Four Stage Liquid Chromatographic Selection of Methionyl Peptides for Peptide-Centric Proteome Analysis:  The Proteome of Human Multipotent Adult Progenitor Cells

Serial application of strong cation-exchange and diagonal reversed-phase chromatography selecting methionyl peptides by stepwise shifting them from their reduced to their sulfoxide and sulfone forms generates a four-stage fractionation system, allowing high coverage analysis of complex proteome dige...

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Bibliographic Details
Published in:Journal of proteome research 2006-06, Vol.5 (6), p.1415-1428
Main Authors: Gevaert, Kris, Pinxteren, Jef, Demol, Hans, Hugelier, Koen, Staes, An, Damme, Jozef Van, Martens, Lennart, Vandekerckhove, Joël
Format: Article
Language:English
Subjects:
Adult
Cell Differentiation
Cell Line
Chromatography, Liquid
Chromosomes, Human
Humans
Methionine - metabolism
Multipotent Stem Cells - cytology
Multipotent Stem Cells - metabolism
Peptides - metabolism
Protein-Tyrosine Kinases - metabolism
Proteome - analysis
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Ubiquitin - metabolism
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Summary:Serial application of strong cation-exchange and diagonal reversed-phase chromatography selecting methionyl peptides by stepwise shifting them from their reduced to their sulfoxide and sulfone forms generates a four-stage fractionation system, allowing high coverage analysis of complex proteome digests by LC−MALDI−MS/MS. Application to the proteome of a human multipotent adult progenitor cell line (MAPC) identified 2151 proteins with high confidence as on average four MS/MS-spectra were linked to each protein. Our dataset contains several novel, potential marker proteins that may be evaluated as affinity-anchors for isolating different adult stem cells in further studies. Furthermore, at least 2 tyrosine kinases that were previously linked to the self-renewal potential of stem cells were identified, validating the stemness of the analyzed cells. We also present data hinting at possible involvement of the ubiquitin/proteasome machinery in steering proliferation and/or differentiation of MAPC. Finally, following comparison of the MAPC proteome with proteomes of four human differentiated cell lines reveals differential usage of chromosomal information:  compared to differentiated cells, MAPC do not appear to hold any preference for expressing genes located on specific chromosomes. Keywords: diagonal chromatography • gel-free proteomics • COFRADIC • multidimensional chromatography
ISSN:1535-3893
1535-3907
DOI:10.1021/pr060026a