MassIVE MSV000083090

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Description

To identify the molecular changes underlying this decreased ability for MECP2-mutant NPCs to differentiate into glia, we applied stable isotope labeling by amino acids in cell culture (SILAC) with quantitative multidimensional protein identification technology (MudPIT) mass spectrometry (MS)-based shotgun proteomics. By metabolically incorporating heavy isotopically labeled amino acids into the synthesized proteins, one culture produces a heavy version of each protein, allowing the mass spectrometer to discriminate between heavy labeled proteins from one culture and unlabeled light proteins from a second culture. By mixing the light and heavy extracts in a 1:1 ratio, we quantitatively compared their proteomes. In order to narrow our focus to only the proteins most perturbed in both MECP2 mutant populations, we used two distinct analytical paradigms, both of which involved determining ratios of light to heavy proteins to calculate the Mutant / WT ratio. In the Ratio of Ratios (RoR) paradigm, quantified proteins are normalized using a common internal standard that can accurately correct for incomplete labeling and other instrument-based biases. In the Label Swap (LS) paradigm, we generated two ratios for each protein from four samples. In this way, we focused on those proteins that were significantly altered in both MECP2-mutant son / paternal control comparisons. [doi:10.25345/C5R30C] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: MECP2 ; iPS cells ; SILAC

Contact

Principal Investigators:
(in alphabetical order) 		John R. Yates III, The Scripps Research Institute, USA
Submitting User: titusj
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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
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