Project PXD000672

PRIDE Assigned Tags:
Biomedical Dataset

Summary

Title

PCT-SWATH kidney tissues

Description

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.

Sample Processing Protocol

SWATH data: biopsy tissues were lysed and digested using pressure cycling technology (PCT) (lys-c and trypsin), and analyzed using SWATH-MS. DDA data 1: a pool of kidney tissues were separated using SDS-PAGE into 15 fractions and digested in gel. The peptides were analyzed in tripleTOF. DDA data 2: each kidney tissue were lyzed and digested using PCT, and analyzed in tripleTOF.

Data Processing Protocol

DDA data were analyzed using iPortal, and Trans Proteome Pipeline. Spectrast was used to generate spectral library for SWATH data analysis. SWATH data were analyzed using OpenSWATH software and the library produced from the DDA data.

Contact

Tiannan Guo, Westlake University
Ruedi Aebersold, ETH Zurich, Switzerland ( lab head )

Submission Date

08/01/2014

Publication Date

04/02/2015

Tissue

kidney

Cell Type

epithelial cell

Disease

kidney cancer

Instrument

TripleTOF 5600

Software

Not available

Experiment Type

Shotgun proteomics

Publication

    Guo T, Kouvonen P, Koh CC, Gillet LC, Wolski WE, Röst HL, Rosenberger G, Collins BC, Blum LC, Gillessen S, Joerger M, Jochum W, Aebersold R. Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nat Med. 2015 Apr;21(4):407-13 PubMed: 25730263