PXD004699-4

PXD004699 is an original dataset announced via ProteomeXchange.

Title	Secretome analysis to elucidate metalloprotease-dependent ectodomain shedding of glycoproteins during neuronal cells differentiation
Description	N1E-115 cells were seeded two days before sample preparation, and cultured in fresh medium containing 2% fetal bovine serum for 12 h before sample preparation. Cells were washed with serum-free medium for three times, and cultured in fresh serum-free DMEM with or without 50 μM GM6001 for 9 h. The conditioned media were collected and centrifuged to remove cell debris, and concentrated up to ~45-fold. Concentrated media were acidified by acetate acidic buffer, and oxidized by NaIO4. Proteins were precipitated with methanol and chloroform, reduced, alkylated, and digested by trypsin. Digested peptides were purified using C18 column, concentrated, diluted with coupling buffer (Biorad), and incubated with Aff-Gel Hydrazide Gel (Biorad). N-glycosylated peptides were eluted and labeled with 18O by treatment with PNGase F (NEB). Eluted peptides were labeled with CH2O (light, DMSO-treated samples) or 13CD2O (heavy, GM6001-treated samples). Each sample was divided into two parts and subjected to LC-MS/MS analysis respectively.
HostingRepository	jPOST
AnnounceDate	2017-01-15
AnnouncementXML	Submission_2018-09-18_22:45:22.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD004699
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Kazuya Tsumagari
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	S-carboxymethyl-L-cysteine; L-methionine sulfoxide; alpha-amino dimethylated residue; Dimethyl:2H(4)13C(2); N6,N6-dimethyl-L-lysine; 2x(13)C,4x(2)H labeled dimethylated L-lysine; Asn->Asp; Delta:H(1)N(-1)18O(1)
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-08-01 18:26:29	ID requested
1	2017-01-15 01:40:01	announced
2	2017-03-29 23:09:31	announced	Updated Repository support.
3	2017-03-29 23:27:24	announced	Updated Repository support.
⏵ 4	2018-09-18 22:45:23	announced	Updated CV, FTP location and Modification list.
5	2021-02-04 17:05:11	announced	2021-02-04: Updated FTP location.
6	2022-09-18 03:53:32	announced	2022-09-18: Updated FTP location.

Tsumagari K, Shirakabe K, Ogura M, Sato F, Ishihama Y, Sehara-Fujisawa A, Secretome analysis to elucidate metalloprotease-dependent ectodomain shedding of glycoproteins during neuronal differentiation. Genes Cells, 22(2):237-244(2017) [pubmed]

submitter keyword: metalloprotease, ADAM, ectodomain shedding, proteomics, secretome, N-glycosylation

Atsuko Sehara-Fujisawa
lab head
Kazuya Tsumagari
contact affiliation	Kyoto University
dataset submitter

jPOST dataset URI

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