Abstract
Omics approaches have significantly impacted knowledge about molecular signaling pathways driving cell function. Induced pluripotent stem cells (iPSC) have revolutionized the field of biological sciences and proteomics and, in particular, has been instrumental in identifying key elements operating during the maintenance of the pluripotent state and the differentiation process to the diverse cell types that form organisms. This review covers the evolution of conceptual and methodological strategies in proteomics; briefly describes the generation of iPSC from a historical perspective, the state-of-the-art of iPSC-based proteomics; and compares data on the proteome and transcriptome of iPSC to that of embryonic stem cells (ESC). Finally, proteomics of healthy and diseased cells and organoids differentiated from iPSC are analyzed.
Highlights
A historical View and Evolution of Conceptual and Methodological Strategies in ProteomicsProteomics is a large-scale protein analysis that includes the identification, quantification, and posttranslational modification, among other relevant information regarding proteins in a tissue, cell, or biofluid
The analysis showed that the biological processes which were enriched in induced pluripotent stem cells (iPSC) when compared to embryonic stem cells (ESC)
The pluripotent potential of iPSC is represented by their capability to differentiate into cell types from the 3 embryonic germ layers: ectoderm, mesoderm, and endoderm, a property initially limited to embryonic stem cells (ESC) [22,23,31]
Summary
A historical View and Evolution of Conceptual and Methodological Strategies in Proteomics. Several studies have described novel methods to evaluate the presence of PTMs in mammalian cells, such as phosphorylation, glycosylation, acetylation, and ubiquitination In this case, additional steps are required during sample preparation, aiming to enrich the proteins presenting the PTMs of interest before the mass spectrometry analysis. Due to the technological limitations of Fourier transform-based mass spectrometry, proteins with higher masses cannot be analyzed by top-down proteomics In this regard, better protein ionization must be achieved, as well as improvements in protein fragmentation in the collision cell of the mass spectrometer for the MS2 or MSn spectra generation, associated with new bioinformatics tools and databases [21].
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