Proteome Profiling - Quality and Quantifiability using the Orbitrap Astral MS (LoadingCurve: 24min5ms, 14min3p5ms, 8min3p5ms)

ABSTRACT: Biomarker development has two key challenges; the high rate of false positives in discovery and the slow validation phase. To address these challenges we have developed and rigorously tested the Targeted Evaluation and Assessment of Quality (TEAQ) software package. This innovative tool for identifying and selecting precursors, peptides, and proteins that meet the stringent criteria of targeted assays, thus overcoming the limitations faced in the current biomarker development landscape. We implemented the TEAQ to evaluate the performance of the Orbitrap Astral MS using Data-Independent Acquisition Mass Spectrometry (DIA-MS) on plasma samples. This assessment focused on crucial parameters such as proteome linearity, specificity, repeatability, reproducibility, and others essential for substituting dedicated targeted techniques in the more rigorous discovery phase of biomarker development. Through the application of TEAQ on a clinical cohort comprising individuals with inflammation bowel disease (n=493) and an 11-point loading curve, our software successfully identified the signature precursors of quantifiable proteins. A signature peptide or precursor, as per our definition, is a unique peptide or precursor sequence specific to the target protein, exhibiting no miss-cleavages, a linearity R2 value exceeding 0.8, and a coefficient of variation (CV) below 20%. Furthermore, deviations should be less than 20% at low limited quantification concentrations. In instances where multiple peptides or precursors originate from the same protein, it is imperative that all peptides demonstrate a correlation coefficient within the same proteins (>0.7) in the study. Our data set has been made available to as a resource for targeted assay development. This comprehensive approach ensures the reliability and accuracy of our biomarker identification process, paving the way for advancements in clinical practice.

INSTRUMENT(S): Orbitrap Astral

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

SUBMITTER: Jennifer Van Eyk  

PROVIDER: MSV000094136 | MassIVE | Tue Feb 20 19:26:00 GMT 2024

SECONDARY ACCESSION(S): PXD049978

REPOSITORIES: MassIVE