Targeted and Untargeted Proteomics Approaches in Biomarker Development

Abstract

An enormous amount of research effort has been devoted to biomarker discovery and validation. With the completion of the human genome, proteomics is now playing an increasing role in this search for new and better biomarkers. Here, what leads to successful biomarker development is reviewed and how these features may be applied in the context of proteomic biomarker research is considered. The "fit-for-purpose" approach to biomarker development suggests that untargeted proteomic approaches may be better suited for early stages of biomarker discovery, while targeted approaches are preferred for validation and implementation. A systematic screening of published biomarker articles using MS-based proteomics reveals that while both targeted and untargeted technologies are used in proteomic biomarker development, most researchers do not combine these approaches. i) The reasons for this discrepancy, (ii) how proteomic technologies can overcome technical challenges that seem to limit their translation into the clinic, and (iii) how MS can improve, complement, or replace existing clinically important assays in the future are discussed.

Fast and low-cost detection of SARS-CoV-2 peptides by tandem mass spectrometry in clinical samples

“…Even though data on specificity and sensitivity of immunoassays targeted to virus proteins are still scarce, targeted proteomics most likely present higher specificity. Moreover, selectivity is an intrinsic feature for mass spectrometry-based tests and combined with unique peptide sequences increases the potential application for this strategy 20,21 .…”

Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models

“…Depending on the goal of a study, either targeted or untargeted proteomic approaches can be applied, and sometimes combined for improved analysis. [ 47 ] In untargeted proteomics, all possible proteins expressed from a sample are detected and quantified without a priori knowledge. On the other hand, a targeted platform is used to detect specific proteins especially when the desired proteins are known to be present in low abundance a priori.…”

“…[ 48 ] Therefore, targeted approaches are more precise but have lower coverage than untargeted methods. [ 47 ] For data acquisition using tandem mass spectrometry (MS/MS), two modes exist—data‐dependent acquisition (DDA) mode and data‐independent acquisition (DIA) mode. In DDA, a subset of the most abundant precursor ions that exceed a predefined intensity threshold are selected from the first MS scan to the next MS scan.…”

Systematic Optimization of the iMALDI Workflow for the Robust and Straightforward Quantification of Signaling Proteins in Cancer Cells

“…Additionally, these methods often lead to only "relative" results (i.e., up or down regulation), whereas, in a clinical context, the precise determination of protein/peptide levels is often required. [10] A more appropriate technique for clinical analysis using mass spectrometry is "absolute" quantification using targeted proteomics. [10,11] Combining anti-peptide antibody-based immuno-enrichment of peptides with mass spectrometry as quantitative readout has been shown to be a simple approach for improving selectivity and for achieving high sensitivity and throughput in complex biological samples.…”

“…[10] A more appropriate technique for clinical analysis using mass spectrometry is "absolute" quantification using targeted proteomics. [10,11] Combining anti-peptide antibody-based immuno-enrichment of peptides with mass spectrometry as quantitative readout has been shown to be a simple approach for improving selectivity and for achieving high sensitivity and throughput in complex biological samples. [12] In immuno-matrix assisted laser desorption/ionization time of flight (iMALDI) mass spectrometry (MS), endogenous, or proteolytically derived peptides are enriched using antibodies that are coupled to magnetic beads, which then are directly spotted onto a MALDI plate, eluted by the matrix solvent, and analyzed using MALDI-time-of-flight (TOF) MS (Figure 1).…”