Dataset Information

PCT-SWATH kidney tissues - Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

ABSTRACT: DDA and SWATH analysis of human kidney tissues. Data set used for PCT-SWATH paper. PCT-SWATH provides the first method to generate a digital map representing the proteome of biopsy level clinical samples from which thousands of proteins can be accurately quantified with a high degree of reproducibility across sample sets.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Kidney

DISEASE(S): Kidney Cancer

SUBMITTER: Tiannan Guo

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD000672 | Pride | 2015-02-04

REPOSITORIES: Pride

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Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps.

Guo Tiannan T Kouvonen Petri P Koh Ching Chiek CC Gillet Ludovic C LC Wolski Witold E WE Röst Hannes L HL Rosenberger George G Collins Ben C BC Blum Lorenz C LC Gillessen Silke S Joerger Markus M Jochum Wolfram W Aebersold Ruedi R

Nature medicine 20150302 4

Clinical specimens are each inherently unique, limited and nonrenewable. Small samples such as tissue biopsies are often completely consumed after a limited number of analyses. Here we present a method that enables fast and reproducible conversion of a small amount of tissue (approximating the quantity obtained by a biopsy) into a single, permanent digital file representing the mass spectrometry (MS)-measurable proteome of the sample. The method combines pressure cycling technology (PCT) and seq ...[more]

PMID: 25730263

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Project description:Intra-tumor heterogeneity (ITH) has been studied at the morphologic, genomic, and transcriptomic level, but not proteomic level. Recent advances in mass spectrometric (MS) proteome quantification techniques, exemplified by SWATH-MS, a massively parallel targeting method, now also support precise quantitative proteomic comparisons across multiple samples, thus identifying molecular and implied functional differences. Here we used SWATH-MS to analyze the proteome profiles of a set of fresh-frozen prostate tissue samples derived from radical prostatectomy specimens. A high confidence set of 1,906 proteins were consistently quantified across 60 biopsy-level tissue samples from three prostatectomy patients, each consisting of 1.0 mm punch biopsies from histologically malignant (acinar and ductal adenocarcinoma) and matching benign prostatic hyperplasia tissues. The quantitative protein profiles allowed independent quantification of the degree of intra-tumor heterogeneity for each protein in benign and malignant tissues. We found that while majority of the proteins showed comparably low intra-tumor variability, 122 proteins were highly variable in malignant and/or matching benign tissues. We observed that proteins that varied between patients or tissue types also tended to be highly variable within prostate tissues, suggesting that these variability patterns will be a critical selection criterion in future protein biomarker studies. The data also permitted investigation of the heterogeneity of multiple biochemical pathways. The high variability of several of the pathways, including Glypican-1 network, alpha-linolenic acid metabolism and celecoxib pathway, explained contradictory results regarding them in the literature. In conclusion, we demonstrated a methodology for investigating proteomic intra-tumor heterogeneity from biopsy-level tissue samples, and quantified the degree of intra-tumor heterogeneity of 1,906 proteins in prostate tumors. The method and data presented here have advanced our understanding of tumor biology and offered critical insights for future biomarker development.

			Action	DRS
	consensus.splib	Other
	guot_L121121_001.wiff	Wiff
	guot_L121121_001.wiff.mtd	Wiff
	guot_L121121_001.wiff.scan	Wiff
	guot_L121121_002.wiff	Wiff