PXD000109

PXD000109 is an original dataset announced via ProteomeXchange.

Title	ThinPrep Cervical Smear iTRAQ LC-MS/MS
Description	The protein content from ThinPrep cervical smear specimens was purified with TCA precipitation. The protein pellets were dissolved and protein concentration was measured with the Bradford assay. 100 ug of protein for each sample were reduced with TCEP, cysteines were blocked with MMTS and finally digested overnight with trypsin. The resultant peptides were labeled with the iTRAQ 8plex reagents and after mixing were subjected to off-line high pH C18 fractionation. The peptide fractions were further analyzed with low pH C18 LC-Orbitrap Elite HCD MS/MS (MS resolution 120,000, top 10 precursors, isolation width 1.2 m/z, 100 min gradient method). Protein Identification was performed using Proteome Discoverer 1.3 software. SEQUEST node included prec. mass tolerance: 10 ppm, fragment mass tolerance 0.5 Da, iTRAQ8plex Nterm and K,Y static modification, Methylthio static modification, Phospho S variable modification, Oxidation M variable modification, Deamidation N,Q variable modification. All spectra were search against a Uniprot fasta file containing all reviewed Human entries and all reviewed and un-reviewed human papillomavirus entries. Peptide and PTM validation was performed with Percolator and PhosphoRS nodes respectively. Protein quantitation was performed with the Reporter Ions Quantifier node.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:16:49.636.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Theodoros Roumeliotis
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue; phosphorylated residue; iTRAQ8plex-116 reporter+balance reagent acylated residue; monohydroxylated residue; deamidated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2012-12-14 05:49:17	ID requested
1	2013-05-09 15:14:03	announced
1	2014-07-25 00:47:34	announced
2	2013-05-09 15:16:31	announced	Add reference
⏵ 3	2024-10-22 04:16:50	announced	2024-10-22: Updated project metadata.

10.1021/pr301067r;

Papachristou EK, Roumeliotis TI, Chrysagi A, Trigoni C, Charvalos E, Townsend PA, Pavlakis K, Garbis SD, The shotgun proteomic study of the human ThinPrep cervical smear using iTRAQ mass-tagging and 2D LC-FT-Orbitrap-MS: the detection of the human papillomavirus at the protein level. J Proteome Res, 12(5):2078-89(2013) [pubmed]

submitter keyword: HPV, Orbitrap Elite,ThinPrep, iTRAQ

Theodoros Roumeliotis
contact affiliation	WTSI
contact email	tr6@sanger.ac.uk
lab head
Theodoros Roumeliotis
contact affiliation	WTSI
contact email	tr6@sanger.ac.uk
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/2013/05/PXD000109

PRIDE project URI

• PRIDE
  1. PXD000109
     1. Label: PRIDE project
     2. Name: ThinPrep Cervical Smear iTRAQ LC-MS/MS