Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps.
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 sequential window acquisition of all theoretical fragment ion spectra (SWATH)-MS. The resulting proteome maps can be analyzed, re-analyzed, compared and mined in silico to detect and quantify specific proteins across multiple samples. We used this method to process and convert 18 biopsy samples from nine patients with renal cell carcinoma into SWATH-MS fragment ion maps. From these proteome maps we detected and quantified more than 2,000 proteins with a high degree of reproducibility across all samples. The measured proteins clearly distinguished tumorous kidney tissues from healthy tissues and differentiated distinct histomorphological kidney cancer subtypes.
Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
Tiannan
T
Guo
1] Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland. [2] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
Petri
P
Kouvonen
1] Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland. [2] BioQuant, Heidelberg University, Heidelberg, Germany.
Ching Chiek
CC
Koh
Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
Ludovic C
LC
Gillet
1] Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland. [2] Systems Biology IT, SystemsX.ch, Zurich, Switzerland.
Witold E
WE
Wolski
1] Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland. [2] PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland.
Hannes L
0000000309907488
HL
Röst
1] Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland. [2] PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland.
George
G
Rosenberger
Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
Ben C
BC
Collins
1] Systems Biology IT, SystemsX.ch, Zurich, Switzerland. [2] Scientific IT Services, ETH Zurich, Zurich, Switzerland.
Lorenz C
LC
Blum
Department of Oncology/Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland.
Silke
S
Gillessen
Department of Oncology/Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland.
Markus
M
Joerger
Institute of Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland.
Wolfram
W
Jochum
1] Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland. [2] Faculty of Science, University of Zurich, Zurich, Switzerland.
Ruedi
R
Aebersold
D001706:Biopsy; D002292:Carcinoma, Renal Cell / Q000378:metabolism; D006801:Humans; D007477:Ions; D007668:Kidney / Q000378:metabolism; D007680:Kidney Neoplasms / Q000378:metabolism; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry; D011312:Pressure; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results
D007477:Ions; D010455:Peptides; D020543:Proteome