MassIVE MSV000079440

Partial Public PXD003392

Tagless Analysis of Protein-Protein Interactions in Desufovibrio vulgaris.

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Description

A quantitative tagless method that employs iTRAQ mass spectrometry to measure the co-purification of endogenous proteins through orthogonal chromatographic fractionation was employed to characterize protein-protein interactions in D.vulgaris. 5,273 fractions from a four step fractionation of a D. vulgaris protein extract were assayed, leading to the detection of 1,242 proteins. Shotgun LC MALDI utilized AB Sciex 4800 and 5800 mass spectrometers. ProteinPilot software was used for protein identification and relative quantitation. Pearson cross-correlation values were computed for each iTRAQ multiplex for both the SEC and separately the HIC dimensions. Interologs of protein pairs in the established benchmark protein-protein interaction sets are much more likely to have high maximum CC values in both the HIC and SEC dimensions than seen for all protein pairs or for negative protein pairs. We identified 200 high confidence D. vulgaris PPIs based on tagless co-purification and co-localization in the genome, 140 of which are not part of our D. vulgaris affinity purification-MS interactome. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Protein-protein interactions, tagless strategy, iTRAQ, LC MALDI TOF/TOF, Desulvofibrio

Contact

Principal Investigators:
(in alphabetical order) 		Mark D. Biggin
Submitting User: halinaewa
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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 protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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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.