MassIVE MSV000083969

Imported Reanalysis Dataset Public PXD000603

Lung cancer and Normal Lung Tissue LC-MS/MS

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Description

The Chromosome-centric Human Proteome Project (C-HPP) was recently initiated as an international collaborative effort. Our team adopted chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic analysis to catalog Chr 9-encoded proteins from normal tissues, lung cancer cell lines and lung cancer tissues. TQ orbitrap, Orbitrap full MS scans were acquired from m/z 350 to 1500 at a resolution of 15 000 (at m/z 400). Parent ions were fragmented using the LTQ (isolation width of 2 m/z units) , with a maximum injection time of 100 ms combined with an AGC value of 1 x104 using three fragmentation modes such as collision-induced dissociation (CID) alone, the reagent ion source emission current, reagent ion electron energy, and reagent ion source chemical ionization pressure were set to 35 mA, 70 V, and 26 psi, respectively. Database : UniProt database (rel. 2012-06, 86,875 entries). Search software : MASCOT software (version 2.2.04). Database search criteria were as follows: taxonomy Homo sapiens, carboxyamidomethylated (+57 Da) at cysteine residues for fixed modifications, oxidized at methionine (+16 Da) residues for variable modi?cations, two maximum allowed missed cleavage, 10 ppm MS tolerance. Only peptides resulting from trypsin digestion were considered. PeptideProphet and ProteinProphet were used to estimate the false discovery rate (FDR). We identified proteins using two or more unique peptides with an FDR < 1% at the protein level. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Lung cancer ; Normal Lung Tissue ; LC-MS/MS

Contact

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

Publications

Ahn JM, Kim MS, Kim YI, Jeong SK, Lee HJ, Lee SH, Paik YK, Pandey A, Cho JY.
Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues.
J. Proteome Res. 2014 Jan 3;13(1):137-46. Epub 2013 Dec 6.

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Owner Reanalyses
Experimental Design
    Conditions:
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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.