# Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data

## TL;DR

The LINCS program created a standardized, accessible proteomics data library to support research on cellular responses to various perturbations.

## Contribution

Development of metadata standards and integrative tools to harmonize and share LINCS proteomics data across multiple platforms.

## Key findings

- LINCS proteomics data from four centers use diverse technologies like P100, tandem mass tags, and SWATH.
- Metadata standards ensure compatibility with community platforms and FAIR data principles.
- Tools like the LINCS Data Portal and piNET enable exploration and analysis of proteomics signatures.

## Abstract

The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function and molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive to cells. Because of the importance of proteins and their modifications to the response of specific cellular perturbations, four of the six LINCS centers have included significant proteomics efforts in the characterization of the resulting phenotype. This manuscript aims to describe this effort and the data harmonization and integration of the LINCS proteomics data discussed in recent LINCS papers.

•The Library of Integrated Network-Based Cellular Signatures (LINCS) has diverse data.•Targeted proteomics, data-dependent/independent acquisition technologies utilized.•Metadata standards harmonize data and ensure compatibility with community platforms.•LINCS tools make proteomics signatures accessible for exploration and analysis.

The Library of Integrated Network-Based Cellular Signatures (LINCS) has diverse data.

Targeted proteomics, data-dependent/independent acquisition technologies utilized.

Metadata standards harmonize data and ensure compatibility with community platforms.

LINCS tools make proteomics signatures accessible for exploration and analysis.

The Library of Integrated Network-Based Cellular Signatures (LINCS) built a FAIR-aligned library of cellular response signatures to support disease research and drug discovery. LINCS proteomics data were generated at four centers using diverse technologies like P100, tandem mass tags, and SWATH to study cancer, cardiotoxicity, and neurodegenerative diseases. Metadata standards were developed to harmonize data and ensure compatibility with community platforms. LINCS tools, such as the Data Portal and piNET, make these proteomics signatures easily accessible for exploration and analysis.