PXD000063

PXD000063 is an original dataset announced via ProteomeXchange.

Title	iTRAQ MS of mouse LbetaT2 cells transfected with Galphas siRNA vs. scrambled siRNA
Description	Twenty million LbetaT2 cells were transfected with either control or Galphas siRNA, then were seeded in 100-mm cell culture plates in DMEM + 10% FBS. Two days later, cells were washed twice with pre-warmed PBS. Conditioned media was harvested another 24 h later, and centrifuged at 20,000 g for 10 min at 4°C to remove cell debris. To enrich secreted proteins in the conditioned media, conditioned media samples were centrifuged using Amicon centrifugal filters with a 3kDa cutoff (Millipore, Billerica, MA). A total of 8 concentrated conditioned media samples were independently prepared: 4 samples from control siRNA-treated cells, and 4 samples from Galphas siRNA-treated cells. Samples were stored at –70°C until they were sent to the Mount Sinai Proteomics Core Facility.HPLC-isobaric tags for relative and absolute quantitation mass-spectrometry (iTRAQ MS) - Data analysis ProteinPilot 3.0 (AB Sciex) was used to search the MS/MS spectra for protein identification and quantitation with its searching algorithm Paragon 3.0.0.0 (*Reference). The protein database used for searching was Uniprot mouse fasta file (release-2010_11). The search parameters include quantitation for iTRAQ 8-plex (peptide-labeled), MMTS for cysteine alkylation, trypsin for enzyme digestion, biological modifications for ID focus, and taxonomy set for Mus musculus. The detected protein threshold was set to 1.3 (95% confidence). Additionally, we converted our AB Sciex mass spectral data (TOF/TOF data) into an mzML format, using the AB Sciex MS Data Converter (beta version 1.3) tool. Finally, we used the command line tool group2xml, which is included with ProteinPilot Software, to convert the .group search engine result file to an XML file.
HostingRepository	PRIDE
AnnounceDate	2016-09-27
AnnouncementXML	Submission_2016-09-27_16:19:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hanna Pincas
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	methylthiolated residue; iTRAQ8plex-116 reporter+balance reagent acylated residue; monohydroxylated residue; deamidated residue
Instrument	4800 Proteomics Analyzer

Revision	Datetime	Status	ChangeLog Entry
0	2012-11-02 08:02:20	ID requested
1	2016-09-27 05:30:52	announced
⏵ 2	2016-09-27 16:19:15	announced	Updated publication reference for PubMed record(s): 27466366.

Choi SG, Wang Q, Jia J, Chikina M, Pincas H, Dolios G, Sasaki K, Wang R, Minamino N, Salton SR, Sealfon SC, Characterization of Gonadotrope Secretoproteome Identifies Neurosecretory Protein VGF-derived Peptide Suppression of Follicle-stimulating Hormone Gene Expression. J Biol Chem, 291(40):21322-21334(2016) [pubmed]

submitter keyword: Mouse, pituitary gonadotrope-derived LbetaT2 cells, AB SCIEX TOF/TOF 5800

Stuart C. Sealfon
contact affiliation	Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, NY 10029, and Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, NY 10029
contact email	stuart.sealfon@mssm.edu
lab head
Hanna Pincas
contact affiliation	Neurology
contact email	hanna.pincas@mssm.edu
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/2016/09/PXD000063

PRIDE project URI

• PRIDE
  1. PXD000063
     1. Label: PRIDE project
     2. Name: iTRAQ MS of mouse LbetaT2 cells transfected with Galphas siRNA vs. scrambled siRNA