MassIVE MSV000079945

Imported Reanalysis Dataset Public PXD000065

HiRIEF deep proteomics of A431 human vulvar cancer cell line and N2A mouse neuroblastoma cell line

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Description

Here we present high resolution data from two cancer cell lines. A human cell line, A431 was treated with a drug at different time points and then fractionated into its different subcellular compartments (nuclear, organellar, soluble,whole cell). Protein extracts were trypsinized, peptides separated by HiRIEF (high resolution isoelectric focusing) and analysed by LC-MS. From the mouse cell line N2A proteins were extracted and subjected to the same HiRIEF-LC-MS procedure. All MS/MS spectra were searched by Sequest/Percolator under the software platform Proteome Discoverer (PD, v1.3.0.339, Thermo Scientific) using a target-decoy strategy. The reference databases used were the human protein subset of Ensembl 63 and the mouse protein subset of Ensembl 64. Precursor mass tolerance of 10 ppm and product mass tolerances of 0.02 Da for HCD-FTMS and 0.8 Da for CID-ITMS were used. Additional settings were: trypsin with 1 missed cleavage; Lys-Pro and Arg-Pro not considered as cleavage sites; carbamidomethylation on cysteine and iTRAQ-8plex on lysine and N-terminal as fixed modifications; and oxidation of methionine and phosphorylation on serine, threonine or tyrosine as variable modifications. Quantitation of iTRAQ-8plex reporter ions was done using an integration window tolerance of 20ppm. Peptides found at 1% FDR (false discovery rate) were used by the protein grouping algorithm in PD to infer protein identities. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: A431 ; N2A ; human ; mouse ; LC-MS ; HiRIEF ; isoelectric focusing ; cancer

Contact

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

Publications

Branca RM, Orre LM, Johansson HJ, Granholm V, Huss M, Pérez-Bercoff �, Forshed J, Käll L, Lehtiö J.
HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.
Nat. Methods. 2014 Jan;11(1):59-62. Epub 2013 Nov 17.

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Identification Results
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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.

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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.

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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.

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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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Total number of peptide-spectrum matches (i.e. spectrum identifications) 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.

"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.