Discovery of Native Protein Complexes by Liquid Chromatography Followed by Quantitative Mass Spectrometry.
Adv Exp Med Biol
; 1336: 105-128, 2021.
Article
en En
| MEDLINE
| ID: mdl-34628629
ABSTRACT
Discovering protein complexes in vivo is of vital importance to understand the evolution and function of biological systems. Proteomics analysis has evolved as a state-of-the-art technique in elucidating the above information. A combination of liquid chromatography (LC) and liquid chromatography coupled to shotgun mass spectrometry (LC-MS) provides the most exhaustive information in this regard. However, a significant amount of computational effort is required for the meaningful interpretation of the generated datasets. In this chapter we describe in detail the state-of-the-art pipeline to discover soluble protein complexes and provide practical advice focusing on typical situations a biologist faces while analyzing such proteomics datasets. Furthermore, we briefly describe two commonly used software packages to solve the described problem:
Weka for training protein-protein interactions (PPIs) using machine learning (ML) and Cytoscape for clustering the interaction network.Palabras clave
Data-independent data acquisition (DIA); Denoising protein-protein interaction matrices; Label-based protein quantification; Label-free protein quantification; Liquid chromatography; Machine learning; Mass spectrometry; Network analysis; Network display; Protein networks; Protein-protein interactions; Shotgun proteomics; Spectral libraries; Weighted cross correlation
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Proteómica
Idioma:
En
Revista:
Adv Exp Med Biol
Año:
2021
Tipo del documento:
Article
País de afiliación:
Alemania