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LC-MS Proteomics: Mapping the Future of Drug Discovery
Liquid chromatography-mass spectrometry (LC-MS)-based technology has become a cornerstone in modern drug discovery screenings. It provides comprehensive, quantitative information about protein networks, drug-target interactions, and disease mechanisms. Furthermore, it enables global and targeted insights essential for chemoproteomics, target deconvolution, drug safety, and mode of action studies, and biomarker discovery in precision medicine research.
The challenge
From mapping protein-protein interactions and profiling cell type-specific signaling pathways to analyzing plasma-derived, druggable biomarkers in genetic or metabolic diseases, successful proteomics-driven drug discovery relies not only on powerful instrumentation—such as robust and sensitive LC-MS systems—but also on the quality of prepared samples. High-quality sample preparation is essential for confidently identifying true interactions and establishing biological relevance.
The solution
PreOmics® empowers researchers with a comprehensive portfolio of robust, automatable solutions designed to unlock the full potential of proteomics for drug discovery and development. The iST, BeatBox® and ENRICH technologies address the most pressing challenges in sample preparation—variability, sample complexity, and low abundance targets—ensuring reproducible, deeper access to the proteome and biological relevance for a broad range of applications, aiming to streamline hands-on steps and standardize workflows in proteomics.
With its compact, plug-and-play design and unmatched reproducibility, the BeatBox simplifies tissue homogenization and cell lysis, making it the perfect tool for scalable, high-quality protein extraction, particularly relevant in target validation or biomarker discovery in tissue. The iST technology enables efficient lysis, digestion, and clean-up with minimal effort, ideal for large-scale cell screening and chemoproteomics. The ENRICH technology offers tailored enrichment strategies to discover specific plasma proteins representing potential drug targets or for studying the mechanism of action. As fully automatable solutions, the iST and ENRICH sample preparation kits can be seamlessly integrated on liquid handling platforms, enabling standardized high-throughput processing in cohort studies and laboratories.
Unlock the full potential of LC-MS-based proteomics. Discover how PreOmics solutions can transform complexity into clarity for your Drug Discovery approach.
Results
Enhanced plasma membrane protein coverage with BeatBox®
A comparison of plasma membrane (PM) protein extraction using the BeatBox homogenizer and a conventional bead-based sonication method demonstrated improved performance with BeatBox. The samples prepared with BeatBox exhibited higher protein intensities and a greater number of peptides identified for the exemplary drug target GABAB receptor with its subunits, Gabbr1 and Gabbr2, as determined by LC-MS-based proteomic analysis.
A comparison of plasma membrane (PM) protein extraction using the BeatBox homogenizer and a conventional bead-based sonication method demonstrated improved performance with BeatBox. The samples prepared with BeatBox exhibited higher protein intensities and a greater number of peptides identified for the exemplary drug target GABAB receptor with its subunits, Gabbr1 and Gabbr2, as determined by LC-MS-based proteomic analysis.
Harnessing iST technology to decode drug sensitivity in multiple myeloma
Researchers from ETH Zurich analyzed 101 bone marrow samples from 70 multiple myeloma patients, revealing diverse ex vivo drug sensitivities driven by genetic and microenvironmental factors. Using iST sample preparation, the team identified key biomarkers, such as EYA3 and HLA-DRB5, that predicted specific therapy responses. The study supports personalized therapeutic strategies, advancing precision medicine in multiple myeloma treatment.
Researchers from ETH Zurich analyzed 101 bone marrow samples from 70 multiple myeloma patients, revealing diverse ex vivo drug sensitivities driven by genetic and microenvironmental factors. Using iST sample preparation, the team identified key biomarkers, such as EYA3 and HLA-DRB5, that predicted specific therapy responses. The study supports personalized therapeutic strategies, advancing precision medicine in multiple myeloma treatment.
