Protein biomarkers are routinely used to characterize stem cells by cell state, cell type and function. Methods such as immunostaining, Western Blot analysis and FACS have been used to enrich, localize and quantify singular proteins in pluripotent and differentiated cells. However, future needs in stem cell biology require greater throughput and sensitivity to enable global and target-specific analysis. Protein-based applications in stem cell biology include:

• Profile stem cells by cell state (self renewal or early differentiation) or cell type (e.g., pluripotent vs. lineage specific) using cell surface antigens, transcription factors and secreted proteins.
• Discover novel cell surface antigens for lineage specific cells (neural, hematopoietic and mesenchymal stem cells) to enhance cell isolation and enrichment by FACS.
• Investigate the biological relevance of target genes in key biological processes, such as maintenance of pluripotency, differentiation or plasticity by correlating differential expression of proteins in response to gene regulation by miRNA or gene knockdown by siRNA.
• Develop defined media conditions (such as including growth factors, extracellular matrix proteins and small molecules) for the growth, stability and directed differentiation of cultured stem cells.

• Mass Spectrometry is high throughput, sensitive method for global and targeted protein profiling, and is widely used for discovery and characterization of novel proteins, modifications and interactions. Applied Biosystems/MDS SCIEX are the leading providers of mass spectrometry systems including the 4800 Plus MALDI TOF/TOF™ Analyzer, QSTAR® Elite Hybrid LC/MS/MS System, 4000 Q TRAP® LC/MS/MS System, iTRAQ® reagents and ProteinPilot™ 2.0 Software.
  
  To learn more, visit our Protein Biomarker Solutions site.
  
  
• Western Blotting analysis a versatile method to assay for protein markers of pluripotency or differentiation pathways, and could be correlated with gene expression analysis and methylation profiling. The Western-Star™ Immunodetection System is a non-isotopic chemiluminescence substrate that offers greater sensitivity to detect low abundance proteins, such as transcription factors.
  
  
• Fluorescence-Activated Cell Sorting (FACS) ) is critical tool for working with heterogenous sample populations. For example, FACS is often used upstream of microarray analysis or TaqMan Real-Time PCR to enrich sample populations based on the expression of cell surface antigens, such as CD34+. Once isolated, stem cell researchers can utilize the TaqMan® Cells-to-CT® Kits to rapidly characterize cultured stem cells by mRNA or microRNA profiling. Researchers working with neural, mesenchymal and hematopoietic stem cells are using mass spectrometry, such as the 4800 Plus MALDI TOF/TOF™ Analyzer, to identify novel cell surface antigens expressed in adult stem cells.
  

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