Experimental Details - HuPA_00661
Experiment type Mass spectrometry
Short description Immature Dendritic cell proteome analysis
Experimental description Gene expression is commonly used to study the activation of dendritic cells (DCs) to identify proteins that determine whether these cells induce an immunostimulatory or tolerogenic immune response. RNA expression however, not necessarily predicts protein expression and often requires large numbers of experiments for statistical significance. Proteomics provides a direct view on protein expression but is costly and time consuming. Here, we combined a comprehensive label free quantitative proteome and transcriptome analysis on a single batch of immature and cytokine cocktail matured human DCs and integrated mRNA and protein expression at the pathway level. Although the overall correlation between changes in mRNA and protein expression was low, correlation between components of DC relevant pathways was significantly higher. We could identify 5 dominant pathways, which confirmed the importance of cytokines, adhesion and migration, but also identified a fundamental role for lipid metabolism in DC maturation. From these pathways we could extract novel prognostic markers that might potentially improve DC vaccine design.
Principal Investigator's NameDr. Edwin Lasonder
AddressRadboud University Medical Centre
PO Box 9101
Nijmegen, Gelderland 6500 HB
CountryThe Netherlands
Published/Unpublished Published
Journal name
PubMed ID Published
Sample source
Tissue: Immature Dendritic cell
Cell line:
Source organism Homo sapiens [Taxonomy:9606]
Labeling technique No
Protease used Trypsin
Is the sample from in gel Yes
Reduction and Alkylation Yes
Mass spectrometer
Instrument: LTQ-FT
Vendor: Thermo Fisher
Ionization method ESI
Fragmentation method CID
Mass tolerance used for database searching (MS) 10 PPM
Mass tolerance used for database searching (MS/MS) 0.5 Da
Database used for searching IPI_Human 3.25
Search engine used Mascot 2.1
Download MS raw dataset  
Download processed files  

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