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In-depth membrane proteomic study of breast cancer tissues

ABSTRACT: Proteomics on Human breast cancer tissue samples. 9 patients with high risk or 9 patiens low risk MammaPrint breast cancer. Membran fraction. Proteins were reduced, alkylated, digested with Lys-C and Trypsin, and labelled with iTRAQ4plex: 114; high risk; 115; low risk.

REANALYSED by: PAe004084

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: satoshi muraoka

PROVIDER: PXD000066 | Pride | 2013-01-08

REPOSITORIES: Pride

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			Action	DRS
	BreastCancerMem_Fr1.raw	Raw
	BreastCancerMem_Fr10.raw	Raw
	BreastCancerMem_Fr11.raw	Raw
	BreastCancerMem_Fr12.raw	Raw
	BreastCancerMem_Fr13.raw	Raw

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In-depth membrane proteomic study of breast cancer tissues for the generation of a chromosome-based protein list.

Muraoka Satoshi S Kume Hideaki H Adachi Jun J Shiromizu Takashi T Watanabe Shio S Masuda Takeshi T Ishihama Yasushi Y Tomonaga Takeshi T

Journal of proteome research 20121115 1

The Chromosome-centric Human Proteome Project (C-HPP) aims to define all proteins encoded in each chromosome and especially to identify proteins that currently lack evidence by mass spectrometry. The C-HPP also prioritizes particular protein subsets such as membrane proteins, post-translational modifications, and low-abundance proteins. In this study, we aimed to generate deep profiling of the membrane proteins of human breast cancer tissues on a chromosome-by-chromosome basis using shotgun prot ...[more]

PMID: 23153008

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In-depth membrane proteomic study of breast cancer tissues

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Reanalysis dataset of JPST000201

Project description:Human breast cancer tissue samples from 18 patients with high-risk or low-risk MammaPrint breast cancer were analyzed. The membrane fractions were enriched, and the extracted proteins were reduced, alkylated, digested with Lys-C and Trypsin, and labelled with iTRAQ4plex: 114; high risk; 115; low risk. For this reanalysis, MS Datasets were processed for peak picking with MaxQuant v1.6.2.10, and the generated peak lists were searched against human entries of UniProt/Swiss-Prot release 2018_10 using three search engines: MaxQuant v1.6.2.10, X!Tandem v2015.04.01.1, and Comet 2015.02 rev. 0. The decoy database was generated by reversing sequences from the database. Then, the sum of the total number of matched b/y ions and the total number of amino acids comprising the peptide sequence tag were counted to score the reliability of peptide identification independent of these search engines. Finally, the 1% false discovery rate was controlled by the target-decoy approach with this score.

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Molecular Characterization of Breast Cancer Subtypes from Joint Analysis of High Throughput miRNA and mRNA Data (II)

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Gene expression analysis of pre-defined sets of neoplastic tissues

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E.coli and Human proteome

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