Key differences identified in mitochondrial proteins and lipid metabolism with ENRICH-iST
In a proteomic study of kidney transplant recipients, researchers from the University of Bergen identified distinct molecular profiles between individuals with pre-existing type 2 diabetes and those who developed post-transplant diabetes. Using ENRICH-iST, they uncovered key differences in mitochondrial proteins and lipid metabolism, which could support the development of targeted therapies and early diagnostic markers to improve transplant outcomes.
In a proteomic study of kidney transplant recipients, researchers from the University of Bergen identified distinct molecular profiles between individuals with pre-existing type 2 diabetes and those who developed post-transplant diabetes. Using ENRICH-iST, they uncovered key differences in mitochondrial proteins and lipid metabolism, which could support the development of targeted therapies and early diagnostic markers to improve transplant outcomes.
What do our customers say?
Hyonson Hwang
Ph.D., Research Scientist, Caris Life Sciences
"[...] I’ve since tested a variety of PreOmics®' other products, the BeatBox®, iST kit, and ENRICH kit, and have been equally impressed. Instead of spending time trying to optimize mass spec sample preparation protocols like before, using PreOmics®’ products, I have more time for data analysis and interpretation, experimental design, and development of mass spec data collection methods."
Ghaith Hamza
Senior Proteomics Scientist at AstraZeneca, Boston, USA
"After stress testing the iST kits, we quickly found that they reproducibly provide superior quality data in a fraction of the time compared to conventional bottom-up sample preparation protocols. We were also excited to see the breadth of protocols established by PreOmics® for the variety of biological material we routinely process and utilize for our work."
Andreas-David Brunner
Scientist R&D Drug Discovery Sciences at Boehringer Ingelheim Pharma GmbH & Co. KG
"We routinely work with biofluid cohorts collected from preclinical species. The novel ENRICH-iST technology from PreOmics® allowed us to achieve reliable and in-depth proteomic data without laborious method development. The new kit worked out of the box; the workflow is intuitive and can be completely automated. This solution allows us to standardize our processes completely and significantly improve our throughput."
Advancing Drug Discovery Applications
References & Further Reading
Chemoproteomics
iST
Automated High-Throughput Affinity Capture-Mass Spectrometry Platform with Data-Independent Acquisition
Jing, H. et al., Journal of Proteomics Research. 2025; 24(2):537–549
Read
iST
Photoproximity Labeling from Single Catalyst Sites Allows Calibration and Increased Resolution for Carbene Labeling of Protein Partners In Vitro and on Cells
Bartholow, T.G. et al., ACS Central Science. 2024; 10(1):199–208
Read
Mechanism of Action & Drug Safety
iST
Toxicoproteomics reveals an effect of clozapine on autophagy in human liver spheroids
Nury, C. et al., Toxicology Mechanisms and Methods. 2022; 33(5):401–410
Read
iST
Efficacy of IDOR-1117-2520, a novel, orally available CCR6 antagonist in preclinical models of skin dermatitis
Kulig, P. et al., British Journal of Pharmacology. 2025; 1–24
Read
ENRICH-iST
Proteomic analysis of plasma at the preterminal stage of rhesus nonhuman primates exposed to a lethal total-body dose of gamma-radiation
Carpenter, A.D. et al., Scientific Reports. 2024; 14:13571
Read
Precision Medicine
iST
Cellular Heterogeneity of Activated Primary Human Macrophages and Associated Drug–Gene Networks: From Biology to Precision Therapeutics
Decano, J.L. et al., Circulation. 2023; 148(19):1459–1478
Read
iST
Proteomic Profiling of Cerebrospinal Fluid and Its Extracellular Vesicles from Extraventricular Drainage in Pediatric Pilocytic Astrocytoma, towards Precision Oncology
Spinelli, S. et al., Cancers. 2024; 16(6):1223
Read
Drug Target Screening
BeatBox
GLP-1-directed NMDA receptor antagonism for obesity treatment
Petersen, J. et al., Nature. 2024; 629:1133–1141
Read
iST-NHS
A clinically compatible drug‐screening platform based on organotypic cultures identifies vulnerabilities to prevent and treat brain metastasis
Zhu, L. et al., EMBO Molecular Medicine. 2022; 14:e14552
Read
