PXD000457

PXD000457 is an original dataset announced via ProteomeXchange.

Title	Large scale proteomics of cholesteatoma
Description	The study describes comprehensive proteomics data of the cholesteatoma disease. Cholesteatoma is a serious and destructive growth of keratinizing squamous epithelium in the middle ear, with a poorly understood etiopathogenesis. The large scale proteomics approach used in this study highly expands our molecular knowledge of cholesteatoma and implicates several biological functions in its pathology. Human samples of cholesteatoma, neck of cholesteatoma, tympanic membrane, external auditory canal skin, and middle ear mucosa were analyzed. Approximately two thousand unique proteins were identified by label-free nanoLC-MS/MS proteomics. The protein and peptide identification data were obtained by Proteome Discoverer (Thermo Scientific, version 1.3.0.339) processing of LTQ Orbitrap raw files using the Mascot algorithm (Matrix Sciences, version 2.4.0). To yield comprehensive proteome data the tissue biopsy was separated into ten protein fractions, which were MS analysed separately, and the resulting MS files were subsequently merged in the database analysis. Precursor mass tolerance was 5 ppm and fragment mass tolerance was 0.5 Da. Dynamic Modification was Oxidation (M) and Static Modification was Carbamidomethyl (C); annotated in the PRIDE files as mass deviations (e g for double charged peptides m/z deviation of approximately 8.00 and 28.51 for modification of Met and Cys, respectively). FASTA file was SwissProt_2012_03.fasta (containing 20,255 Homo sapiens sequences). MudPit scoring was applied, and up to two missed trypsin cleavages were accepted. Peptide cut off Score was 10 and protein relevance threshold was 20.
HostingRepository	PRIDE
AnnounceDate	2014-10-23
AnnouncementXML	Submission_2014-10-23_02:44:18.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000457
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Johan Palmfeldt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap; instrument model: LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-09-11 02:45:33	ID requested
1	2014-06-04 02:24:59	announced
2	2014-07-24 03:50:13	announced	Updated project metadata.
3	2014-08-08 06:06:34	announced	Updated project metadata.
⏵ 4	2014-10-23 02:44:19	announced	Updated project metadata.

Britze A, Birkler RI, Gregersen N, Ovesen T, Palmfeldt J, Large-scale proteomics differentiates cholesteatoma from surrounding tissues and identifies novel proteins related to the pathogenesis. PLoS One, 9(8):e104103(2014) [pubmed]

curator keyword: Biomedical

submitter keyword: Patient, middle ear, biopsy, Cholesteatoma, tympanic membrane, mucosa, epithel

Johan Palmfeldt
contact affiliation	Research Unit of Molecular Medicine
contact email	johan.palmfeldt@ki.au.dk
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/PXD000457

PRIDE project URI

• PRIDE
  1. PXD000457
     1. Label: PRIDE project
     2. Name: Large scale proteomics of cholesteatoma