Gene expression analyses of stem cells (SCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal, pluripotency, and/or multipotency. In recent years, proteomic approaches have produced a wealth of data identifying proteins and mechanisms involved in SC proliferation and differentiation. Although many proteomics techniques have been developed and improved in peptide and protein separation, as well as mass spectrometry, several important issues, including sample heterogeneity, post-translational modifications, protein-protein interaction, and high-throughput quantification of hydrophobic and low-abundance proteins, still remain to be addressed and require further technical optimization. This review summarizes the methodologies used and the information gathered with proteome analyses of SCs, and it discusses biological and technical challenges for proteomic study of SCs. Disclosure of potential conflicts of interest is found at the end of this article.
Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases
Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it
A luminescent ruthenium complex for ultrasensitive detection of proteins immobilized on membrane supports
Quantitation of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using (18)O-labeled internal standards
Direct neural fate specification from embryonic stem cells: a primitive mammalian neural stem cell stage acquired through a default mechanism
Identification of a subpopulation of rapidly self-renewing and multipotential adult stem cells in colonies of human marrow stromal cells
Proteomic characterization of early-stage differentiation of mouse embryonic stem cells into neural cells induced by all-trans retinoic acid in vitro
Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology
SAGE identification of gene transcripts with profiles unique to pluripotent mouse R1 embryonic stem cells
Proteome analysis of conditioned medium from mouse embryonic fibroblast feeder layers which support the growth of human embryonic stem cells
Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes
Differentiation of human embryonic stem cells to cardiomyocytes: role of coculture with visceral endoderm-like cells
Comprehensive proteomic profiling of the membrane constituents of a Mycobacterium tuberculosis strain.
Multivariate proteomic analysis of murine embryonic stem cell self-renewal versus differentiation signaling
Proteomics applied to the clinical follow-up of patients after allogeneic hematopoietic stem cell transplantation.
Gene expression profiling of embryonic stem cells leads to greater understanding of pluripotency and early developmental events
Developmental toxicity testing in the 21st century: the sword of Damocles shattered by embryonic stem cell assays?
p57(Kip2) and p27(Kip1) cooperate to maintain hematopoietic stem cell quiescence through interactions with Hsc70
Stable isotope labeling by amino acids in cell culture (SILAC) and quantitative comparison of the membrane proteomes of self-renewing and differentiating human embryonic stem cells.
Generation of motor neurons by coculture of retinoic acid-pretreated embryonic stem cells with chicken notochords
Proteomic validation of multifunctional molecules in mesenchymal stem cells derived from human bone marrow, umbilical cord blood and peripheral blood
Quantitative proteomics analysis highlights the role of redox hemostasis and energy metabolism in human embryonic stem cell differentiation to neural cells
Phenotypic and proteomic characteristics of human dental pulp derived mesenchymal stem cells from a natal, an exfoliated deciduous, and an impacted third molar tooth
Quantitative proteomic analysis of mouse embryonic fibroblasts and induced pluripotent stem cells using 16O/18O labeling
Identification of cytoplasmic and membrane-associated complexes in human embryonic stem cells using blue native PAGE
An orthogonal comparison of the proteome of human embryonic stem cells with that of human induced pluripotent stem cells of different genetic background
Proteomic comparison of human embryonic stem cells with their differentiated fibroblasts: Identification of 206 genes targeted by hES cell-specific microRNAs
Proteomic analysis of human mesenchymal stromal cells derived from adipose tissue undergoing osteoblast differentiation
Adaptation of a commonly used, chemically defined medium for human embryonic stem cells to stable isotope labeling with amino acids in cell culture
Comparative proteome and transcriptome analyses of embryonic stem cells during embryoid body-based differentiation
A novel role for proteomics in the discovery of cell-surface markers on stem cells: Scratching the surface
Modulation of cancer cell line differentiation: A neglected proteomic analysis with potential implications in pathophysiology, diagnosis, prognosis, and therapy of cancer
Proteomic analysis of membrane proteins expressed specifically in pluripotent murine embryonic stem cells
Chaperoning stem cells: a role for heat shock proteins in the modulation of stem cell self-renewal and differentiation?
Proteome alteration of early-stage differentiation of mouse embryonic stem cells into hepatocyte-like cells
Mortalin and DJ-1 coordinately regulate hematopoietic stem cell function through the control of oxidative stress.
Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins.
Proteomic profiling of secreted proteins for the hematopoietic support of interleukin-stimulated human umbilical vein endothelial cells
Loss of a proteostatic checkpoint in intestinal stem cells contributes to age-related epithelial dysfunction
Comparative Proteomics Analysis of Four Commonly Used Methods for Identification of Novel Plasma Membrane Proteins
Identification of cell surface proteins for antibody-based selection of human embryonic stem cell-derived cardiomyocytes
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