# C-COMPASS: a user-friendly neural network tool profiles cell compartments at protein and lipid levels

## TL;DR

C-COMPASS is a user-friendly tool that uses neural networks to predict the distribution of proteins and lipids in cell compartments, enabling multiomic studies of organelle dynamics.

## Contribution

C-COMPASS introduces a neural network-based model that extends organelle profiling to lipids and handles complex multilocalization patterns.

## Key findings

- C-COMPASS successfully models organelle composition changes across conditions using protein abundance data.
- The tool enables spatial profiling of lipids by training on co-generated marker protein profiles.
- Applications in humanized mouse livers reveal organelle remodeling during metabolic perturbations.

## Abstract

Systematic proteomic organelle profiling methods including protein correlation profiling and LOPIT have advanced our understanding of cellular compartmentalization. To manage the complexity of organelle profiling data, we introduce C-COMPASS, a user-friendly open-source software that employs a neural network-based regression model to predict the spatial cellular distribution of proteins. C-COMPASS handles complex multilocalization patterns and integrates protein abundance to model organelle composition changes across conditions. We apply C-COMPASS to mice with humanized livers to elucidate organelle remodeling during metabolic perturbations. Additionally, by training neural networks with co-generated marker protein profiles, C-COMPASS extends spatial profiling to lipids, overcoming the lack of organelle-specific lipid markers, allowing for determination of localization and tracking of lipid species across different compartments. This provides integrated snapshots of organelle lipid and protein compositions. Overall, C-COMPASS offers an accessible tool for multiomic studies of organelle dynamics without needing advanced computational skills, empowering researchers to explore new questions in lipidomics, proteomics and organelle biology.

C-COMPASS is an open-source software designed to predict the spatial cellular distribution of proteins and lipids from cellular organelle profiling using a neural network-based regression model.