Dataset Information

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

ABSTRACT: 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.

OTHER RELATED OMICS DATASETS IN: MSV000083000

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Testis, Placenta, Tonsil, Liver, Epithelial Cell, Kidney

SUBMITTER: Rui Branca

LAB HEAD: Janne Lehtiö

PROVIDER: PXD006291 | Pride | 2018-01-19

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	A431_HiRIEFII_PSM_table_part_a.txt	Txt
	A431_HiRIEFII_PSM_table_part_b.txt	Txt
	A431_HiRIEFII_peptide_table.txt	Txt
	A431_HiRIEFII_protein_table_genecentric.txt	Txt
	A431_HiRIEFII_protein_table_genesymbolcentric.txt	Txt

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Publications

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

Zhu Yafeng Y Orre Lukas M LM Johansson Henrik J HJ Huss Mikael M Boekel Jorrit J Vesterlund Mattias M Fernandez-Woodbridge Alejandro A Branca Rui M M RMM Lehtiö Janne J

Nature communications 20180302 1

Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and vali ...[more]

PMID: 29500430

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