New‐generation mass spectrometry expands the toolbox of cell and developmental biology

Abstract

Systems cell biology understanding of development requires characterization of all the molecules produced in the biological system. Decades of research and new-generation sequencing provided functional information on key genes and transcripts. However, there is less information available on how differential gene expression translates into the domains of functionally important proteins, peptides, and metabolites, and how changes in these molecules impact development. Mass spectrometry (MS) is the current technology of choice for the detection and quantification of large numbers of proteins and metabolites, because it requires no use of antibodies, functional probes, or a priori knowledge of molecules produced in the system. This review focuses on recent technologies that have improved MS sensitivity for proteins and metabolites and enabled new functionalities to assess their temporal and spatial changes during vertebrate embryonic development. This review highlights case studies, in which new-generation MS tools have enabled the study of hundreds-to-thousands of proteins and metabolites in tissues, cell populations, and single cells in model systems of vertebrate development, particularly the frog (Xenopus), zebrafish, and mouse. New-generation MS expands the toolbox of cell and developmental studies, raising exciting potentials to advance basic and translational research in the life sciences.

Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos

“…To fill this technological gap, we here report MS-based single-cell proteomics of identified cells in live vertebrate embryos of important model organisms. This report follow our initial disclosure of the technology in 2017 28 with the optimized workflow disseminated in 2018 29 . Instead of averaging cells to boost detection sensitivity, as is classical to MS, or dissecting cells, as currently possible in single-cell MS by us and others, [20][21][22] we microfabricated capillaries to aspirate a portion of identified cells directly from live embryos.…”

Xenopus laevis as a Model Organism for the Study of Spinal Cord Formation, Development, Function and Regeneration

“…Xenopus is a classic model for embryology and physiology research and has been perfectly suited for studies on the formation, development, maturation and repair of the spinal cord. The recent completion of the sequencing of the Xenopus laevis genome (Session et al, 2016 ), and Xenopus tropicalis genome since 2010 (Hellsten et al, 2010 ), allows for the use of both in genetic studies; along with the remarkable advances in systems biology, including genomics, metabolomics and proteomics, the opportunities for discovery that this model system offers are reinvigorated (Lombard-Banek et al, 2017 ; Tandon et al, 2017 ). Additionally the accessibility of novel approaches for gene editing like TALENs (transcription activator-like effector nucleases) and CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated nucleases) expand the use of Xenopus as a genetically tractable model for loss and gain of function studies (Tandon et al, 2017 ).…”

Mass spectrometry‐based proteomics reveals the distinct nature of the skin proteomes of photoaged compared to intrinsically aged skin

“…Proteomics, using mass spectrometry (MS) to analyse peptide constituents in a sample allowing post‐hoc identification of protein species , can be used as a non‐targeted method to identify differences in relative abundance between samples. This has frequently been used successfully to identify novel biomarkers of disease .…”