Tags

Type your tag names separated by a space and hit enter

Method and platform standardization in MRM-based quantitative plasma proteomics.
J Proteomics. 2013 Dec 16; 95:66-76.JP

Abstract

There exists a growing demand in the proteomics community to standardize experimental methods and liquid chromatography-mass spectrometry (LC/MS) platforms in order to enable the acquisition of more precise and accurate quantitative data. This necessity is heightened by the evolving trend of verifying and validating candidate disease biomarkers in complex biofluids, such as blood plasma, through targeted multiple reaction monitoring (MRM)-based approaches with stable isotope-labeled standards (SIS). Considering the lack of performance standards for quantitative plasma proteomics, we previously developed two reference kits to evaluate the MRM with SIS peptide approach using undepleted and non-enriched human plasma. The first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). Here, these kits have been refined for practical use and then evaluated through intra- and inter-laboratory testing on 6 common LC/MS platforms. For an identical panel of 22 plasma proteins, similar concentrations were determined, regardless of the kit, instrument platform, and laboratory of analysis. These results demonstrate the value of the kit and reinforce the utility of standardized methods and protocols.

BIOLOGICAL SIGNIFICANCE

The proteomics community needs standardized experimental protocols and quality control methods in order to improve the reproducibility of MS-based quantitative data. This need is heightened by the evolving trend for MRM-based validation of proposed disease biomarkers in complex biofluids such as blood plasma. We have developed two kits to assist in the inter- and intra-laboratory quality control of MRM experiments: the first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). In this paper, we report the use of these kits in intra- and inter-laboratory testing on 6 common LC/MS platforms. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.

Authors+Show Affiliations

University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23933160

Citation

Percy, Andrew J., et al. "Method and Platform Standardization in MRM-based Quantitative Plasma Proteomics." Journal of Proteomics, vol. 95, 2013, pp. 66-76.
Percy AJ, Chambers AG, Yang J, et al. Method and platform standardization in MRM-based quantitative plasma proteomics. J Proteomics. 2013;95:66-76.
Percy, A. J., Chambers, A. G., Yang, J., Jackson, A. M., Domanski, D., Burkhart, J., Sickmann, A., & Borchers, C. H. (2013). Method and platform standardization in MRM-based quantitative plasma proteomics. Journal of Proteomics, 95, 66-76. https://doi.org/10.1016/j.jprot.2013.07.026
Percy AJ, et al. Method and Platform Standardization in MRM-based Quantitative Plasma Proteomics. J Proteomics. 2013 Dec 16;95:66-76. PubMed PMID: 23933160.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Method and platform standardization in MRM-based quantitative plasma proteomics. AU - Percy,Andrew J, AU - Chambers,Andrew G, AU - Yang,Juncong, AU - Jackson,Angela M, AU - Domanski,Dominik, AU - Burkhart,Julia, AU - Sickmann,Albert, AU - Borchers,Christoph H, Y1 - 2013/08/07/ PY - 2013/05/14/received PY - 2013/07/11/revised PY - 2013/07/26/accepted PY - 2013/8/13/entrez PY - 2013/8/13/pubmed PY - 2014/7/8/medline KW - Kits KW - LC/MS/MS KW - Multiple reaction monitoring KW - Plasma KW - Quantitative proteomics KW - Standardization SP - 66 EP - 76 JF - Journal of proteomics JO - J Proteomics VL - 95 N2 - UNLABELLED: There exists a growing demand in the proteomics community to standardize experimental methods and liquid chromatography-mass spectrometry (LC/MS) platforms in order to enable the acquisition of more precise and accurate quantitative data. This necessity is heightened by the evolving trend of verifying and validating candidate disease biomarkers in complex biofluids, such as blood plasma, through targeted multiple reaction monitoring (MRM)-based approaches with stable isotope-labeled standards (SIS). Considering the lack of performance standards for quantitative plasma proteomics, we previously developed two reference kits to evaluate the MRM with SIS peptide approach using undepleted and non-enriched human plasma. The first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). Here, these kits have been refined for practical use and then evaluated through intra- and inter-laboratory testing on 6 common LC/MS platforms. For an identical panel of 22 plasma proteins, similar concentrations were determined, regardless of the kit, instrument platform, and laboratory of analysis. These results demonstrate the value of the kit and reinforce the utility of standardized methods and protocols. BIOLOGICAL SIGNIFICANCE: The proteomics community needs standardized experimental protocols and quality control methods in order to improve the reproducibility of MS-based quantitative data. This need is heightened by the evolving trend for MRM-based validation of proposed disease biomarkers in complex biofluids such as blood plasma. We have developed two kits to assist in the inter- and intra-laboratory quality control of MRM experiments: the first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). In this paper, we report the use of these kits in intra- and inter-laboratory testing on 6 common LC/MS platforms. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics. SN - 1876-7737 UR - https://www.unboundmedicine.com/medline/citation/23933160/Method_and_platform_standardization_in_MRM_based_quantitative_plasma_proteomics_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1874-3919(13)00431-4 DB - PRIME DP - Unbound Medicine ER -