PXD047657-1

PXD047657 is an original dataset announced via ProteomeXchange.

Title	ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics
Description	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.
HostingRepository	PRIDE
AnnounceDate	2024-09-03
AnnouncementXML	Submission_2024-09-03_15:28:59.684.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ziyi Li
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-08 08:26:57	ID requested
⏵ 1	2024-09-03 15:29:12	announced
2	2024-10-22 06:57:37	announced	2024-10-22: Updated project metadata.

Li Z, Weller CA, Shah S, Johnson N, Hao Y, Roberts J, Bereda C, Klaisner S, Machado P, Fratta P, Petrucelli L, Prudencio M, Oskarsson B, Staff NP, Dickson DW, Cookson MR, Ward ME, Singleton AB, Nalls MA, Qi YA, ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics. bioRxiv, ():(2023) [pubmed]

10.1101/2023.12.12.571327;

submitter keyword: Human, pipline, MS

Andy Qi
contact affiliation	Center for Alzheimer’s Disease and Related Dementias (CARD) National Institute on Aging (NIA) National Institutes of Health (NIH)
contact email	andy.qi@nih.gov
lab head
Ziyi Li
contact affiliation	NIH
contact email	liz36@nih.gov
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/09/PXD047657

PRIDE project URI

• PRIDE
  1. PXD047657
     1. Label: PRIDE project
     2. Name: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics