Dataset Information

Human triple negative breast cancer tissues

ABSTRACT: Tissue samples were cut into 8-µm frozen sections and then microdissected to obtain ~4,000 breast cancer epithelial cells using a P.A.L.M. MicroBeam system (Carl Zeiss MicroImaging, GmbH, Munich, Germany). Proteins were extracted from microdissected cells, followed by denaturation, reduction and alkylation. Protein samples were digested at 37oC for 4 h using MS-grade trypsin (Promega, Madison, WI, USA) at a 1:4 (enzyme:protein) ratio, and then acidified for further analysis. Global proteomic profiles of 126 TNBC samples were recorded on a nanoscale LC hyphenated LTQ-Orbitrap-XL MS system (ThermoElectron, Bremen, Germany). Peptide mixtures were separated on the nLC system (Ultimate 3000, Dionex, Amsterdam, The Netherlands) with a 3-h binary gradient (mobile phase A: H2O, mobile phase B: ACN) in a 3-μm C18 silica packed 50-cm capillary column with 75-μm inner-diameter. Mass spectra were acquired over a mass-to-charge ratio (m/z) range of 400–1,800 at a resolving power of 30,000 at 400 m/z. The top five most intensive parent ions from the full scan were isolated and fragmented by collisional activated dissociation in the linear ion trap. Dynamic exclusion was used to increase number of parent ions selected for fragmentation. MaxQuant search used Carbamidomethylation as a fixed modification for cysteine-containing peptides, and oxidation of methionine and N-terminal acetylation as variable modification.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Ning Qing Liu

LAB HEAD: Ning Qing Liu

PROVIDER: PXD000260 | Pride | 2014-01-13

REPOSITORIES: pride

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			Action	DRS
	100531OTc2_RB-AU-0033-100426-001_029.RAW	Raw
	100531OTc2_RB-AU-0033-100426-002_034.RAW	Raw
	100531OTc2_RB-AU-0033-100426-003_039.RAW	Raw
	100531OTc2_RB-AU-0033-100426-005_049.RAW	Raw
	100531OTc2_RB-AU-0033-100426-006_054.RAW	Raw

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Publications

Comparative proteome analysis revealing an 11-protein signature for aggressive triple-negative breast cancer.

Liu Ning Qing NQ Stingl Christoph C Look Maxime P MP Smid Marcel M Braakman René B H RB De Marchi Tommaso T Sieuwerts Anieta M AM Span Paul N PN Sweep Fred C G J FC Linderholm Barbro K BK Mangia Anita A Paradiso Angelo A Dirix Luc Y LY Van Laere Steven J SJ Luider Theo M TM Martens John W M JW Foekens John A JA Umar Arzu A

Journal of the National Cancer Institute 20140107 2

<h4>Background</h4>Clinical outcome of patients with triple-negative breast cancer (TNBC) is highly variable. This study aims to identify and validate a prognostic protein signature for TNBC patients to reduce unnecessary adjuvant systemic therapy.<h4>Methods</h4>Frozen primary tumors were collected from 126 lymph node-negative and adjuvant therapy-naive TNBC patients. These samples were used for global proteome profiling in two series: an in-house training (n = 63) and a multicenter test (n = 6 ...[more]

PMID: 24399849

Publication: 1/2

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