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 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.
Gevaert
Kris
K
Department of Biochemistry and Medical Protein Research, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B9000 Ghent, Belgium. kris.gevaert@ugent.be
Pinxteren
Jef
J
Demol
Hans
H
Hugelier
Koen
K
Staes
An
A
Van Damme
Jozef
J
Martens
Lennart
L
Vandekerckhove
Joël
J
D000328:Adult; D002454:Cell Differentiation; D002460:Cell Line; D002853:Chromatography, Liquid; D002877:Chromosomes, Human; D006801:Humans; D008715:Methionine / Q000378:metabolism*; D039902:Multipotent Stem Cells / Q000166:cytology / Q000378:metabolism*; D010455:Peptides / Q000378:metabolism*; D011505:Protein-Tyrosine Kinases / Q000378:metabolism; D020543:Proteome / Q000032:analysis*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D025801:Ubiquitin / Q000378:metabolism
D010455:Peptides; D020543:Proteome; D025801:Ubiquitin; D008715:Methionine; D011505:Protein-Tyrosine Kinases