command line from the terminal (here).

3 Nextflow pipeline

We schematically describe what is happening in this workflow here

4 GPMelt outputs

After this, we explore the different outputs of the GPMelt pipeline, and describe how they can be used, from the most important outputs to the Nextflow reports.

5 Additional examples

We finish by providing the parameters.txt files that can be used to test the other real datasets presented in GPMelt (Le Sueur, Rattray, and Savitski 2024).

References

Le Sueur, Cecile, Magnus Rattray, and Mikhail Savitski. 2024. “GPMelt: A Hierarchical Gaussian Process Framework to Explore the Dark Meltome of Thermal Proteome Profiling Experiments.” PLOS Computational Biology 20 (9): e1011632.

Sridharan, Sindhuja, Nils Kurzawa, Thilo Werner, Ina Günthner, Dominic Helm, Wolfgang Huber, Marcus Bantscheff, and Mikhail M Savitski. 2019. “Proteome-Wide Solubility and Thermal Stability Profiling Reveals Distinct Regulatory Roles for ATP.” Nature Communications 10 (1): 1155.