Meet ProtPipe: Your Multitool for Proteomics and Peptidomics Data

Mass spectrometry (MS) is like a superhero in the world of science, helping us find and understand proteins. It's key in personalized medicine, systems biology, and biomedical research. But analyzing MS data can be tough. That's where ProtPipe steps in. It's a tool designed to make MS data analysis easier. ProtPipe is like a streamlined assembly line for your data. It helps with quality control, sample filtering, and normalization. This makes sure your data is top-notch for further analysis. It even does downstream analyses, like finding differences in protein and peptide amounts, exploring pathways, and checking protein interactions. Plus, it can tell you how strongly some proteins bind to Major histocompatibility complex (MHC).The cool thing about ProtPipe is that it generates annotated tables and visualizations. It does this by crunching numbers and comparing conditions in your experiments. All this is done with a tool called DIA-NN, which comes preinstalled. ProtPipe is open-source and well-documented. You can find it online and even use a user-friendly web interface. It's like having a helpful guide always with you.