Proteomics

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The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells


ABSTRACT: Assessing relevant molecular differences between human-induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) is important, given that such differences may impact their potential therapeutic use. Controversy surrounds recent gene expression studies comparing hiPSCs and hESCs. Here, we present an in-depth quantitative mass spectrometry-based analysis of hESCs, two different hiPSCs and their precursor fibroblast cell lines. Our comparisons confirmed the high similarity of hESCs and hiPSCS at the proteome level as 97.8% of the proteins were found unchanged. Nevertheless, a small group of 58 proteins, mainly related to metabolism, antigen processing and cell adhesion, was found significantly differentially expressed between hiPSCs and hESCs. A comparison of the regulated proteins with previously published transcriptomic studies showed a low overlap, highlighting the emerging notion that differences between both pluripotent cell lines rather reflect experimental conditions than a recurrent molecular signature. See the Data Processing section of the published paper concerning the bioinformatics pipeline used. PMCID: PMC3261715 PMID: 22108792 Mol Syst Biol. 2011 Nov 22;7:550. doi: 10.1038/msb.2011.84. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Munoz J, Low TY, Kok YJ, Chin A, Frese CK, Ding V, Choo A, Heck AJ. Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.

INSTRUMENT(S): LTQ Orbitrap Velos, LCQ Classic

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Teck Yew Low  

PROVIDER: PXD000134 | Pride | 2013-02-01

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
4Skin_Mix1_SCX_F08_OR5.raw Raw
4Skin_Mix1_SCX_F09_OR5.raw Raw
4Skin_Mix1_SCX_F10_OR5.raw Raw
4Skin_Mix1_SCX_F10rep_OR5.raw Raw
4Skin_Mix1_SCX_F11_OR5.raw Raw
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The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells.

Munoz Javier J   Low Teck Y TY   Kok Yee J YJ   Chin Angela A   Frese Christian K CK   Ding Vanessa V   Choo Andre A   Heck Albert J R AJ  

Molecular systems biology 20111122


Assessing relevant molecular differences between human-induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) is important, given that such differences may impact their potential therapeutic use. Controversy surrounds recent gene expression studies comparing hiPSCs and hESCs. Here, we present an in-depth quantitative mass spectrometry-based analysis of hESCs, two different hiPSCs and their precursor fibroblast cell lines. Our comparisons confirmed the high similarity of h  ...[more]

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