What am I looking at?
Each point is one proteome: the model’s sample summary token for one PRIDE run, reduced to two dimensions. Samples that the model represents similarly sit close together.
Without ever seeing a tissue label, samples from the same tissue land together even when they come from different projects, instruments and years. Samples are still often organised by project, but the projects themselves are organised biologically relative to one another. Where a project does not sit with the rest of its tissue, two explanations compete and are often confounded: technical variability (a batch effect from sample preparation, labelling or instrument) or biological variability, such as disease. Take : annotated as skin, its samples sit mostly in brain. PRIDE describes it as brain metastases of melanoma, so its position is biologically plausible. Isolate a tissue and show its projects to find your own cases.
Hovera point to read its metadata.
Clickto pin it and see its ten nearest neighbours in the model’s space.
Legendclick a class to isolate it, then “Show projects” to colour its PRIDE projects.
Searcha PXD or instrument to light up matching samples.
