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nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows.
Allen, Carolyn; Meinl, Rico; Paez, J Sebastian; Searle, Brian C; Just, Seth; Pino, Lindsay K; Fondrie, William E.
Afiliación
  • Allen C; Talus Bioscience, Seattle, Washington 98122, United States.
  • Meinl R; Talus Bioscience, Seattle, Washington 98122, United States.
  • Paez JS; Talus Bioscience, Seattle, Washington 98122, United States.
  • Searle BC; Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, United States.
  • Just S; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, United States.
  • Pino LK; Proteome Software, Inc., Portland, Oregon 97219, United States.
  • Fondrie WE; Proteome Software, Inc., Portland, Oregon 97219, United States.
J Proteome Res ; 22(8): 2743-2749, 2023 08 04.
Article en En | MEDLINE | ID: mdl-37417926
Data-independent acquisition (DIA) mass spectrometry methods provide systematic and comprehensive quantification of the proteome; yet, relatively few open-source tools are available to analyze DIA proteomics experiments. Fewer still are tools that can leverage gas phase fractionated (GPF) chromatogram libraries to enhance the detection and quantification of peptides in these experiments. Here, we present nf-encyclopedia, an open-source NextFlow pipeline that connects three open-source tools, MSConvert, EncyclopeDIA, and MSstats, to analyze DIA proteomics experiments with or without chromatogram libraries. We demonstrate that nf-encyclopedia is reproducible when run on either a cloud platform or a local workstation and provides robust peptide and protein quantification. Additionally, we found that MSstats enhances protein-level quantitative performance over EncyclopeDIA alone. Finally, we benchmarked the ability of nf-encyclopedia to scale to large experiments in the cloud by leveraging the parallelization of compute resources. The nf-encyclopedia pipeline is available under a permissive Apache 2.0 license; run it on your desktop, cluster, or in the cloud: https://github.com/TalusBio/nf-encyclopedia.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Proteómica Idioma: En Revista: J Proteome Res Asunto de la revista: BIOQUIMICA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
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XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Proteómica Idioma: En Revista: J Proteome Res Asunto de la revista: BIOQUIMICA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos