High-Throughput Mass Spectrometry for Targeted Protein Degradation

Targeted protein degraders are a promising class of drugs that have gained significant attention in recent years due to their potential to treat previously "undruggable" targets in diseases such as cancer. However, the development of these drugs come with its own set of challenges and can benefit significantly from modern mass spectrometry (MS) analysis.

MS analysis plays a vital role in the drug discovery process, enabling researchers to identify and measure proteins related to disease pathways and detect proteome-level changes. This step is crucial for understanding and characterizing the specificity of potential degraders or molecular glue candidates, providing direct biophysical information on potential off-target effects. To achieve accurate quantification for extensive sample cohorts, it is essential to establish a workflow that combines high throughput, deep proteome identification, and high selectivity.

Maximize sensitivity and efficiency in complex biological systems analysis
The 4D-Proteomics™ ecosystem by Bruker offers researchers a comprehensive solution for maximizing sensitivity and efficiency in sample preparation, data generation, and analysis, enabling true discovery workflows. This powerful ecosystem seamlessly integrates sample preparation, separation, data acquisition, and analysis, providing researchers with a highly efficient and streamlined approach to analyzing complex biological systems. Equip your lab with advanced tools such as trapped ion mobility spectrometry (TIMS), PepSep™ C18 HPLC columns, and Bruker ProteoScape™ software, for a complete solution for high-quality and reproducible data generation.

Sensitive and reproducible measurements start with high-quality separation methods. PepSep™ MAX HPLC columns enhance the performance of instruments, providing a crucial tool for researchers in their request for the next protein degraders. When combined with cutting-edge methodologies, PepSep™ HPLC C18 columns empower scientists to achieve better sensitivity in their TPD analysis. Streamline your investigation, and dive deeper into the intricate world of cellular processes. Prepare to embark on a transformative journey where scientific possibilities know no bounds with PepSep™ MAX.

With the rise of targeted protein degraders, high-resolution analysis of samples, including gas-phase separation of chimeric species, is critical to understand the impact of these drugs on protein homeostasis. TIMS technology simultaneously improves sensitivity by focusing precursor ions and selectivity by separating ions in the gas-phase based on their collisional cross section (CCS).

Leveraging Parallel Accumulation-Serial Fragmentation (PASEF^®), TIMS technology enables fast and high-sensitivity analysis of complex protein mixtures. PASEF^® allows for the simultaneous analysis of multiple precursor ions, increasing sensitivity and specificity in the detection of protein targets. 

Expect better identification and quantification of complex peptide mixtures, including post-translational modifications (PTMs). The high sensitivity of TIMS technology enables the detection of low-abundance peptides, which is crucial for targeted protein degraders analysis, as these drugs typically work on specific, low-expressing protein targets. 

Unlock high-resolution peptide separation, rapid and accurate detection of low-abundance proteins, and improved quantification of protein targets. Experience reliable and accurate data that can aid in the development of new drugs for treating diseases such as cancer.

Take your targeted protein degrader analysis to the next level with Bruker ProteoScape™, the software which includes TIMScore™. Leveraging machine learning and cross-collision section (CCS) values, Bruker ProteoScape™ delivers improved sensitivity and specificity of targeted protein degrader detection.

With both dependent acquisition (dda-PASEF) and data-independent acquisition (dia-PASEF^®) options, researchers can access a comprehensive view of protein degradation pathways in real time. dda-PASEF allows for building rich spectra libraries, while dia-PASEF^® provides deep quantification of the proteome at unmatched speed. And with Bruker ProteoScape™, researchers can have it all. Get the precision and accuracy you need to uncover novel insights into targeted protein degrader analysis.

Overcoming the common challenge of achieving high throughput without compromising sensitivity in TPD studies is now possible with Spectronaut^® 18. With data-independent acquisition (DIA) and Spectronaut^® 18, you are empowered to maintain exceptional sensitivity while maximizing throughput.

With its deep-learning augmented peptide identification, Spectronaut^® enables the discovery of a broader range of precursors and proteins, enhancing sensitivity for comprehensive analysis. Take advantage of Linux and cloud compatibility to optimize your computational resources, ensuring efficient data processing and analysis.

Spectronaut^® 18 also comes with an improved directDIA+ workflow that maximizes productivity by allowing you to start analyzing your dataset immediately after acquiring the first sample, reducing the time from injection to actionable data by over 80%. Accelerate your TPD analysis, gain critical insights into drug mechanisms, and elevate your research capabilities with Spectronaut^®.

Outsourcing to a specialist MS-based CRO service provider can be invaluable, even with in-house instruments and expertise. Biognosys will help you in securing overflow capacity, accelerating large-scale studies, and accessing novel workflows. The Biognosy’s TrueDiscovery™ platform delivers deep, unbiased profiling of proteomes with unmatched specificity, enabling the characterization of degradation profiles and protein turnover rates. 

Conduct your studies at Biognosys' state-of-the-art facility, a leading Good Laboratory Practice (GLP)-certified and Good clinical practice (GCP)-compliant mass spectrometry laboratory for large-scale proteomics research.