Citations 2
ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics
Li, Ziyi , Weller, Cory A. , Shah, Syed Islamuddin , Johnson, Nicholas L. , Hao, Ying , Roberts, Jessica P. , Guha, Deyaan, Bereda, Colleen , Klaisner, Sydney, Machado, Pedro , Zanovello, Matteo , Prudencio, Mercedes , Staff, Nathan P. , Fratta, Pietro , Petrucelli, Leonard , Cookson, Mark , Ward, Michael E. , Singleton, Andrew , Nalls, Mike A. , Fratta, Pietro , Shah, Syed I , Jarreau, Paige B , Roberts, Jessica , Guha, Deyaan , Bereda, Colleen , Klaisner, Sydney , Machado, Pedro M , Zanovello, Matteo , Prudencio, Mercedes , Oskarsson, Björn , Staff, Nathan P , Dickson, Dennis W , Fratta, Pietro , Petrucelli, Leonard , Narayan, Priyanka , Ward, Michael E , Singleton, Andrew B , Nalls, Mike A , Qi, Yue A , Li, Ziyi , Fratta, Pietro , Johnson, Nicholas L , Oskarsson, Björn , Dickson, Dennis W. , Qi, Yue
Genomics, Proteomics & Bioinformatics | November 22, 2024 | Volume: 22 | Issue: 6 | Pages: No page available
Abstract Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, with personalized medicine, systems biology, and biomedical applications. 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–protein interaction analysis, and major histocompatibility complex (MHC)–peptide 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.
Advancements in APOE and dementia research: Highlights from the 2023 AAIC Advancements: APOE conference
Kloske, Courtney M. , Blue, Elizabeth , Carrillo, María C. , Chen, Xiaoying , Chiba‐Falek, Ornit , Davis, Albert A. , Paolo, Gilbert Di , Garretti, Francesca , Golden, Lesley R. , Heinecke, Jay W. , Herz, Joachim, Huang, Yadong , Kanekiyo, Takahisa , Khvorova, Anastasia, Hertog, Sascha J. Koppes‐den, Lamb, Bruce T. , Lawler, Paige E. , Litvinchuk, Alexandra , Liu, Chia‐Chen , Michaelson, D. M., Miller, Justin J. , Morganti, Josh M. , Oosthoek, Marlies , Ramachandran, Kapil V. , Ramakrishnan, Abhirami , Robert, Aiko, Sexton, Claire E. , Shah, Nilomi, Shue, Francis , Strickland, Michael R. , TCW, Julia , Thierry, Manon, Tuckey, Ryan A. , Ulrich, Jason D. , Wang, Na , Weninger, Stacie, Zhao, Na , Goate, Alison , Liu, Chia-Chen , Shue, Francis , Zhao, Na , Goate, Alison M , Belloy, Michaël E. , Bowman, Gregory R. , Gate, David M , Iadecola, Costantino , Johnson, Lance A. , Karch, Celeste M. , Khvorova, Anastasia , Hertog, Sascha Koppes-den , Le Guen, Yann , Mahinrad, Simin , Marcora, Edoardo , Mariño, Claudia , Narayan, Priyanka , Naslavsky, Michel Satya , Raulin, Ana‐Caroline , Saleh, Rasha N.M. , Sible, Isabel J. , Soranno, Andrea , Tsai, Li‐Huei , Kant, Rik van der , Wellington, Cheryl L. , Yassine, Hussein N. , Bu, Guojun , Holtzman, David M.
Alzheimer's & Dementia | July 19, 2024 | Volume: 20 | Issue: 9 | Pages: 6590-6605
AbstractINTRODUCTIONThe apolipoprotein E gene (APOE) is an established central player in the pathogenesis of Alzheimer's disease (AD), with distinct apoE isoforms exerting diverse effects. apoE influences not only amyloid‐beta and tau pathologies but also lipid and energy metabolism, neuroinflammation, cerebral vascular health, and sex‐dependent disease manifestations. Furthermore, ancestral background may significantly impact the link between APOE and AD, underscoring the need for more inclusive research.METHODSIn 2023, the Alzheimer's Association convened multidisciplinary researchers at the “AAIC Advancements: APOE” conference to discuss various topics, including apoE isoforms and their roles in AD pathogenesis, progress in apoE‐targeted therapeutic strategies, updates on disease models and interventions that modulate apoE expression and function.RESULTSThis manuscript presents highlights from the conference and provides an overview of opportunities for further research in the field.DISCUSSIONUnderstanding apoE's multifaceted roles in AD pathogenesis will help develop targeted interventions for AD and advance the field of AD precision medicine.Highlights APOE is a central player in the pathogenesis of Alzheimer's disease. APOE exerts a numerous effects throughout the brain on amyloid‐beta, tau, and other pathways. The AAIC Advancements: APOE conference encouraged discussions and collaborations on understanding the role of APOE.