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bioRxiv · 10.1101/2024.10.17.618892

Joint Protein Inference Analysis with PyProteinInference Elucidates Biological Understanding of Tandem Mass Spectrometry Data

Hinkle, T. B.·Bakalarski, C. E.
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Abstract

Selection and application of protein inference algorithms can have a significant impact on the data output from tandem mass spectrometry (MS/MS) experiments, yet its use is often an afterthought in proteomics research due to the inability to apply different inference algorithms in existing analysis systems today. PyProteinInference provides a comprehensive suite of tools to guide researchers through the application of multiple inference algorithms and computation of protein-level, set-based false discovery rates (FDR) from tandem mass spectrometry (MS/MS) data using a unified interface. Here, we describe the software and its application to a K562 whole-cell lysate as well as in a CRAF affinity-purification mass spectrometry experiment to demonstrate its utility in facilitating conclusions about underlying biological mechanisms in proteomic data.

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Hinkle, T. B., Bakalarski, C. E.. 2024-10-20. Joint Protein Inference Analysis with PyProteinInference Elucidates Biological Understanding of Tandem Mass Spectrometry Data. https://doi.org/10.1101/2024.10.17.618892

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