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The application of MS-based proteomics advances our understanding of protein function, cellular signaling, and complex biological systems. MS data analysis is a critical process that includes identifying and quantifying proteins and peptides and then exploring their biological functions in downstream analyses. To address the complexities associated with MS data analysis, we developed ProtPipe to streamline and automate the processing and analysis of high-throughput proteomics and peptidomics datasets with DIA-NN preinstalled. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analyses. ProtPipe provides downstream analyses, including protein and peptide differential abundance identification, pathway enrichment analysis, protein\u2013protein interaction analysis, and major histocompatibility complex (MHC)\u2013peptide binding affinity analysis. ProtPipe generates annotated tables and visualizations by performing statistical post-processing and calculating fold changes between predefined pairwise conditions in an experimental design. It is an open-source, well-documented tool available at https:\/\/github.com\/NIH-CARD\/ProtPipe, with a user-friendly web interface.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae083","type":"journal-article","created":{"date-parts":[[2024,11,22]],"date-time":"2024-11-22T11:51:34Z","timestamp":1732276294000},"source":"Crossref","is-referenced-by-count":5,"title":["ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5165-8772","authenticated-orcid":false,"given":"Ziyi","family":"Li","sequence":"first","affiliation":[{"name":"Center for Alzheimer\u2019s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda, MD 20892,","place":["USA"]},{"name":"DataTecnica LLC , Washington, DC 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Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London , London, WC1N 3BG,","place":["UK"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3343-1547","authenticated-orcid":false,"given":"Matteo","family":"Zanovello","sequence":"additional","affiliation":[{"name":"UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London , London, WC1N 3BG,","place":["UK"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4894-4858","authenticated-orcid":false,"given":"Mercedes","family":"Prudencio","sequence":"additional","affiliation":[{"name":"Department of Neuroscience, Mayo Clinic , Jacksonville, FL 32224,","place":["USA"]},{"name":"Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences , Jacksonville, FL 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