PXD000584-2

PXD000584 is an original dataset announced via ProteomeXchange.

Title	Shotgun Imaging Analyzer Gastric Cancer
Description	The data discloses mass spectra of a gastric cancer biopsy sectioned into ten parts, each one subjected to a four step MudPIT analysis (i.e., increasing KCL concentrations of 85, 150, 250, and 400 mM). The biopsy was acquired from an area along the stomach that included tumor and resection margin, during the operation procedures on a male patient. Briefly, the tumor was located in the gastric antrum and the resection margin was macroscopically defined during the surgery as a 10 cm rim of healthy-looking tissue surrounding the tumor. The histological type was determined to be adenocarcinoma and classified as T4. Data analysis: The ProLuCID search engine (v 1.3) was used to compare experimental tandem mass spectra against those theoretically generated from our sequence database and select the most likely peptide spectrum matches (PSMs). Briefly, the search was limited to fully and semi-tryptic peptide candidates and imposed carbamidomethylation and oxidation of methionine as fixed and variable modification, respectively. The search engine accepted peptide candidates within a 50-ppm tolerance from the measured precursor m/z and used the XCorr and Z-Score as the primary and secondary search engine scores, respectively. The validity of the PSMs was assessed using the Search Engine Processor (SEPro, v 2.1.0.23). Identifications were grouped by charge state (+2 and > +3) and then by tryptic status (fully tryptic, semi-tryptic), resulting in four distinct subgroups. For each result, the ProLuCID XCorr, DeltaCN, and ZScore values were used to generate a Bayesian discriminator. Additionally, a minimum sequence length of six amino acid residues was required. Results were post-processed to only accept PSMs with less than 5 ppm and proteins supported by two or more independent evidences (e.g., identification of a peptide with different charge states, a modified and a non-modified version of the same peptide, or two different peptides).
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_03:48:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paulo Carvalho
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-11-17 13:40:22	ID requested
1	2013-12-05 04:18:47	announced
1	2013-12-06 02:02:47	announced
⏵ 2	2014-07-24 03:48:03	announced	Updated project metadata.

Aquino PF, Lima DB, de Saldanha da Gama Fischer J, Melani RD, Nogueira FC, Chalub SR, Soares ER, Barbosa VC, Domont GB, Carvalho PC, Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer. J Proteome Res, 13(1):314-20(2014) [pubmed]

ProteomeXchange project tag: Chromosome-centric Human Proteome Project (C-HPP), Human Proteome Project

curator keyword: Biomedical

submitter keyword: gastric cancer lc/lc/ms/ms

Paulo Carvalho
contact affiliation	Laboratory for proteomics and protein engineering
contact email	paulo@pcarvalho.com
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/2013/12/PXD000584

PRIDE project URI

• PRIDE
  1. PXD000584
     1. Label: PRIDE project
     2. Name: Shotgun Imaging Analyzer Gastric Cancer