PXD013132

PXD013132 is an original dataset announced via ProteomeXchange.

Title	TMT10plex_cTEC_mTEC_beta5tKO-cTEC
Description	TEC cells (K5D1 cTECs in quadruplicate, K5D1 mTECs in triplicate, and K5D1-β5tKO cTECs in triplicate) were lysed in 6 M guanidine-HCl containing 100 mM Tris-HCl, pH 8.0, and 2 mM DTT. The clarified lysates were reduced in 5 mM DTT and alkylated in 27.5 mM iodoacetamide. Proteins were purified by methanol/chloroform precipitation and solubilized by 0.1% RapiGest SF in 50 mM triethylammonium bicarbonate buffer. The proteins were digested with trypsin/Lys-C mix for 16 hr. Approximately 10 µg of peptides for each sample were labeled with 0.2 mg of TMT10-plex reagents for 1 hr at room temperature. After the reaction was quenched with hydroxylamine, all the TMT-labeled samples were pooled, acidified with TFA and fractionated using Pierce high pH reversed-phase peptide fractionation kit. Ten fractions were collected using 5%, 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, 50%, and 80% ACN. Each fraction was evaporated in a SpeedVac concentrator and dissolved in 0.1% TFA. LC-MS/MS analysis of the resultant peptides (1 µg each) was performed on an EASY-nLC 1200 UHPLC connected to a Q Exactive Plus mass spectrometer through a nanoelectrospray ion source. The peptides were separated on a 75 µm inner diameter × 150 mm C18 reversed-phase column. The mass spectrometer was operated in a data-dependent acquisition mode with a top 15 MS/MS method. MS1 spectra were measured with a resolution of 70,000, an automatic gain control (AGC) target of 3×106 and a mass range from 375 to 1,400 m/z. HCD MS/MS spectra were acquired at a resolution of 35,000, an AGC target of 1×105, an isolation window of 0.4 m/z, a maximum injection time of 100 msec and a normalized collision energy of 32. Dynamic exclusion was set to 30 sec. Raw data were directly analyzed against the Swiss-Prot database restricted to Mus musculus using Proteome Discoverer version 2.2 with Mascot search engine version 2.5 for identification and TMT quantification. Peptides and proteins were filtered at a false-discovery rate (FDR) of 1 % using the percolator node and the protein FDR validator node, respectively.
HostingRepository	jPOST
AnnounceDate	2019-10-08
AnnouncementXML	Submission_2022-09-18_02:36:59.548.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hidetaka Kosako
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-18 22:18:14	ID requested
1	2019-10-07 22:37:39	announced
2	2019-10-07 22:46:16	announced	2019-10-08: Updated announcement date.
3	2020-01-09 18:32:29	announced	2020-01-10: Updated PubMed.
4	2021-02-04 16:59:13	announced	2021-02-04: Updated FTP location.
⏵ 5	2022-09-18 02:37:00	announced	2022-09-18: Updated FTP location.

Ohigashi I, Tanaka Y, Kondo K, Fujimori S, Kondo H, Palin AC, Hoffmann V, Kozai M, Matsushita Y, Uda S, Motosugi R, Hamazaki J, Kubota H, Murata S, Tanaka K, Katagiri T, Kosako H, Takahama Y, Trans-omics Impact of Thymoproteasome in Cortical Thymic Epithelial Cells. Cell Rep, 29(9):2901-2916.e6(2019) [pubmed]

submitter keyword: TMT

Hidetaka Kosako
lab head
Hidetaka Kosako
contact affiliation	Tokushima University
dataset submitter

jPOST dataset URI

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.jpostdb.org/JPST000568/