Visualisation of proteome-wide ordered protein abundances in Trypanosoma brucei.

Michele Tinti,Michael A J Ferguson

doi:10.12688/wellcomeopenres.17607.1

Michele Tinti, Michael A J Ferguson

Open Access

https://doi.org/10.12688/wellcomeopenres.17607.1

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Abstract

Background: Trypanosoma brucei is a protozoan parasite and etiological agent of human and animal African trypanosomiasis. It has a complex life cycle, but the most studied cellular types are the in vitro cultivated bloodstream- and procyclic-forms. These correspond to the replicating, mammalian host bloodstream-dwelling, slender trypomastigotes and tsetse vector midgut-dwelling procyclic lifecycle stages, respectively. Several proteomics studies have reported the differential abundance of proteins between these in vitro cultivated cell types. However, there are no datasets providing protein abundance, from most to least abundant, within and between both cell types. Methods: We used MaxQuant software 1.6.10.4 to reprocess a recent large-scale proteomics experiment from our laboratory and extracted intensity-based quantifications of the bloodstream and procyclic form proteomes. Results: We created a web interface to visually explore protein abundances within and between the in vitro cultivated T. brucei bloodstream and procyclic form proteomes. Conclusions: The protein abundance visualization tool, searchable by protein name(s) and attribute(s), is likely to be useful to the trypanosome research community. It will allow users to contextualise their proteins of interest in terms of their abundances in the T. brucei bloodstream and procyclic form proteomes.

Highlights

The protozoan parasite Trypanosoma brucei is transmitted to its human and animal hosts by the tsetse fly (Glossina species), which is found only in sub-Saharan Africa[1]
After data re-processing with MaxQuant[8] we considered only the intensity-based absolute quantification (iBAQ) values of the H labelled samples retrieved from the proteinGroups.txt file
We computed the numerical data ranks from the median iBAQ values starting from 1 to n where n is the number of the protein group identified

Summary

Introduction

The protozoan parasite Trypanosoma brucei is transmitted to its human and animal hosts by the tsetse fly (Glossina species), which is found only in sub-Saharan Africa[1]. Some of these differentiate into the replicating epimastigote form as they migrate to the tsetse salivary glands These differentiate into non-dividing metacyclic trypomastigote forms that are adapted for transmission to the mammalian host during a tsetse bloodmeal. The proteomes of in vitro cultivated BSF and PCF cells have been analysed quite extensively[2,3,4,5]; the focus of such studies has been the determination of the differential protein abundances between the two lifecycle forms rather than ranked-order relative protein abundance values. The latter can be useful when assessing protein functions. The iBAQ method estimates protein abundances in a complex proteome by integrating all the peptide intensities measured by mass spectrometry for each detected protein group and dividing them by the number of theoretical observable tryptic peptides (i.e., between six and 30 amino acids) contained within them

Methods

Conclusions

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