PXD000335

PXD000335 is an original dataset announced via ProteomeXchange.

Title	VHL Cancer
Description	The loss of von Hippel-Lindau (VHL) protein function leads to highly vascular renal tumors characterized by an aggressive course of disease and refractoriness to chemotherapy and radiotherapy. Loss of VHL in renal tumors also differs from tumors of other organs in that the oncogenic cascade is mediated by an increase in the levels of hypoxia-inducible factor-2alpha (HIF2alpha) instead of hypoxia-inducible factor-1alpha (HIF1alpha). MS/MS data generated by data dependent acquisition via the LTQ-FT were extracted by BioWorks version 3.3 and searched against a composite IPI human protein sequence database (IPI _human_v 3.73.par) containing both forward and randomized sequences using Mascot version 2.2 (Matrix Science, Boston, MA) search algorithm. Mascot was searched with a fragment ion mass tolerance of 0.80 Da and a parent ion tolerance of 15.0 ppm assuming trypsin as the digestion enzyme with the possibility of one missed cleavage. Carbamidomethylation of cysteine was specified as a fixed modification, while oxidation of methionine, N-terminal protein acetylation, N-terminal peptide and lysine carbamoylation, and phosphorylation of serine and threonine were specified as variable modifications. The analysis of VHL-wt (Caki-2) human RCC and VHL-mut (786-O) cells was carried out from three independent, biological samples from each cell line (tryptic digests of Caki-2 and 786-O, respectively) and duplicate injections were made for each sample. Data processing was accomplished using two software tools: Scaffold (version Scaffold 3.0, Proteome Software Inc., Portland, OR) and Progenesis LC-MS (version 3.0, Nonlinear Dynamics, Durham, NC). Scaffold was employed to validate MS/MS-based peptide and protein identifications from Mascot database searching. Initial peptide identifications were accepted if they could be established at greater than 95% probability as specified by the Peptide Prophet algorithm [20]. Protein probabilities were assigned by the Protein Prophet algorithm [21]. Protein identifications were accepted, if they reached greater than 99% probability and contained at least 2 identified unique peptides. These identification criteria typically established < 0.01% false discovery rate based on a decoy database search strategy at the protein level. Extracted peptide intensities were evaluated with Progenesis LC-MS to obtain label-free relative quantification from the raw data files. The software created a single aggregate run based on LC retention time of each analysis to contain all MS data with distinguished peptide ions and, then, further feature outline maps were generated for detection and quantification of peptide ions from individual analyses using default program parameters. Peptide quantifications were performed by summing peak intensities followed by normalization, data filtering to retain only ions with positive charges (z) of two and three, and exporting peak lists to query against the IPI human protein sequence database using Mascot (see Database Search subsection above). Proteins were accepted as differentially expressed following analysis of variance (ANOVA, P<0.05), requiring at least a twofold change in expression and also passing validation by Peptide Prophet and Protein Prophet using protein identifications from Scaffold.
HostingRepository	PRIDE
AnnounceDate	2014-07-28
AnnouncementXML	Submission_2014-07-28_00:41:16.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000335
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Laszlo Prokai
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	instrument model: LTQFT

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-11 01:52:17	ID requested
1	2013-08-12 03:30:03	announced
1	2013-10-08 03:17:04	announced
⏵ 2	2014-07-28 00:41:16	announced	Updated project metadata.

Dataset with its publication pending

submitter keyword: Human, VHL, Cancer, HIF-2a, LC-MS/MS

Laszlo Prokai
contact affiliation	Department of Molecular Biology and Immunology
contact email	advancedms@unthsc.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/2013/08/PXD000335

PRIDE project URI

• PRIDE
  1. PXD000335
     1. Label: PRIDE project
     2. Name: VHL Cancer