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RPXD000667

RPXD000667 is an old-style reanalysis announcement missing a container. This dataset should be updated with a proper container and revision following 2019 ProteomeXchange protocols.

Outdated Reanalysis Missing a Container Summary
TitleReprocessed: Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives
DescriptionTet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC) and 5-carboxylcytosine (caC). The exact function of these oxidative cytosine bases remains elusive. We applied quantitative mass spectrometry-based proteomics to identify readers for mC and hmC in mouse embryonic stem cells (mESC), neuronal progenitor cells (NPC) and adult mouse brain tissue. Readers for these modifications are only partially overlapping and some readers, such as Rfx proteins, display strong specificity. Interactions are dynamic during differentiation, as for example evidenced by the mESC-specific binding of Klf4 to mC and the NPC-specific binding of Uhrf2 to hmC, suggesting specific biological roles for mC and hmC. Oxidized derivatives of mC recruit distinct transcription regulators as well as a large number of DNA repair proteins in mouse ES cells, implicating the DNA damage response as a major player in active DNA demethylation. Peptides were separated on an EASY-nLC (Proxeon) connected online to an LTQ-Orbitrap-Velos mass spectrometer. Spectra were recorded in CID mode. A gradient of organic solvent (5-30% acetonitrile) was applied (120 minutes) and the top 15 most abundant peptides were fragmented for MS/MS, using an exclusion list of 500 proteins for 45 seconds. Reprocessed by PeptideAtlas;
HostingRepositoryPeptideAtlas
AnnounceDate2013-12-23
AnnouncementXMLSubmission_2013-12-23_12:17:39.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginReanalysis of PXD000143
RepositorySupportSupported dataset by repository
PrimarySubmitterZhi Sun
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListisotope labeled residue; 6x(13)C labeled L-arginine; 6x(13)C,4x(15)N labeled L-arginine; 6x(13)C,2x(15)N labeled L-lysine; L-methionine sulfoxide; S-carboxamidomethyl-L-cysteine
InstrumentLTQ Orbitrap Velos
Dataset History
ReanalysisRevisionDatetimeStatusTitle / ChangeLog Entry
02013-12-23 11:33:14ID requested
12013-12-23 12:17:59announcedReprocessed: Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives
Publication List
no publication
Keyword List
curator keyword: 5-hydroxymethylcytosine, stem cells, differentiation, quantitative mass spectrometry, chromatin readers
Contact List
Zhi Sun
contact affiliationInstitute for Systems Biology
contact emailzhi.sun@systemsbiology.org
dataset submitter
Eric Deutsch
contact affiliationInstitute for Systems Biology
contact emailedeutsch@systemsbiology.org
lab head
Full Dataset Link List
PeptideAtlas dataset URI