On-Target with Targeted Quantitative Proteomics

What is targeted quantitative proteomics?

Targeted quantitative proteomics is a powerful approach to biochemical characterization that leverages mass spectrometry to detect and quantify up to one hundred proteins of interest from complex biological samples with high sensitivity and accuracy. This technique can be applied in high throughput across multiplexed samples representing different cell lines, patient samples, etc., to enable quantification of clinically relevant proteins. Targeted quantitative proteomics unites the broad scope of untargeted global proteomics with the superior quantitative precision and reproducibilityassociated with single-target studies. This balance of advantages is critical when studying low-abundance targets, making targeted quantitative proteomics especially useful for the identification of biomarkers to track disease progression and treatment efficacy. Thanks to ongoing technological advances, targeted quantitative proteomic methods continue to become more sophisticated, more sensitive, and more widely accessible to researchers, advancing therapeutic innovation across the biopharmaceutical industry.

How does targeted quantitative proteomics work?

In targeted quantitative proteomics, proteins or peptides of interest are defined before samples are subjected to mass spectrometry, and data acquisition is tailored for the collection of high-quality profiles for the selected targets. This approach is particularly beneficial for researchers seeking to quantify low-abundance proteins, which can be overlooked or inaccurately assessed by non-targeted (or “shotgun”) experiments. On a technical level, this targeted acquisition can be accomplished by a number of experimental strategies, including selected or multiple reaction monitoring (SRM/MRM) and parallel reaction monitoring (PRM). These approaches enable the precise and consistent quantification of selected targets from biological samples and can be applied across cell line panels, xenograft models, or patient tissue/fluid samples to facilitate drug and biomarker discovery. Modified applications of targeted quantitative proteomics can expand its utility beyond standard protein targets to enable precise evaluation of post-translationally modified species, including targets that have been phosphorylated, glycosylated, or ubiquitinated.

The target list for a targeted quantitative proteomics experiment can be generated in a number of ways. For example, targets may represent ‘hits’ from a prior non-targeted discovery experiment, such that the targeted analysis is used to validate candidates and prioritize a subset for further investigation or development. These candidates may correspond to potential drug targets or to biomarkers associated with disease progression or treatment efficacy. For example, one research group used non-targeted transcriptomics and shotgun proteomics to identify 40 potential biomarkers associated with colorectal tumorigenesis, then leveraged targeted quantitative proteomics to validate their discriminatory power across patient tissue samples. In other cases, the target list may be defined a priori based on biological or clinical hypotheses, such as in the targeted analysis of proteins in the HER2 pathwayto better understand HER2-positive breast cancer, the targeted interrogation of heat shock proteins (HSPs) in patients with early missed abortion to elucidate underlying pathological mechanisms, and the development of a targeted kinome-wide panel to facilitate profiling of human kinases across patient samples.

How is targeted quantitative proteomics used in drug discovery and development?

The most common biomedical application of targeted quantitative proteomics is for the discovery and validation of biomarkers. Indeed, this technology has been successfully leveraged to identify biomarkers associated with cardiovascular disease, chronic obstructive pulmonary disease, acute liver injury, and oral cancer, among many other diseases. Beyond their diagnostic potential, the identification of disease-associated factors can facilitate significant insights into the mechanisms underlying a disorder and provide critical information to support the development of novel therapeutics. For example, one research group used targeted quantitative proteomics to pinpoint the specific glycosyltransferases that are affected in congenital disorders of glycosylation (CDGs), while another group leveraged a PRM-based strategy to identify the protein expression changes driving dilated cardiomyopathy. Targeted quantitative proteomics can also be used to validate the mechanism by which a drug exerts its therapeutic effect, while its application to the blood-brain barrier has yielded valuable information to inform the development of drugs targeting the central nervous system.

Across many stages of the drug discovery and development process, targeted quantitative proteomics enables high-quality, reproducible profiling of relevant proteins, particularly low-abundance species that can be challenging to quantify accurately via traditional non-targeted methods. These targeted techniques facilitate the identification, validation, and interrogation of clinically valuable biomarkers to improve understanding of disease biology and accelerate therapeutic innovation. In particular, targeted quantitative proteomics can provide invaluable support for the advancement of precision medicine by allowing high-throughput analysis of individual patient samples for the construction of pharmacokinetic and pharmacodynamic models. Whether performed in-house or through commercially available services like QuantScout, targeted quantitative proteomics offers unmatched insight into the biology underlying human disease and treatment.

To learn more about our targeted quantitative proteomics service offerings and how they could super-charge your biopharmaceutical research, send us a message.

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