Dataset Information

Platform independent protein-based cell-of-origin subtyping of diffuse large B-cell lymphoma in formalin-fixed paraffin-embedded tissue

ABSTRACT: 10 µm formalin-fixed paraffin-embedded tissue sections were deparaffinized with xylene; homogenization was performed in lysis-buffer (20 mM Tris-HCl, pH 8.8, 200 mM glycine, 200 mM DTT, 4% SDS)in an ultrasonic bath; samples were incubated under continuous agitation first at 99 °C for 30 min, then at 80 °C for 60 min, afterwards centrifuged at 12,000xg for 10 min. 50 µg of protein lysate were further processed according the GASP (Gel-assisted sample preparation) protocol; peptide identification (IDA, information dependent acquisition) and SWATH measurements by LC-MS/MS on TripleTOF5600 (AB Sciex)

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Primary Cell

DISEASE(S): Lymphoma

SUBMITTER: Katharina Limm

LAB HEAD: Prof. Dr. Peter Oefner

PROVIDER: PXD012317 | Pride | 2020-05-18

REPOSITORIES: Pride

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			Action	DRS
	160722LymphomTraining1.wiff	Wiff
	160722LymphomTraining1.wiff.scan	Wiff
	160722LymphomTraining10.wiff	Wiff
	160722LymphomTraining10.wiff.scan	Wiff
	160722LymphomTraining11.wiff	Wiff

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Platform independent protein-based cell-of-origin subtyping of diffuse large B-cell lymphoma in formalin-fixed paraffin-embedded tissue.

Reinders Jörg J Altenbuchinger Michael M Limm Katharina K Schwarzfischer Philipp P Scheidt Tamara T Strasser Lisa L Richter Julia J Szczepanowski Monika M Huber Christian G CG Klapper Wolfram W Spang Rainer R Oefner Peter J PJ

Scientific reports 20200512 1

Diffuse large B-cell lymphoma (DLBCL) is commonly classified by gene expression profiling according to its cell of origin (COO) into activated B-cell (ABC)-like and germinal center B-cell (GCB)-like subgroups. Here we report the application of label-free nano-liquid chromatography - Sequential Window Acquisition of all THeoretical fragment-ion spectra - mass spectrometry (nanoLC-SWATH-MS) to the COO classification of DLBCL in formalin-fixed paraffin-embedded (FFPE) tissue. To generate a protein ...[more]

PMID: 32398793

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