MassIVE MSV000083000

Imported Reanalysis Dataset Public PXD006291

HiRIEFII proteomics and proteogenomics of A431 cells and five histologically normal tissues

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Description

High Resolution Isoelectric Focusing (HiRIEF) LC-MS was used to analyze samples from the human A431 cell line and also samples of histologically normal tissues. The high analytical depth afforded by HiRIEF permitted proteogenomics on these two sample sets (A431 cells and normal tissues). The A431 data was obtained from a time course experiment upon Gefitinib treatment (EGFR inhibition) of A431 cells with harvests at 2h, 6h and 24h after treatment as well of untreated cells. Isobaric tag labelling of peptide samples with TMT10plex was used. Biological triplicate controls (TMT channels 126, 127N, 127C), duplicate 2h (128N, 128C), duplicate 6h (129N, 129C) and triplicate 24h (130N, 130C, 131) samples were employed. The normal tissues data was obtained from two separate TMT10plex sets. TMT set1 was composed of 9 samples, all from different individuals, including three placenta samples (126, 127N, 127C) two liver samples (128N, 128C), two kidney samples (129N, 129C), two tonsil samples (130N, 130C), plus an internal pooled standard (131). TMT set2 was composed of 8 samples, all from different individuals, including one tonsil sample (126), two liver samples (127C, 128N), two kidney samples (128C, 129N), three testis samples (129C, 130N, 130C), plus an internal pooled standard (131). The internal pooled standard was made by combining equal aliquots of the tryptic peptide mixtures from each of the 17 tissue samples. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: human ; A431 ; kidney ; placenta ; testis ; tonsil ; liver

Contact

Principal Investigators:
(in alphabetical order) 		Janne Lehti�, Department of Oncology-Pathology, Karolinska Institutet, and Science For Life Laboratory, Stockholm, Sweden, N/A
Submitting User: ccms

Publications

Zhu Y, Orre LM, Johansson HJ, Huss M, Boekel J, Vesterlund M, Fernandez-Woodbridge A, Branca RMM, Lehtiö J.
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.
Nat Commun. 2018 Mar 2;9(1):903. Epub 2018 Mar 2.

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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.

"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.