![]() MaxQuant supports all common protein quantification methods such as label-free, label-based and isobaric labeling 1, 5. MaxQuant is a standalone freeware that takes raw data as input and performs protein identification and quantification. Together they allow for a typical quantitative shotgun proteomics analysis workflow. Two standard software tools for data dependent acquisition (DDA)-based quantitative proteomics are MaxQuant 1, 2 and MSstats 3, 4. A common aim is to identify proteins that are differentially abundant between conditions of interest. Mass spectrometry-based proteomics is a standard technique for the identification and relative quantification of thousands of proteins in complex samples. The integration of MaxQuant and MSstats into the Galaxy framework enables their usage in a reproducible way on accessible large computational infrastructures, hence realizing the foundation for high throughput proteomics data science for everyone. To further increase accessibility, we provide detailed hands-on training materials. Galaxy tracks all metadata and intermediate results in analysis histories, which can be shared privately for collaborations or publicly, allowing full reproducibility and transparency of published analysis. ![]() MaxQuant and MSstats in Galaxy can be applied in conjunction with thousands of existing Galaxy tools and integrated into standardized, sharable workflows. This enables the web-based analysis of label-free and isobaric labeling proteomics experiments via Galaxy’s graphical user interface on To enable accessible and reproducible quantitative proteomics analyses in a cloud environment, we have integrated MaxQuant (including TMTpro 16/18plex), Proteomics Quality Control (PTXQC), MSstats and MSstatsTMT into the open-source Galaxy framework. Two de facto standard tools, MaxQuant and MSstats, allow for the analysis of raw data and finding proteins with differential abundance between conditions of interest. Quantitative mass spectrometry-based proteomics has become a high-throughput technology for the identification and quantification of thousands of proteins in complex biological samples.
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