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001-es BibID:	BIBFORM121570
035-os BibID:	(scopus)85179616172 (wos)001137562900001
Első szerző:	Bouyssié, David
Cím:	WOMBAT-P : Benchmarking Label-Free Proteomics Data Analysis Workflows / Bouyssié David, Altner Pnar, Capella-Gutierrez Salvador, Fernández José M., Hagemeijer Yanick Paco, Horvatovich Peter, Hubálek Martin, Levander Fredrik, Mauri Pierluigi, Palmblad Magnus, Raffelsberger Wolfgang, Rodríguez-Navas Laura, Di Silvestre Dario, Kunkli Balázs Tibor, Uszkoreit Julian, Vandenbrouck Yves, Vizcaíno Juan Antonio, Winkelhardt Dirk, Schwämmle Veit
Dátum:	2024
ISSN:	1535-3893
Megjegyzések:	The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-Pipelines. ? 2023 American Chemical Society
Tárgyszavak:	Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk benchmarking data analysis label-free proteomics quality metrics workflow
Megjelenés:	Journal Of Proteome Research. - 23 : 1 (2024), p. 418-429. -
További szerzők:	Altner, Pnar Capella-Gutierrez, Salvador Fernández, José M. Hagemeijer, Yanick Paco Horvatovich, Peter Hubálek, Martin Levander, Fredrik Mauri, Pierluigi Palmblad, Magnus Raffelsberger, Wolfgang Rodríguez-Navas, Laura Di Silvestre, Dario Kunkli Balázs (1990-) (bioinformatikus, biokémikus) Uszkoreit, Julian Vandenbrouck, Yves Vizcaíno, Juan Antonio Winkelhardt, Dirk Schwämmle, Veit
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