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Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks

Kuras, Magdalena LU ; Betancourt, Lazaro Hiram LU ; Rezeli, Melinda LU ; Rodriguez, Jimmy LU ; Szasz, Marcell LU ; Zhou, Qimin LU ; Miliotis, Tasso LU ; Andersson, Roland LU and Marko-Varga, Gyorgy LU (2019) In Journal of Proteome Research p.548-556
Abstract

Large cohorts of carefully collected clinical tissue materials play a central role in acquiring sufficient depth and statistical power to discover disease-related mechanisms and biomarkers of clinical significance. Manual preparation of such large sample cohorts requires experienced laboratory personnel. This carries other possible downsides such as low throughput, high risk of errors, and low reproducibility. In this work, three automated technologies for high-throughput proteomics of frozen sectioned tissues were compared. The instruments evaluated included the Bioruptor for tissue disruption and protein extraction; the Barocycler, which is able to disrupt tissues and digest the proteins; and the AssayMAP Bravo, a microchromatography... (More)

Large cohorts of carefully collected clinical tissue materials play a central role in acquiring sufficient depth and statistical power to discover disease-related mechanisms and biomarkers of clinical significance. Manual preparation of such large sample cohorts requires experienced laboratory personnel. This carries other possible downsides such as low throughput, high risk of errors, and low reproducibility. In this work, three automated technologies for high-throughput proteomics of frozen sectioned tissues were compared. The instruments evaluated included the Bioruptor for tissue disruption and protein extraction; the Barocycler, which is able to disrupt tissues and digest the proteins; and the AssayMAP Bravo, a microchromatography platform for protein digestion, peptide desalting, and fractionation. Wide varieties of tissue samples from rat spleen, malignant melanoma, and pancreatic tumors were used for the assessment. The three instruments displayed reproducible and consistent results, as was proven by high correlations and low coefficients of variation between technical replicates and even more importantly, between replicates that were processed in different batches or at different time points. The results from this study allowed us to integrate these technologies into an automated sample preparation workflow for large-scale proteomic studies that are currently ongoing. Data are available via ProteomeXchange with identifiers PXD010296 and PXD011295.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
AssayMAP Bravo, Barocycler, Bioruptor, clinical proteomics, mass spectrometry, tissue
in
Journal of Proteome Research
pages
548 - 556
publisher
The American Chemical Society
external identifiers
  • scopus:85058626323
ISSN
1535-3893
DOI
10.1021/acs.jproteome.8b00792
language
English
LU publication?
yes
id
737e5ea2-70af-45a2-82b7-b32200d2ed2b
date added to LUP
2019-01-09 12:51:40
date last changed
2019-01-10 03:00:10
@article{737e5ea2-70af-45a2-82b7-b32200d2ed2b,
  abstract     = {<p>Large cohorts of carefully collected clinical tissue materials play a central role in acquiring sufficient depth and statistical power to discover disease-related mechanisms and biomarkers of clinical significance. Manual preparation of such large sample cohorts requires experienced laboratory personnel. This carries other possible downsides such as low throughput, high risk of errors, and low reproducibility. In this work, three automated technologies for high-throughput proteomics of frozen sectioned tissues were compared. The instruments evaluated included the Bioruptor for tissue disruption and protein extraction; the Barocycler, which is able to disrupt tissues and digest the proteins; and the AssayMAP Bravo, a microchromatography platform for protein digestion, peptide desalting, and fractionation. Wide varieties of tissue samples from rat spleen, malignant melanoma, and pancreatic tumors were used for the assessment. The three instruments displayed reproducible and consistent results, as was proven by high correlations and low coefficients of variation between technical replicates and even more importantly, between replicates that were processed in different batches or at different time points. The results from this study allowed us to integrate these technologies into an automated sample preparation workflow for large-scale proteomic studies that are currently ongoing. Data are available via ProteomeXchange with identifiers PXD010296 and PXD011295.</p>},
  author       = {Kuras, Magdalena and Betancourt, Lazaro Hiram and Rezeli, Melinda and Rodriguez, Jimmy and Szasz, Marcell and Zhou, Qimin and Miliotis, Tasso and Andersson, Roland and Marko-Varga, Gyorgy},
  issn         = {1535-3893},
  keyword      = {AssayMAP Bravo,Barocycler,Bioruptor,clinical proteomics,mass spectrometry,tissue},
  language     = {eng},
  pages        = {548--556},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks},
  url          = {http://dx.doi.org/10.1021/acs.jproteome.8b00792},
  year         = {2019},
}