Future Trends and Perspectives of Quantitative Clinical Proteomics
Main Article Content
Abstract
ABSTRACT
Protein quantitation is an important clinical parameter for diagnosis, prognosis, and treatment monitoring such as drug response. In the past the assays were done mostly using antibody-based immunoassays such as radio-immunoassay (RIA) assays or enzyme-linked immunosorbent assay (ELISA). As novel changes that locate beyond the epitopes regions recognized by the antibody render the immunoassays non useful, detection methods that can sense chemical structural changes becomes desirable. Mass spectrometry offers speed, versatility, and sensitivity for the assay without the needs of a priori knowledge of the target molecules. The instrument can measure thousands of proteins (proteomics) simultaneously without losing the sensitivity. Specific novel mass spectra denote specific novel modifications on the target molecules. The report reviews quantitative proteomics using mass spectrometry with emphasis on biomarkers for diagnostics; biological fluids proteomics, tagging functional groups of proteins and eventually non-tagging quantitative proteomics which can offer great potential for emerging biomedical advanced technologies for better management of diseases.
Article Details
How to Cite
MUNOZ, San Juanita; LUI, Lokai Miranda; EASTWOOD LEUNG, Hon-chiu.
Future Trends and Perspectives of Quantitative Clinical Proteomics.
Medical Research Archives, [S.l.], n. 3, june 2015.
ISSN 2375-1924.
Available at: <https://esmed.org/MRA/mra/article/view/93>. Date accessed: 19 apr. 2024.
Keywords
immunoassays; biomarkers; mass spectrometry; quantitative proteomics
Issue
Section
Review Articles
The Medical Research Archives grants authors the right to publish and reproduce the unrevised contribution in whole or in part at any time and in any form for any scholarly non-commercial purpose with the condition that all publications of the contribution include a full citation to the journal as published by the Medical Research Archives.
References
Abbatiello, S. E., B. Schilling, D. R. Mani, L. J. Zimmerman, S. C. Hall, B. MacLean, M. Albertolle, S. Allen, M. Burgess, M. P. Cusack, M. Ghosh, V. Hedrick, J. M. Held, H. D. Inerowicz, A. Jackson, H. Keshishian, C. R. Kinsinger, J. Lyssand, L. Makowski, M. Mesri, H. Rodriguez, P. Rudnick, P. Sadowski, N. Sedransk, K. Shaddox, S. J. Skates, E. Kuhn, D. Smith, J. R. Whiteaker, C. Whitwell, S. Zhang, C. H. Borchers, S. J. Fisher, B. W. Gibson, D. C. Liebler, M. J. MacCoss, T. A. Neubert, A. G. Paulovich, F. E. Regnier, P. Tempst and S. A. Carr (2015). "Large-scale inter-laboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma." Mol Cell Proteomics. Epub ahead of print. http://www.ncbi.nlm.nih.gov/pubmed/25693799
Arntzen, M. O., C. J. Koehler, A. Treumann and B. Thiede (2011). "Quantitative proteome analysis using isobaric peptide termini labeling (IPTL)." Methods Mol Biol 753: 65-76.
Blonder, J., M. L. Hale, K. C. Chan, L. R. Yu, D. A. Lucas, T. P. Conrads, M. Zhou, M. R. Popoff, H. J. Issaq, B. G. Stiles and T. D. Veenstra (2005). "Quantitative profiling of the detergent-resistant membrane proteome of iota-b toxin induced vero cells." J Proteome Res 4(2): 523-531.
Boersema, P. J., T. T. Aye, T. A. van Veen, A. J. Heck and S. Mohammed (2008). "Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates." Proteomics 8(22): 4624-4632.
Carr, S. A., S. E. Abbatiello, B. L. Ackermann, C. Borchers, B. Domon, E. W. Deutsch, R. P. Grant, A. N. Hoofnagle, R. Huttenhain, J. M. Koomen, D. C. Liebler, T. Liu, B. MacLean, D. R. Mani, E. Mansfield, H. Neubert, A. G. Paulovich, L. Reiter, O. Vitek, R. Aebersold, L. Anderson, R. Bethem, J. Blonder, E. Boja, J. Botelho, M. Boyne, R. A. Bradshaw, A. L. Burlingame, D. Chan, H. Keshishian, E. Kuhn, C. Kinsinger, J. S. Lee, S. W. Lee, R. Moritz, J. Oses-Prieto, N. Rifai, J. Ritchie, H. Rodriguez, P. R. Srinivas, R. R. Townsend, J. Van Eyk, G. Whiteley, A. Wiita and S. Weintraub (2014). "Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach." Mol Cell Proteomics 13(3): 907-917.
el-Shabrawi, Y., C. Livir-Rallatos, W. Christen, S. Baltatzis and C. S. Foster (1998). "High levels of interleukin-12 in the aqueous humor and vitreous of patients with uveitis." Ophthalmology 105(9): 1659-1663.
Engwegen, J. Y., H. H. Helgason, A. Cats, N. Harris, J. M. Bonfrer, J. H. Schellens and J. H. Beijnen (2006). "Identification of serum proteins discriminating colorectal cancer patients and healthy controls using surface-enhanced laser desorption ionisation-time of flight mass spectrometry." World J Gastroenterol 12(10): 1536-1544.
Fenyo, D., J. Qin and B. T. Chait (1998). "Protein identification using mass spectrometric information." Electrophoresis 19(6): 998-1005.
