We are proud to announce our participation at US HUPO 2025. This year, we are heading to Philadelphia, PA with several exciting activities including:
Birgit Schilling (Buck Institute for Research on Aging)
Post-translational modifications (PTMs) dynamically regulate proteins and biological pathways, typically through the combined effects of multiple PTMs. Thus, novel and innovative workflows using data-independent acquisition (DIA) ensure confident PTM identification, precise site localization, and accurate and robust label-free quantification. In this study, we present a powerful novel data processing approach using Spectronaut 19, that highlights greatly improved site localization and novel features for PTM site collapse, input normalization and relative PTM site occupancy (stoichiometry). These new features will be presented analyzing bone tissues quantifying typically ~2,000 proteins and thousands of hydroxy-proline post-translational modifications. These PTMs, predominantly in collagens, greatly influence crosslinking in the collagen extracellular matrices, which directly relates to bone stiffness and bone quality. We present a project of tissue crosstalk involving the skeleton (bones), specifically in the context of the “Bone-Brain” axis. Briefly, clinically, many skeletal and neurodegenerative diseases have high correlation in aged populations, especially diseases such as Alzheimer’s Disease (AD) and Osteoporosis or Osteoarthritis (OA). Here, we analyzed bones from an Alzheimer’s disease mouse model with isogenic APOE alleles, APOE2, APOE3 and APOE4. APOE4 carriers are typically at higher risk for AD. Hydroxy-proline modifications are highly abundant in these bones and are differentially regulated based on APOE allele status. An additional study investigates the “Bone-Gut” axis where we analyzed the hydroxy-proline PTM landscapes of bones in the context of different microbiota and antibiotic treatments in mice.
Yi-Kai Liu (Purdue Center for Cancer Research)
Extracellular vesicles (EVs) have gained increasing attention as their molecular cargoes serve as potential biomarkers for various diseases, including cancers. EV proteomics and phosphoproteomics have emerged as powerful tools for discovering biomarkers for disease diagnosis, monitoring, and therapeutics. However, the low abundance of EV proteins and phosphoproteins compared to cellular counterparts necessitates sensitive and accurate quantitative proteomic approaches. Multiplexed proteomics combined with data-independent acquisition (mDIA) offers advantages over traditional DDA and label-free approaches in sensitivity and quantification. In this seminar, we will introduce a robust mDIA pipeline based on dimethyl labeling for quantitative proteomics and phosphoproteomics of EVs. EVs were efficiently isolated using the extracellular vesicle total recovery and purification (EVtrap) technique, and EV peptides were subjected to stable isotope dimethyl labeling. We then compared different pipelines, including conventional DDA, library-free DIA, and library-based DIA, on the timsTOF HT platform. In addition, various types of spectral libraries and search software suites were evaluated. Using the optimal pipeline, we successfully detected proteome changes associated with the IDH1 mutation in cholangiocarcinoma cell-derived EVs. We also identified EV proteins showing responses to the treatment of inhibitor AG-120 on mutant cells. In summary, this study establishes an optimized mDIA pipeline for sensitive and accurate EV proteomics, unveiling for the first time the proteomic impact of IDH1 mutations and inhibitor treatment in EVs. These findings underscore the potential of mDIA for advancing EV biomarker discovery.
Presenter: Rachel Mehaffey
Date and time: Tuesday, February 25, 4:30 PM – 6:00 PM
Poster Session 2
Poster number: P05.14
Presenter: Brendan Rickert
Date and time: Monday, February 24, 4:30 PM – 6:00 PM
Poster Session 1
Poster number: P08.05
Presenter: Yuehan Feng
Date and time: Tuesday, February 25, 4:30 PM – 6:00 PM
Poster Session 2
Poster number: P02.08
Our Sr. Director, Application Sciences, Yuehan Feng, will speak during Alamar Biosciences’ Breakfast Symposium on Tuesday, February 25.