Simultaneous targeted and discovery-driven clinical proteotyping using hybrid-PRM/DIA

ABSTRACT: Background MS-based proteotyping has been widely used for biomarker discovery. However, the clinical/translational proteotyping community requires strategies that not only enable the discovery of novel biomarker candidates but also increase the likelihood of establishing these protein-based biomarker assays as clinical routine, and improve the speed of analytical and clinical assay validation. Methods Here, we applied hybrid-DIA as an intelligent data acquisition strategy that allows the comprehensive digitization of a clinical sample at the proteotype level, while at the same time increasing the measurement sensitivity for a specific set of markers of clinical interest by the intelligent triggering of multiplexed parallel reaction monitoring (MSxPRM). Heavy-labeled reference peptides were utilized as triggers for MSxPRM and monitoring of endogenous peptides. Results We first evaluated hybrid-DIA on a pool of 185 selected proteotypic peptides for tumor-associated antigens (TAA) derived from 64 annotated human proteins. We demonstrated improved reproducibility and sensitivity of detection of endogenous peptides even at lower concentrations near the limit of detection, and MSxPRM scans were shown not to affect overall DIA performance. We then applied hybrid-DIA to biobanked melanoma samples using a set of 30 AQUA peptides against 28 proteins. Our measurements showed increased validity in determining clinical markers of interest. Conclusions In conclusion, Hybrid-DIA MS offers a way to expedite the translation and utilization of protein biomarkers in clinical practice while also offering insights into disease progression and treatment paths.

INSTRUMENT(S): Orbitrap Fusion Lumos, Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Bernd Wollscheid  

PROVIDER: MSV000092996 | MassIVE |

REPOSITORIES: MassIVE