PXD000243

PXD000243 is an original dataset announced via ProteomeXchange.

Title	Telomeric protein composition deriving from q-TIP analysis comparing Hela supertelomerase cells, Hela TRF2 knockdown cells or Hela POT1 knockdown cells with Hela control cells, proteomes by 2D-LC-MS/MS
Description	All samples derived from the q-TIP experiments were analysed using reverse-phase chromatography coupled to orbitrap high-resolution mass spectrometer using trypsin digestion. MS/MS files were searched against the UniProt human protein database (release date 18-04-2012) by MaxQuant software (version 1.2.2.5 and 1.3.0.5). Mass spectra were searched with an initial mass tolerance of 7 ppm in MS mode and 0.5 Da in MS/MS mode. Up to two missed cleavages were allowed. Carbamidomethylation was set as a fixed modification, whereas oxidation (M) and acetylation (Protein N-term) were considered as variable modifications. Phospho (STY) was set as variable modifications for the approach B as well. Minimum required peptide length was set to six amino acids (seven for the approach B) and at least two (unique + razor) peptides were required for protein identification. A cut-off was fixed at 1% FDR at the peptide and protein level. Reverse and contaminants sequences were removed and proteins with a Posterior Error Probability (PEP) lower than 0.1 were accepted for further data treatment. Protein quantification was performed with razor and unique peptides, using only unmodified, oxidated (M) and acetylated (Protein N-term) peptides. A minimum of two ratio counts was required to quantify proteins. A FDR < 0.05 was applied on the Significances B to accept proteins significantly differentially quantified between conditions. In the article and the supplementary table 2, Rep3 corresponds to the forward experiment or the second replicate (Rep2)
HostingRepository	PRIDE
AnnounceDate	2014-07-25
AnnouncementXML	Submission_2014-07-25_01:09:12.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Romain Hamelin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; phosphorylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2013-05-07 02:51:43	ID requested
1	2013-11-26 03:13:58	announced
1	2013-11-26 05:49:52	announced
⏵ 2	2014-07-25 01:09:12	announced	Updated project metadata.

Dataset with its publication pending

submitter keyword: Human, SILAC, LC-MS/MS, telomers, chromatin, telomer length

Romain Hamelin
contact affiliation	PCF
contact email	romain.hamelin@epfl.ch
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/2013/11/PXD000243

PRIDE project URI

• PRIDE
  1. PXD000243
     1. Label: PRIDE project
     2. Name: Telomeric protein composition deriving from q-TIP analysis comparing Hela supertelomerase cells, Hela TRF2 knockdown cells or Hela POT1 knockdown cells with Hela control cells, proteomes by 2D-LC-MS/MS