PXD000186

PXD000186 is an original dataset announced via ProteomeXchange.

Title	AtT 20 endogenous peptides
Description	We performed LC-MSMS analysis using both CID and ETD for the identification of endogenous peptides. Endogenous peptides were extracted from mouse AtT 20 cells by acidified methanol method and all large molecules including proteins were removed by centrifugation. The supernatant containing endogenous peptides was freeze-dried. For LC-MSMS analysis, extracted peptides were resuspended and injected to Ultimate 3000 HPLC system and analysed on LTQ Orbitrap XL mass spectrometer. A 60 min gradient from 2% acetonitrile to 50% acetonitrile, both containing 0.1% formic acid was used to separate peptides on C18 column.The LTQ-Orbitrap mass spectrometer was operated in data-dependent mode, automatically switching between MS and MS/MS acquisition for the three most abundant peaks in a given MS spectrum. A chosen precursor ion was first fragmented by CID and ETD. Data processing: The raw data files were processed with Proteome Discoverer 1.3. The CID and ETD spectra were then written to Mascot generic files. OMSSA (version 2.1.9) was used and b- and y- ions were selected for CID data, and c-, y- and z- ions were used for ETD. The spectra were searched by setting the parent ion mass accuracy to +/- 0.02 Da. For fragment ions, the mass tolerance was set to +/- 0.4 Da. For the genome-wide peptide search, the mouse genomic sequence (NCBI build 37.61) was directly translated in its 6 reading frames, and used for spectral searching. No enzymatic cleavage was taken into account during the database searches. No variable PTMs were included.
HostingRepository	PRIDE
AnnounceDate	2014-12-02
AnnouncementXML	Submission_2014-12-02_00:30:22.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eisuke Hayakawa
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-03-18 10:23:04	ID requested
1	2014-06-09 03:13:53	announced
2	2014-07-25 01:00:01	announced	Updated project metadata.
⏵ 3	2014-12-02 00:30:23	announced	Updated project metadata.

Hayakawa E, Menschaert G, De Bock PJ, Luyten W, Gevaert K, Baggerman G, Schoofs L, Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation. J Proteome Res, 12(12):5410-21(2013) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: peptidome

Eisuke Hayakawa
contact affiliation	Biology Department
contact email	Eisuke.Hayakawa@bio.kuleuven.be
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/PXD000186

PRIDE project URI

• PRIDE
  1. PXD000186
     1. Label: PRIDE project
     2. Name: AtT 20 endogenous peptides