Simplified and Efficient Quantification of Low-abundance Proteins at Very High Multiplex via Targeted Mass Spectrometry

Molecular & Cellular Proteomics - Tập 13 - Trang 1137-1149 - 2014
Michael W. Burgess1, Hasmik Keshishian1, D.R. Mani1, Michael A. Gillette1,2, Steven A. Carr1
1Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142;
2Massachusetts General Hospital, Boston, Massachusetts 02114

Tài liệu tham khảo

Gillette, 2012, Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry, Nat. Methods, 10, 28, 10.1038/nmeth.2309 Keshishian, 2007, Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution, Mol. Cell. Proteomics, 6, 2212, 10.1074/mcp.M700354-MCP200 Keshishian, 2009, Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution, Mol. Cell. Proteomics, 8, 2339, 10.1074/mcp.M900140-MCP200 Addona, 2011, A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease, Nat. Biotechnol, 29, 635, 10.1038/nbt.1899 Kuhn, 2009, Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry, Clin. Chem, 55, 1108, 10.1373/clinchem.2009.123935 Kuhn, 2012, Inter-laboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma, Mol. Cell. Proteomics, 11, 10.1074/mcp.M111.013854 Whiteaker, 2010, An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers, Mol. Cell. Proteomics, 9, 184, 10.1074/mcp.M900254-MCP200 Whiteaker, 2011, A targeted proteomics-based pipeline for verification of biomarkers in plasma, Nat. Biotechnol, 29, 625, 10.1038/nbt.1900 Whiteaker, 2011, Peptide immunoaffinity enrichment coupled with mass spectrometry for peptide and protein quantification, Clin. Lab. Med, 31, 385, 10.1016/j.cll.2011.07.004 Thakur, 2011, Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation, Mol. Cell. Proteomics, 9, 2529 MacLean, 2010, Skyline: an open source document editor for creating and analyzing targeted proteomics experiments, Bioinformatics, 26, 966, 10.1093/bioinformatics/btq054 Abbatiello, 2010, Automated detection of inaccurate and imprecise transitions in quantitative assays of peptides by multiple monitoring mass spectrometry, Clin. Chem, 56, 291, 10.1373/clinchem.2009.138420 Desmet, 2005, Geometry-independent plate height representation methods for the direct comparison of the kinetic performance of LC supports with a different size of morphology, Anal. Chem, 77, 4058, 10.1021/ac050160z Broeckhoven, 2010, The kinetic plot method applied to gradient chromatography: theoretical framework and experimental validation, J. Chromatogr. A, 1217, 2787, 10.1016/j.chroma.2010.02.023 Vaast, 2012, Comparison of the gradient kinetic performance of silica monolithic capillary columns with columns packed with 3mm porous and 2.7mm fused-core silica particles, J. Chromatogr. A, 1228, 270, 10.1016/j.chroma.2011.07.089 Gilar, 2004, Implications of column peak capacity on the separation of complex peptide mixtures in single- and two-dimensional high-performance liquid chromatography, J. Chromatogr, 1061, 183, 10.1016/j.chroma.2004.10.092 Liu, 2007, Effects of column length, particle size, gradient length and flow rate on peak capacity of nano-scale liquid chromatography for peptide separations, J. Chromatogr, 1147, 30, 10.1016/j.chroma.2007.02.016 Hsieh, 2012, Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS/MS of complex proteomic samples, J. Am. Soc. Mass Spectrom, 24, 148, 10.1007/s13361-012-0508-6 Nagaraj, 2012, System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap, Mol. Cell. Proteomics, 11, 10.1074/mcp.M111.013722 Shi, 2013, Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis, Anal. Chem, 85, 9196, 10.1021/ac402105s Shi, 2012, Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum, Proc. Natl. Acad. Sci. U.S.A, 109, 15395, 10.1073/pnas.1204366109 Liu, 2013, Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS, Proteomics, 13, 1247, 10.1002/pmic.201200417 Egertson, 2013, Multiplexed MS/MS for improved data-independent acquisition, Nat. Methods, 10, 744, 10.1038/nmeth.2528