PXD000501

PXD000501 is an original dataset announced via ProteomeXchange.

Title	In-depth proteomic analysis of secretome and whole cells of mouse astrocyte
Description	In this study, 3 biological replicates with 3 technical replicates for the conditioned media (CM) and the whole cell lysates (WCL) of C8-D1A cell line were analyzed using 108 LC-MS/MS runs. Each peptide sample was separated into 6 fractions using stageTip based High-pH fractionation. The peptide samples were analyzed using LC-MS/MS instrumentation consisting of a Nanoflow Easy-nLC 1000 that was connected to a Q Exactive mass spectrometer through a nanoelectrospray ion source. All raw files were processed in MaxQuant, version 1.3.0.5 and the Andromeda search engine against the IPI mouse database (version 3.87, 59 534 entries), containing both forward and reverse proteins sequences, and common contaminants. MS/MS searches for the secretome and the whole-cell proteome were performed with the following parameters: carbamidomethylation as a fixed modification; oxidation of methionine and protein N-terminal acetylation as variable modifications; a 20-ppm first-search tolerance; a 6-ppm main-search tolerance. Minimum peptide length was set to six residues. The false discovery rate for all peptides, PTM sites, and protein identifications was set to 0.01.
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_03:47:59.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dohyun Han
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; N-acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2013-10-08 03:47:20	ID requested
1	2014-06-05 08:58:25	announced
⏵ 2	2014-07-24 03:48:00	announced	Updated project metadata.

Han D, Jin J, Woo J, Min H, Kim Y, Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation. Proteomics, 14(13-14):1604-9(2014) [pubmed]

curator keyword: Biological

submitter keyword: mouse, astrocyte, secretome, whole cell proteome, High-pH fractionation, LC-MS/MS

Dohyun Han
contact affiliation	Colleage of medicine
contact email	hdh03@snu.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/2014/06/PXD000501

PRIDE project URI

• PRIDE
  1. PXD000501
     1. Label: PRIDE project
     2. Name: In-depth proteomic analysis of secretome and whole cells of mouse astrocyte