PXD029272

PXD029272 is an original dataset announced via ProteomeXchange.

Title	LFQ_TurboID-PSMA6_ETP_Tamavidin2-REV
Description	The control and ETP-treated WI-38 cells stably expressing α1-TurboID were seeded and cultured overnight. The cells were treated with 500 μM biotin for 1 h. Preparation of cell lysates, tryptic digestion, and enrichment of biotinylated peptides using Tamavidin 2-REV were performed as described previously (PMID: 32554809). LC-MS/MS analysis of the resultant peptides was performed on an EASY-nLC 1200 UHPLC connected to a Q Exactive mass spectrometer through a nanoelectrospray ion source (Thermo Fisher Scientific). The peptides were separated on a 75-μm-inner-diameter, 150-mm C18 reversed-phase column (Nikkyo Technos, Tokyo, Japan) with a linear 4–32% ACN gradient for 0–60 min, followed by an increase to 80% ACN for 10 min. The mass spectrometer was operated in data-dependent acquisition mode with a top 10 MS/MS method. MS1 spectra were measured with a resolution of 70,000, an AGC target of 1 × 106, and a mass range from 350 to 1,500 m/z. MS/MS spectra were triggered at a resolution of 17,500, an AGC target of 5 × 104, an isolation window of 2.0 m/z, a maximum injection time of 200 ms, and a normalized collision energy of 27. Dynamic exclusion was set to 15 s. Raw data were directly analyzed against the SwissProt database restricted to Homo sapiens using Proteome Discoverer (v.2.4; Thermo Fisher Scientific) with Sequest HT search engine. The search parameters were the following: (a) trypsin as an enzyme with up to two missed cleavages; (b) precursor mass tolerance of 10 ppm; (c) fragment mass tolerance of 0.02 Da; (d) carbamidomethylation of cysteine as a fixed modification; and (e) acetylation of protein N-terminus, oxidation of methionine, and biotinylation of lysine as variable modifications. Peptides were filtered at a false discovery rate <0.01 using the Percolator node in Proteome Discoverer. Label-free quantification was performed using the Precursor Ions Quantifier node.
HostingRepository	jPOST
AnnounceDate	2022-10-21
AnnouncementXML	Submission_2022-10-20_08:00:11.974.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shu Yasuda
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; N6-biotinyl-L-lysine; L-methionine sulfoxide; alpha-amino acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-21 07:50:01	ID requested
⏵ 1	2022-10-20 08:00:12	announced

Dataset with its publication pending

submitter keyword: LFQ, TurboID

Shigeo Murata
lab head
Shu Yasuda
contact affiliation	University of Tokyo
dataset submitter

jPOST dataset URI

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