MassIVE MSV000084868

Imported Reanalysis Dataset Public PXD002875

Proteome-wide quantitative multiplexed profiling of protein expression: Carbon source dependency in S. cerevisiae

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Description

The global proteomic alterations in the budding yeast Saccharomyces cerevisiae due to differences in carbon sources can be comprehensively examined using mass spectrometry-based multiplexing strategies. Here we investigate changes in the S. cerevisiae proteome resulting from cultures grown in minimal media using galactose, glucose, or raffinose as the carbon source. We used a TMT 9-plex strategy to determine alterations in relative protein abundance due to a particular carbon source, in triplicate, thereby permitting subsequent statistical analyses. We quantified over 4700 proteins across all 9 samples, of which 1003 demonstrated statistically significant differences in abundance in at least one condition. The majority of altered proteins were classified as functioning in metabolic processes and as having cellular origins of plasma membrane and mitochondria. In contrast, proteins remaining relatively unchanged in abundance included those having nucleic acid-related processes, such as transcription and RNA processing. In addition, the comprehensiveness of the dataset enabled the analysis of subsets of functionally-related proteins, such as phosphatases, kinases, and transcription factors. Moreover, alterations in protein abundance levels of full sets of proteins that comprise distinct biological pathways, such as galactose metabolism and the TCA cycle, can be examined collectively. As a resource, these data can be mined further in efforts to understand better the roles of carbon source fermentation in yeast metabolic pathways and potentially utilize observed alterations for industrial applications, such as biofuel feedstock production. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: : yeast ; glucose ; galactose ; raffinose ; TMT ; Fusion

Contact

Principal Investigators:
(in alphabetical order) 		Joao A. Paulo, Harvard Medical School, Boston, MA, USA, N/A
Submitting User: ccms

Publications

Paulo JA, O'Connell JD, Gaun A, Gygi SP.
Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae.
Mol. Biol. Cell. 2015 Nov 5;26(22):4063-74. Epub 2015 Sep 23.

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Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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

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Number of distinct technical 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.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

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.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.