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

• Published in: Nature medicine Vol. 21; no. 4; pp. 407 - 413
• Main Authors: Guo, Tiannan, Kouvonen, Petri, Koh, Ching Chiek, Gillet, Ludovic C, Wolski, Witold E, Röst, Hannes L, Rosenberger, George, Collins, Ben C, Blum, Lorenz C, Gillessen, Silke, Joerger, Markus, Jochum, Wolfram, Aebersold, Ruedi
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.04.2015; Nature Publishing Group
• Subjects: 13/106; 692/308/1892; 82/16; 82/58; 82/81; Biomedicine; Biopsy; Cancer; Cancer Research; Carcinoma, Renal Cell - metabolism; Comparative analysis; Conversion; Digital mapping; Humans; Infectious Diseases; Ions; Kidney - metabolism; Kidney cancer; Kidney Neoplasms - metabolism; Kidneys; Mass spectrometry; Mass Spectrometry - methods; Mass spectroscopy; Metabolic Diseases; Methods; Molecular Medicine; Neurosciences; Peptides - chemistry; Physiological aspects; Pressure; Protein research; Proteins; Proteome; Proteomes; Proteomics; Proteomics - methods; Renal cell carcinoma; Reproducibility; Reproducibility of Results; Scientific imaging; Spectroscopy; technical-report; Tissues
• ISSN: 1078-8956; 1546-170X
• DOI: 10.1038/nm.3807

A method for converting biopsy-size tissue samples into digital files containing the mass spectrometry–measurable proteome of the sample will allow analysis and re-analysis of limited tissue samples. 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.