PCT-SWATH kidney tissues
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.
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