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

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 - Nat. Med. (2015)

Bottom Line: 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.From these proteome maps we detected and quantified more than 2,000 proteins with a high degree of reproducibility across all samples.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.

ABSTRACT
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.

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Variation analysis of human kidney tissue proteomes by SWATH-MSThe violin plots show the distribution of CV values from injection replicates, within-patient proteomic variation based on all RCC and ccRCC tissues, and among-patient variation based on all RCC and ccRCC tissues.
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Figure 5: Variation analysis of human kidney tissue proteomes by SWATH-MSThe violin plots show the distribution of CV values from injection replicates, within-patient proteomic variation based on all RCC and ccRCC tissues, and among-patient variation based on all RCC and ccRCC tissues.

Mentions: The availability of PCT-SWATH maps of the 9 paired kidney biopsies allowed us to again determine the technical and biological variation of PCT-SWATH analysis. The median CV of the injection batch variation was below 6%, consistent with the 12 kidney tissue test replicates data discussed above (Fig. 5). To estimate biological variation within an individual, we calculated the median CV of all proteins in the SWATH data quantified in every pair of tissue biopsies, either non-tumorous or tumorous, from each of the 9 RCC patients. The median of median CV values indicating within-patient variation rose to close to 40% (Fig.5). Inter-patient CV values in paired kidney biopsies were slightly higher than intra-patient CV. Interestingly, the median CV value of non-tumorous tissues from patients with ccRCC was 19%, significantly lower than the CV observed in all other variations, except injection batch variation. The tumor tissues among patients, even in the ccRCC subtype, displayed relatively high variation (Fig. 5).


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

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 - Nat. Med. (2015)

Variation analysis of human kidney tissue proteomes by SWATH-MSThe violin plots show the distribution of CV values from injection replicates, within-patient proteomic variation based on all RCC and ccRCC tissues, and among-patient variation based on all RCC and ccRCC tissues.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4390165&req=5

Figure 5: Variation analysis of human kidney tissue proteomes by SWATH-MSThe violin plots show the distribution of CV values from injection replicates, within-patient proteomic variation based on all RCC and ccRCC tissues, and among-patient variation based on all RCC and ccRCC tissues.
Mentions: The availability of PCT-SWATH maps of the 9 paired kidney biopsies allowed us to again determine the technical and biological variation of PCT-SWATH analysis. The median CV of the injection batch variation was below 6%, consistent with the 12 kidney tissue test replicates data discussed above (Fig. 5). To estimate biological variation within an individual, we calculated the median CV of all proteins in the SWATH data quantified in every pair of tissue biopsies, either non-tumorous or tumorous, from each of the 9 RCC patients. The median of median CV values indicating within-patient variation rose to close to 40% (Fig.5). Inter-patient CV values in paired kidney biopsies were slightly higher than intra-patient CV. Interestingly, the median CV value of non-tumorous tissues from patients with ccRCC was 19%, significantly lower than the CV observed in all other variations, except injection batch variation. The tumor tissues among patients, even in the ccRCC subtype, displayed relatively high variation (Fig. 5).

Bottom Line: 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.From these proteome maps we detected and quantified more than 2,000 proteins with a high degree of reproducibility across all samples.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus