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

Magdalena Kuras, Lazaro Hiram Betancourt, Melinda Rezeli, Jimmy Rodriguez, A. Szász, Qimin Zhou, Tasso Miliotis, Roland Andersson, Gyorgy Marko-Varga

???family-name???: Article

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 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.

???language???English
???pages???548-556
???numberOfPages???9
???journalAssociation???Journal of Proteome Research
???volume???18
???journalNumber???1
???DOIs???
???publicationStatus???Published - jan. 4 2019

Fingerprint

Proteomics
Mass spectrometry
Mass Spectrometry
Throughput
Tissue
Technology
tetrachloroisophthalonitrile
Laboratory Personnel
Salt removal
Proteins
Workflow
Biomarkers
Fractionation
Proteolysis
Rats
Tumors
Melanoma
Spleen
Personnel
Peptides

Keywords

    ASJC Scopus subject areas

    • Biochemistry
    • Chemistry(all)

    Cite this

    Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks. / Kuras, Magdalena; Betancourt, Lazaro Hiram; Rezeli, Melinda; Rodriguez, Jimmy; Szász, A.; Zhou, Qimin; Miliotis, Tasso; Andersson, Roland; Marko-Varga, Gyorgy.

    ???in???: Journal of Proteome Research, ???journal.volume??? 18, ???journalNumber??? 1, 04.01.2019, ???pages??? 548-556.

    ???family-name???: Article

    Kuras, M, Betancourt, LH, Rezeli, M, Rodriguez, J, Szász, A, Zhou, Q, Miliotis, T, Andersson, R & Marko-Varga, G 2019, 'Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks', Journal of Proteome Research, ???journal.volume??? 18, ???journalNumber??? 1, ???pages??? 548-556. https://doi.org/10.1021/acs.jproteome.8b00792
    Kuras, Magdalena ; Betancourt, Lazaro Hiram ; Rezeli, Melinda ; Rodriguez, Jimmy ; Szász, A. ; Zhou, Qimin ; Miliotis, Tasso ; Andersson, Roland ; Marko-Varga, Gyorgy. / Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks. ???in???: Journal of Proteome Research. 2019 ; ???journal.volume??? 18, ???journalNumber??? 1. ???pages??? 548-556.
    @article{9132b4abc692413cb93d531186884944,
    title = "Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks",
    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 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.",
    keywords = "AssayMAP Bravo, Barocycler, Bioruptor, clinical proteomics, mass spectrometry, tissue",
    author = "Magdalena Kuras and Betancourt, {Lazaro Hiram} and Melinda Rezeli and Jimmy Rodriguez and A. Sz{\'a}sz and Qimin Zhou and Tasso Miliotis and Roland Andersson and Gyorgy Marko-Varga",
    year = "2019",
    month = "1",
    day = "4",
    doi = "10.1021/acs.jproteome.8b00792",
    language = "English",
    volume = "18",
    pages = "548--556",
    journal = "Journal of Proteome Research",
    issn = "1535-3893",
    publisher = "American Chemical Society",
    number = "1",

    }

    TY - JOUR

    T1 - Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks

    AU - Kuras, Magdalena

    AU - Betancourt, Lazaro Hiram

    AU - Rezeli, Melinda

    AU - Rodriguez, Jimmy

    AU - Szász, A.

    AU - Zhou, Qimin

    AU - Miliotis, Tasso

    AU - Andersson, Roland

    AU - Marko-Varga, Gyorgy

    PY - 2019/1/4

    Y1 - 2019/1/4

    N2 - 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.

    AB - 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.

    KW - AssayMAP Bravo

    KW - Barocycler

    KW - Bioruptor

    KW - clinical proteomics

    KW - mass spectrometry

    KW - tissue

    UR - http://www.scopus.com/inward/record.url?scp=85058626323&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=85058626323&partnerID=8YFLogxK

    U2 - 10.1021/acs.jproteome.8b00792

    DO - 10.1021/acs.jproteome.8b00792

    M3 - Article

    VL - 18

    SP - 548

    EP - 556

    JO - Journal of Proteome Research

    T2 - Journal of Proteome Research

    JF - Journal of Proteome Research

    SN - 1535-3893

    IS - 1

    ER -