Network-centric analysis of co-fractionated protein complex profiles using SECAT

The Size-Exclusion Chromatography Analysis Toolkit (SECAT) elucidates protein complex dynamics using co-fractionated bottom-up mass spectrometry (CF-MS) data. Here, we present a protocol for the network-centric analysis and interpretation of CF-MS profiles using SECAT. We describe the technical step...

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Detalles Bibliográficos
Autores principales: Bokor, Benjamin J., Gorhe, Darvesh, Jovanovic, Marko, Rosenberger, George
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10199247/
https://www.ncbi.nlm.nih.gov/pubmed/37182203
http://dx.doi.org/10.1016/j.xpro.2023.102293
Descripción
Sumario:The Size-Exclusion Chromatography Analysis Toolkit (SECAT) elucidates protein complex dynamics using co-fractionated bottom-up mass spectrometry (CF-MS) data. Here, we present a protocol for the network-centric analysis and interpretation of CF-MS profiles using SECAT. We describe the technical steps for preprocessing, scoring, semi-supervised machine learning, and quantification, including common pitfalls and their solutions. We further provide guidance for data export, visualization, and the interpretation of SECAT results to discover dysregulated proteins and interactions, supporting new hypotheses and biological insights. For complete details on the use and execution of this protocol, please refer to Rosenberger et al. (2020).(1)

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