Assessing the Phagosome Proteome by Quantitative Mass Spectrometry

Maria Emilia Dueñas, José Luis Marín-Rubio, Julien Peltier-Heap, Anetta Hartlova, Matthias Trost

Research output: Chapter in Book/Conference paperChapterpeer-review


The process of phagocytosis involves a series of defined steps, including the formation of a new intracellular organelle, i.e., the phagosome, and the maturation of the phagosome by fusion with endosomes and lysosomes to produce an acidic and proteolytic environment in which the pathogens are degraded. Phagosome maturation is associated with significant changes in the proteome of phagosomes due to the acquisition of new proteins or enzymes, post-translational modifications of existing proteins, as well as other biochemical changes that ultimately lead to the degradation or processing of the phagocytosed particle. Phagosomes are highly dynamic organelles formed by the uptake of particles through phagocytic innate immune cells; thus characterization of the phagosomal proteome is essential to understand the mechanisms controlling innate immunity, as well as vesicle trafficking. In this chapter, we describe how novel quantitative proteomics methods, such as using tandem mass tag (TMT) labelling or acquiring label-free data using data-independent acquisition (DIA), can be applied for the characterization of protein composition of phagosomes in macrophages.

Original languageEnglish
Title of host publicationPhagocytosis and Phagosomes
Subtitle of host publicationMethods and Protocols
EditorsRoberto J. Botelho
PublisherHumana Press Inc.
Number of pages14
ISBN (Electronic)978-1-0716-3338-0
ISBN (Print)978-1-0716-3337-3
Publication statusPublished - 27 Jun 2023
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


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