ProteomicsDB: Toward a FAIR Open-source Resource for Life-science Research

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2021 Nov 18

PMID 34791421

Citations 25

Authors

Ludwig Lautenbacher

Patroklos Samaras

Julian Muller

Andreas Grafberger

Marwin Shraideh

Johannes Rank

Simon T Fuchs

Tobias K Schmidt

Matthew The

Christian Dallago

Holger Wittges

Burkhard Rost

Helmut Krcmar

Bernhard Kuster

Mathias Wilhelm

Affiliations

Soon will be listed here.

Abstract

ProteomicsDB (https://www.ProteomicsDB.org) is a multi-omics and multi-organism resource for life science research. In this update, we present our efforts to continuously develop and expand ProteomicsDB. The major focus over the last two years was improving the findability, accessibility, interoperability and reusability (FAIR) of the data as well as its implementation. For this purpose, we release a new application programming interface (API) that provides systematic access to essentially all data in ProteomicsDB. Second, we release a new open-source user interface (UI) and show the advantages the scientific community gains from such software. With the new interface, two new visualizations of protein primary, secondary and tertiary structure as well an updated spectrum viewer were added. Furthermore, we integrated ProteomicsDB with our deep-neural-network Prosit that can predict the fragmentation characteristics and retention time of peptides. The result is an automatic processing pipeline that can be used to reevaluate database search engine results stored in ProteomicsDB. In addition, we extended the data content with experiments investigating different human biology as well as a newly supported organism.

Citing Articles

A Scalable, Web-Based Platform for Proteomics Data Processing, Result Storage and Analysis.

Schneider M, Zolg D, Samaras P, Ben Fredj S, Bold D, Guevende A J Proteome Res. 2025; 24(3):1241-1249.

PMID: 39982847 PMC: 11894649. DOI: 10.1021/acs.jproteome.4c00871.

Protein subinteractomes of human microsomal cytochromes P450.

Ershov P, Yablokov E, Mezentsev Y, Ivanov A Mol Biol Rep. 2025; 52(1):226.

PMID: 39937310 DOI: 10.1007/s11033-025-10341-5.

AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships.

Wu Y, Xie L Comput Struct Biotechnol J. 2025; 27:265-277.

PMID: 39886532 PMC: 11779603. DOI: 10.1016/j.csbj.2024.12.030.

Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response.

Hofer S, Frasch L, Brajkovic S, Putzker K, Lewis J, Schurmann H Mol Syst Biol. 2025; 21(3):231-253.

PMID: 39838187 PMC: 11876601. DOI: 10.1038/s44320-025-00085-6.

PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways.

Muller J, Bayer F, Wilhelm M, Schuh M, Kuster B, The M Nat Commun. 2025; 16(1):510.

PMID: 39779715 PMC: 11711753. DOI: 10.1038/s41467-024-55533-y.

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