Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology

Christoph B. Messner*, Vadim Demichev, Ziyue Wang, Johannes Hartl, Georg Kustatscher, Michael Mülleder, Markus Ralser

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

Abstract / Description of output

There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases.

Original languageEnglish
Article number2200013
Number of pages15
Early online date9 Nov 2022
Publication statusE-pub ahead of print - 9 Nov 2022

Keywords / Materials (for Non-textual outputs)

  • biomarker discovery
  • data-independent acquisition
  • dynamic biological systems
  • gene annotation
  • precision medicine
  • proteomics


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