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PXD000584

PXD000584 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleShotgun Imaging Analyzer Gastric Cancer
DescriptionThe 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).
HostingRepositoryPRIDE
AnnounceDate2014-07-24
AnnouncementXMLSubmission_2014-07-24_03:48:02.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterPaulo Carvalho
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentLTQ Orbitrap Velos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-11-17 13:40:22ID requested
12013-12-05 04:18:47announced
12013-12-06 02:02:47announced
22014-07-24 03:48:03announcedUpdated project metadata.
Publication List
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]
Keyword List
ProteomeXchange project tag: Chromosome-centric Human Proteome Project (C-HPP), Human Proteome Project
curator keyword: Biomedical
submitter keyword: gastric cancer lc/lc/ms/ms
Contact List
Paulo Carvalho
contact affiliationLaboratory for proteomics and protein engineering
contact emailpaulo@pcarvalho.com
dataset submitter
Full Dataset Link List
Dataset FTP location
PRIDE project URI
Repository Record List
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