SpectroPipeR-a streamlining post Spectronaut® DIA-MS data analysis R package.
Where this comes from
- Record sourced from PubMed, PMID 39985446.
- Also identified by DOI 10.1093/bioinformatics/btaf086 and PMC identifier 11893148.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. The SpectroPipeR package (manual: https://stemicha.github.io/SpectroPipeR/) was written in R and is freely available on GitHub (https://github.com/stemicha/SpectroPipeR).
Medical subject headings
- Software
- Proteomics
- Mass Spectrometry
- Proteome