Dataset Information

Shotgun Imaging Analyzer Gastric Cancer

ABSTRACT: 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).

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Paulo Carvalho

PROVIDER: PXD000584 | Pride | 2013-12-05

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20130607_Priscy_A10_150mM_a.raw	Raw
	20130607_Priscy_A10_150mM_a.sqt	Other
	20130607_Priscy_A10_150mM_b.raw	Raw
	20130607_Priscy_A10_150mM_b.sqt	Other
	20130607_Priscy_A10_150mM_c.raw	Raw

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Publications

Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer.

Aquino Priscila Ferreira PF Lima Diogo Borges DB de Saldanha da Gama Fischer Juliana J Melani Rafael Donadélli RD Nogueira Fabio C S FC Chalub Sidney R S SR Soares Elzalina R ER Barbosa Valmir C VC Domont Gilberto B GB Carvalho Paulo C PC

Journal of proteome research 20131127 1

Accessing localized proteomic profiles has emerged as a fundamental strategy to understand the biology of diseases, as recently demonstrated, for example, in the context of determining cancer resection margins with improved precision. Here, we analyze a gastric cancer biopsy sectioned into 10 parts, each one subjected to MudPIT analysis. We introduce a software tool, named Shotgun Imaging Analyzer and inspired in MALDI imaging, to enable the overlaying of a protein's expression heat map on a tis ...[more]

PMID: 24283986

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