PXD000159

PXD000159 is an original dataset announced via ProteomeXchange.

Title	SIRT6 and SIRT7 binding proteome
Description	To find the SIRT6 and SIRT7 binding proteins, we expressed V5-tagged SIRT6 and SIRT7 and pulled down this protein with anti-V5 agarose affinity gel. Sirtuins are a family of NAD-dependent deacetylases which deacetylate not only histones but also a wide range of target proteins. Sirtuins are conserved from yeast to mammal, and are known to regulate many processes such as cellular metabolism, apoptosis, cellular senescence, cell cycle, and organism-level aging. Among the members of sirtuins showing different subcellular localization, SIRT1, SIRT6 and SIRT7 are localized in nucleus. Whereas many functions and interacting proteins of SIRT1 have been studied, functions of SIRT6 and SIRT7 are not extensively revealed yet. Since it is important to understand the molecular function of SIRT6 and SIRT7, we here aimed to identify interacting proteins in mammalian cells. Affinity purification and nano-liquid chromatography/tandem mass spectrometry were used for exploring novel SIRT6 and SIRT7-interacting partners which were validated by co-immunoprecipitation, immunoblot and confocal microscopy. Taken together, our study has identified novel SIRT6 and SIRT7-interacting proteins. Bioinformatics pipeline: We performed peak list generation of MS data, and identification/quantification of peptides and proteins from three technical replicates of LC-MS/MS data using MaxQuant quantification tool with Andromeda search engine (version 1.3.0.5) (Cox and Mann, 2008; Cox et al., 2009; Cox et al., 2011). Top 10 peaks per 100 Da were used for analysis. Enzyme specificity for trypsin was used. The minimal peptide length was six amino-acids, and we allowed two mis-cleavages. Variable modification options were used for the oxidation of methionine (15.995 Da), and carbamidomethylation of cysteine (57.021 Da). The tolerance was set to 10 ppm for precursor ions and 0.8 Da for fragment ions. SwissProt database (Homo sapiens reference proteome set, release 2013_01, 20,226 entries), to which contaminants and reverse sequences were added. For peptide and protein identification the one percent false discovery rate (FDR) was determined by accumulating 1% of reverse database hits. In the case of identified peptides that are all shared between two proteins, these are combined and reported as one protein group. For comparison between samples we used label-free quantification with a minimum of two ratio counts to determine the normalized protein label-free quantification (LFQ) intensity (Luber et al., 2010).
HostingRepository	PRIDE
AnnounceDate	2014-07-25
AnnouncementXML	Submission_2014-07-25_00:55:15.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dae-Kyum Kim
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; carbamoylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-02-26 02:09:24	ID requested
1	2014-04-28 07:17:57	announced
2	2014-05-15 06:10:44	announced	Updated publication reference for PubMed record(s): 24782448.
⏵ 3	2014-07-25 00:55:16	announced	Updated project metadata.

Lee N, Kim DK, Kim ES, Park SJ, Kwon JH, Shin J, Park SM, Moon YH, Wang HJ, Gho YS, Choi KY, Comparative interactomes of SIRT6 and SIRT7: Implication of functional links to aging. Proteomics, 14(13-14):1610-22(2014) [pubmed]

submitter keyword: SIRT6, SIRT7, LC-MS/MS

Dae-Kyum Kim
contact affiliation	Department of Life Science, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
contact email	sses162@postech.ac.kr
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/04/PXD000159

PRIDE project URI

• PRIDE
  1. PXD000159
     1. Label: PRIDE project
     2. Name: SIRT6 and SIRT7 binding proteome