Dataset Information

Locus-specific Retention Predictor (LsRP)

ABSTRACT: LsRP based on amino acid locus information and Support Vector Regression can be used to predict peptide retention time in LC-MS experiments.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Wenyuan Lu

LAB HEAD: Pengyuan Yang

PROVIDER: PXD005572 | Pride | 2017-04-10

REPOSITORIES: Pride

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Publications

Locus-specific Retention Predictor (LsRP): A Peptide Retention Time Predictor Developed for Precision Proteomics.

Lu Wenyuan W Liu Xiaohui X Liu Shanshan S Cao Weiqian W Zhang Yang Y Yang Pengyuan P

Scientific reports 20170317

The precision prediction of peptide retention time (RT) plays an increasingly important role in liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomics. Owing to the high reproducibility of liquid chromatography, RT prediction provides promising information for both identification and quantification experiment design. In this work, we present a Locus-specific Retention Predictor (LsRP) for precise prediction of peptide RT, which is based on amino acid locus information and Sup ...[more]

PMID: 28303880

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Project description:Human pluripotent stem cells hold great potential for regenerative medicine, but available cell types have important limitations. While embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the "gold standard" of pluripotency, they are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) are prone to epigenetic and transcriptional aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming or secondary to the reprogramming method, we generated a genetically matched collection of human IVF-ESCs, iPSCs, and ESCs derived by somatic cell nuclear transfer (SCNT; NT-ESCs), and subjected them to genome-wide genetic, epigenetic and transcriptional analyses. SCNT-based reprogramming is mediated by the full complement of oocyte cytoplasmic factors, thus closely recapitulating early embryogenesis. NT-ESCs and iPSCs derived from the same somatic donor cells contained comparable numbers of de novo copy number variations (CNVs), suggesting that the two reprogramming methods may not differ significantly in mutagenic or selective pressure. On the other hand, the DNA methylation and transcriptome profiles of NT-ESCs corresponded very closely to those of IVF-ESCs, while iPSCs differed markedly from IVF-ESCs and harbored residual DNA methylation patterns typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal candidates for cell replacement therapies. 16 matched samples, two IVF-ESCs, five sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, the parental fibroblast line, and the sperm and oocyte donor were genotyped using the Illumina Omni5, which interrogates 4.3 million SNPs across the human genome. Additionally, matched samples from a patient with Leigh syndrome, a NT-ESC line, three iPSC lines, and the parental fibroblast line were genotyped using the Illumina Omni5.

Dataset Information

Locus-specific Retention Predictor (LsRP)

Publications

Locus-specific Retention Predictor (LsRP): A Peptide Retention Time Predictor Developed for Precision Proteomics.

Similar Datasets

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