PXD000580

PXD000580 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of yeast mutant RNA exosome complexes
Description	The yeast exosome is a conserved multiprotein complex essential for RNA processing and degradation. In this work, we investigated the effects of amino acid substitutions in the exosome subunit Rrp43p on the stability of the complex by comparing the interaction profiles of the complexes purified from the wild type and mutant strains. For that, protein samples were digested with trypsin and the resulting peptides were analyzed by LC-MS/MS (Q-Tof Premier, Waters). The spectra were acquired using software MassLynx v.4.1 and the raw data files were converted to a peak list format (mgf) by the software Mascot Distiller v.2.3.2.0, 2009 (Matrix Science Ldt.) and searched against the yeast database (NCBI- 6702 sequences; 3018299 residues; release data April, 2013) using Mascot engine v.2.3.01 (Matrix Science Ltd.), with carbamidomethylation as fixed modifications, oxidation of methionine as variable modification, one trypsin missed cleavage and a tolerance of 0.1 Da for both precursor and fragment ions. Peptides were considered as unique when it differed in at least 1 amino acid residue. Among these, covalently modified peptides, including N- or C-terminal elongation (i.e. missed cleavages) were counted as unique, but different charge states of the same peptide and modifications were not considered as a criterion to differentiate peptides. Unique peptides with a minimum of five amino acid residues and displaying a significant threshold (p<0.05) in Mascot-based score were considered. The results showed that lower amounts of the exosome subunits are co-purified with the mutant Rrp43p proteins. Additionally, by decreasing the stability of the exosome, other non-specific protein interactions are favored. Therefore, data reported here indicate that complexes containing a mutant Rrp43p exhibit decreased stability and provide information on additional protein interactions.
HostingRepository	PRIDE
AnnounceDate	2014-07-28
AnnouncementXML	Submission_2014-07-28_00:50:55.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000580
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Rogerio Lourenco
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q-Tof Premier; instrument model: Q-Tof Premier

Revision	Datetime	Status	ChangeLog Entry
0	2013-11-14 00:40:22	ID requested
1	2014-04-15 04:19:50	announced
⏵ 2	2014-07-28 00:50:56	announced	Updated project metadata.

Louren, ç, o RF, Leme AF, Oliveira CC, Proteomic analysis of yeast mutant RNA exosome complexes. J Proteome Res, 12(12):5912-22(2013) [pubmed]

submitter keyword: Saccharomyces cerevisiae, LC-MS/MS

Rogerio Lourenco
contact affiliation	Department of Biochemistry/ University of Sao Paulo
contact email	lourenco@iq.usp.br
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000580
     1. Label: PRIDE project
     2. Name: Proteomic analysis of yeast mutant RNA exosome complexes