Dataset Information

ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics

ABSTRACT: Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, personalized medicine, systems biology and biomedical applications. By combining MS with different proteomics approaches such as immunopurification MS, immunopeptidomics, and total protein proteomics, researchers can gain insights into protein-protein interactions, immune responses, cellular processes, and disease mechanisms. The application of MS-based proteomics in these areas continues to advance our understanding of protein function, cellular signaling, and complex biological systems. Data analysis for mass spectrometry is a critical process that includes identifying and quantifying proteins and peptides and exploring biological functions for these proteins in downstream analysis. 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. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analysis. ProtPipe provides downstream analysis including identifying differential abundance proteins and peptides, pathway enrichment analysis, protein-protein interaction analysis, and MHC1-peptide binding affinity. ProtPipe generates annotated tables and diagnostic visualizations from statistical postprocessing and computation of fold-changes across pairwise conditions, predefined in an experimental design. ProtPipe is well-documented open-source software and is available at https://github.com/NIH-CARD/ProtPipe, accompanied by a web interface.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Brain, Blood Plasma, Cerebrospinal Fluid, Cell Culture, Embryonic Stem Cell

SUBMITTER: Ziyi Li

LAB HEAD: Andy Qi

PROVIDER: PXD047657 | Pride | 2024-09-03

REPOSITORIES: Pride

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ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics.

Li Ziyi Z Weller Cory A CA Shah Syed S Johnson Nicholas N Hao Ying Y Roberts Jessica J Bereda Colleen C Klaisner Sydney S Machado Pedro P Fratta Pietro P Petrucelli Leonard L Prudencio Mercedes M Oskarsson Björn B Staff Nathan P NP Dickson Dennis W DW Cookson Mark R MR Ward Michael E ME Singleton Andrew B AB Nalls Mike A MA Qi Yue A YA

bioRxiv : the preprint server for biology 20231213

Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, personalized medicine, systems biology and biomedical applications. By combining MS with different proteomics approaches such as immunopurification MS, immunopeptidomics, and total protein proteomics, researchers can gain insights into protein-protein interactions, immune responses, cellular processes, and disease mechanisms. The application of MS-based proteomics in these areas continu ...[more]

PMID: 38168437

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