SpectroPipeR-a streamlining post Spectronaut® DIA-MS data analysis R package
Stephan Michalik1, Elke Hammer1,2, Leif Steil1
1Department Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, MV 17475, Germany.
Summary:
Proteome studies frequently encounter challenges in down-stream data analysis due to limited bioinformatics resources, rapid data generation, and variations in analytical methods. To address these issues, we developed SpectroPipeR, an R package designed to streamline data analysis tasks and provide a comprehensive, standardized pipeline for Spectronaut® DIA-MS data. This novel package automates various analytical processes, including XIC plots, ID rate summary, normalization, batch and covariate adjustment, relative protein quantification, multivariate analysis, and statistical analysis, while generating interactive HTML reports for e.g. ELN systems.
Availability And Implementation:
The SpectroPipeR package (manual: https://stemicha.github.io/SpectroPipeR/) was written in R and is freely available on GitHub (https://github.com/stemicha/SpectroPipeR).
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