Mühlhäuser, W. W. D. | bioRxiv Science

bioRxiv2024

Autoprot: Processing, Analysis and Visualization of Proteomics Data in Python

MotivationThe increasing numbers of complex quantitative mass spectrometry-based proteomics data sets demand a standardised and reliable analysis pipeline. For this purpose, Python-based analysis, particularly through Jupyter notebooks, serves as a simple yet powerful tool. Nevertheless, the availability of Python software for standardised and accessible MS data analysis is limited, and this software is often constrained to using analysis functions written in Python. This excludes existing and well-tested software, for example written in R. Despite this, Python offers several interactive data visualisation modules that greatly enhance exploratory research and facilitate result communication with collaboration partners. Consequently, there is a need for an integrated and Jupyter-compatible Python analysis pipeline that incorporates R algorithms and interactive visualization for proteomics data analysis. SummaryWe developed autoprot, a Python module for simplified analysis of quantitative mass spectrometry-based proteomics experiments processed with the MaxQuant software. It provides access to established functions written in both Python and R for statistical testing and data transformation. Moreover, it generates JavaScript-based interactive plots that can be integrated into interactive web applications. Thereby, autoprot offers standardised, fast and reliable proteomics data analysis while maintaining the high customisability required to tailor the analysis pipeline to specific experiments. Availability and ImplementationAutoprot is implemented in Python [≥] 3.9 and can be downloaded from https://github.com/ag-warscheid/autoprot. Online documentation is available at https://ag-warscheid.github.io/autoprot/.

bioinformatics↗

bioRxiv2021

Mistargeting of hydrophobic mitochondrial proteins activates a nucleus-mediated posttranscriptional quality control pathway in trypanosomes

Mitochondrial protein import in the parasitic protozoan Trypanosoma brucei is mediated by the atypical outer membrane translocase, ATOM. It consists of seven subunits including ATOM69, the import receptor for hydrophobic proteins. Ablation of ATOM69, but not of any other subunit, triggers a unique quality control pathway resulting in the proteasomal degradation of non-imported mitochondrial proteins. The process requires a protein of unknown function, an E3 ubiquitin ligase and the ubiquitin-like protein (TbUbL1), which all are recruited to the mitochondrion upon ATOM69 depletion. TbUbL1 is a nuclear protein, a fraction of which is released to the cytosol upon triggering of the pathway. Nuclear release is essential as cytosolic TbUbL1 can bind mislocalised mitochondrial proteins and likely transfers them to the proteasome. Mitochondrial quality control has previously been studied in yeast and metazoans. Finding such a pathway in the highly diverged trypanosomes suggests such pathways are an obligate feature of all mitochondria.

biochemistry↗