MassIVE MSV000079580

Imported Reanalysis Dataset Public PXD000737

iTRAQ-based quantitative proteomics analysis of human HNSCC cells

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Description

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer and is major cause of cancer mortality and morbidity. It emerges within oral cavity, lip, tongue, floor of the mouth, nasopharynx, palate, gingival and larynx, is common cancer worldwide especially in Southeast Asia and Southern China. Despite of the advancements in the understanding of the HNSCC as the disease, the 5 year survival rate remains unchanged at 50% since last three decades. Factors such as advanced stage presentation of the patient and consequent delay in diagnosis contributes to the bleak scenario. Thus, therefore there is dire need of useful biomarkers that can predict HNSCC in early stages and can serve as prognostic indicators or targets for treatment. In the present study, We used iTRAQ (isobaric tags for relative and absolute quantitation)-based quantitative proteomic approach followed by liquid chromatography and high resolution tandem mass spectrometry (LC-MS/MS) to identify differential proteins from head and neck cancer cell lines. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: HNSCC ; iTRAQ ; Biomarker

Contact

Principal Investigators:
(in alphabetical order) 		Dr Akhilesh Pandey
Submitting User: ccms

Publications

Syed N, Chavan S, Sahasrabuddhe NA, Renuse S, Sathe G, Nanjappa V, Radhakrishnan A, Raja R, Pinto SM, Srinivasan A, Prasad TS, Srikumar K, Gowda H, Santosh V, Sidransky D, Califano JA, Pandey A, Chatterjee A.
Silencing of high-mobility group box 2 (HMGB2) modulates cisplatin and 5-fluorouracil sensitivity in head and neck squamous cell carcinoma.
Proteomics. 2015 Jan;15(2-3):383-93.

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Experimental Design
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Identification Results
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Quantification Results
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When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
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.

"N/A" means no results of this type were submitted.
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.