MassIVE MSV000082884

Imported Reanalysis Dataset Public PXD000619

Quantitative proteomic analysis of gallbladder cancer

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Description

We carried out an iTRAQ-based quantitative proteomic analysis of gallbladder cancer and adjacent non-tumor tissue to systematically identify differentially expressed proteins in gallbladder cancer. Ten gallbladder adenocarcinoma and ten adjacent non-tumor tissue samples were selected post pathological confirmation for the study. Samples were pooled and In-solution trypsin digestion was carried out. Post digestion, peptides were iTRAQ labeled with 114 and 115 (gallbladder adenocarcinoma) and 116 and 117 (adjacent non-tumor samples). LC-MS/MS analysis of SCX fractions was carried out using a reversed phase analytical C18 column connected to 1200 Series Nanoflow LC interfaced with LTQ-Orbitrap Velos. Data were acquired using Xcalibur 2.1. Proteome Discoverer (v 1.3) suite was used for quantitation and database searches. LC-MS/MS data were searched using Mascot and SEQUEST search algorithms against Human RefSeq 50 supplemented with frequently observed contaminants. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: gallbladder cancer ; iTRAQ ; quantitative proteomics ; prosaposin ; transgelin ; biomarkers

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Principal Investigators:
(in alphabetical order) 		None Listed
Submitting User: ccms

Publications

Sahasrabuddhe NA, Barbhuiya MA, Bhunia S, Subbannayya T, Gowda H, Advani J, Shrivastav BR, Navani S, Leal P, Roa JC, Chaerkady R, Gupta S, Chatterjee A, Pandey A, Tiwari PK.
Identification of prosaposin and transgelin as potential biomarkers for gallbladder cancer using quantitative proteomics.
Biochem. Biophys. Res. Commun. 2014 Apr 18;446(4):863-9. Epub 2014 Mar 20.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.