PXD056457

PXD056457 is an original dataset announced via ProteomeXchange.

Title	C-COMPASS: A user-friendly neural network tool profiles cell compartments at protein and lipid levels
Description	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 liver 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 the localization, and tracking of lipid species across different compartments. This provides, for the first time, integrated snapshots of organelle lipid and protein composition. C-COMPASS offers an accessible tool for multi-omics studies of organelle dynamics without needing advanced computational skills, empowering researchers to explore new questions in lipidomics, proteomics, and organelle biology.
HostingRepository	PRIDE
AnnounceDate	2025-07-18
AnnouncementXML	Submission_2025-07-18_11:38:37.491.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Natalie Krahmer
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-02 09:15:20	ID requested
⏵ 1	2025-07-18 11:38:37	announced

Dataset with its publication pending

ProteomeXchange project tag: Liver (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Diabetes (B/D-HPP), Human Proteome Project

submitter keyword: Organelle proteomics

Natalie Krahmer
contact affiliation	Helmholtz Diabetes Center
contact email	Natalie.krahmer@helmholtz-munich.de
lab head
Natalie Krahmer
contact affiliation	Helmholtz Center Munich
contact email	natalie.krahmer@helmholtz-muenchen.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD056457

PRIDE project URI

• PRIDE
  1. PXD056457
     1. Label: PRIDE project
     2. Name: C-COMPASS: A user-friendly neural network tool profiles cell compartments at protein and lipid levels