Fuhrman, B. J., C. Schairer, M. H. Gail, J. Boyd-Morin, X. Xu, L. Y. Sue, S. S. Buys, C. Isaacs, L. K. Keefer, T. D. Veenstra, C. D. Berg, R. N. Hoover and R. G. Ziegler (2012). "Estrogen metabolism and risk of breast cancer in postmenopausal women." J Natl Cancer Inst 104(4): 326-339.
Gharbi, S., P. Gaffney, A. Yang, M. J. Zvelebil, R. Cramer, M. D. Waterfield and J. F. Timms (2002). "Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system." Mol Cell Proteomics 1(2): 91-98.
Gillet, L. C., P. Navarro, S. Tate, H. Rost, N. Selevsek, L. Reiter, R. Bonner and R. Aebersold (2012). "Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis." Mol Cell Proteomics 11(6): O111 016717.
Gygi, S. P., B. Rist, S. A. Gerber, F. Turecek, M. H. Gelb and R. Aebersold (1999). "Quantitative analysis of complex protein mixtures using isotope-coded affinity tags." Nat Biotechnol 17(10): 994-999.
Hamacher, M., R. Apweiler, G. Arnold, A. Becker, M. Bluggel, O. Carrette, C. Colvis, M. J. Dunn, T. Frohlich, M. Fountoulakis, A. van Hall, F. Herberg, J. Ji, H. Kretzschmar, P. Lewczuk, G. Lubec, K. Marcus, L. Martens, N. Palacios Bustamante, Y. M. Park, S. R. Pennington, J. Robben, K. Stuhler, K. A. Reidegeld, P. Riederer, J. Rossier, J. C. Sanchez, M. Schrader, C. Stephan, D. Tagle, H. Thiele, J. Wang, J. Wiltfang, J. S. Yoo, C. Zhang, J. Klose and H. E. Meyer (2006). "HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy." Proteomics 6(18): 4890-4898.
Hood, B. L., D. A. Lucas, G. Kim, K. C. Chan, J. Blonder, H. J. Issaq, T. D. Veenstra, T. P. Conrads, I. Pollet and A. Karsan (2005). "Quantitative analysis of the low molecular weight serum proteome using 18O stable isotope labeling in a lung tumor xenograft mouse model." J Am Soc Mass Spectrom 16(8): 1221-1230.
Jones, K. A., P. D. Kim, B. B. Patel, S. G. Kelsen, A. Braverman, D. J. Swinton, P. R. Gafken, L. A. Jones, W. S. Lane, J. M. Neveu, H. C. Leung, S. A. Shaffer, J. D. Leszyk, B. A. Stanley, T. E. Fox, A. Stanley, M. J. Hall, H. Hampel, C. D. South, A. de la Chapelle, R. W. Burt, D. A. Jones, L. Kopelovich and A. T. Yeung (2013). "Immunodepletion plasma proteomics by tripleTOF 5600 and Orbitrap elite/LTQ-Orbitrap Velos/Q exactive mass spectrometers." J Proteome Res 12(10): 4351-4365.
Klose, J. and H. Spielmann (1975). "Gel isoelectric focusing of mouse lactate dehydrogenase: heterogeneity of the isoenzymes A4 and X4." Biochem Genet 13(9-10): 707-720.
Listgarten, J. and A. Emili (2005). "Practical proteomic biomarker discovery: taking a step back to leap forward." Drug Discov Today 10(23-24): 1697-1702.
Listgarten, J. and A. Emili (2005). "Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry." Mol Cell Proteomics 4(4): 419-434.
Listgarten, J., R. M. Neal, S. T. Roweis, P. Wong and A. Emili (2007). "Difference detection in LC-MS data for protein biomarker discovery." Bioinformatics 23(2): e198-204.
Little, R. R. and W. L. Roberts (2009). "A review of variant hemoglobins interfering with hemoglobin A1c measurement." J Diabetes Sci Technol 3(3): 446-451.
Liu, H., R. G. Sadygov and J. R. Yates, 3rd (2004). "A model for random sampling and estimation of relative protein abundance in shotgun proteomics." Anal Chem 76(14): 4193-4201.
Lundgren, D. H., S. I. Hwang, L. Wu and D. K. Han (2010). "Role of spectral counting in quantitative proteomics." Expert Rev Proteomics 7(1): 39-53.
Mann, M. (2006). "Functional and quantitative proteomics using SILAC." Nat Rev Mol Cell Biol 7(12): 952-958.
Moore, L. E., R. M. Pfeiffer, Z. Zhang, K. H. Lu, E. T. Fung and R. C. Bast, Jr. (2012). "Proteomic biomarkers in combination with CA 125 for detection of epithelial ovarian cancer using prediagnostic serum samples from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial." Cancer 118(1): 91-100.
Neher, S. B., J. Villen, E. C. Oakes, C. E. Bakalarski, R. T. Sauer, S. P. Gygi and T. A. Baker (2006). "Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon." Mol Cell 22(2): 193-204.
Neubert, T. A. and P. Tempst (2010). "Super-SILAC for tumors and tissues." Nat Methods 7(5): 361-362.
Omenn, G. S. (2004). "Advancement of biomarker discovery and validation through the HUPO plasma proteome project." Dis Markers 20(3): 131-134.
Omenn, G. S. (2007). "THE HUPO Human Plasma Proteome Project." Proteomics Clin Appl 1(8): 769-779.
Ong, S. E., L. J. Foster and M. Mann (2003). "Mass spectrometric-based approaches in quantitative proteomics." Methods 29(2): 124-130.
Petzold, A., A. Altintas, L. Andreoni, A. Bartos, A. Berthele, M. A. Blankenstein, L. Buee, M. Castellazzi, S. Cepok, M. Comabella, C. S. Constantinescu, F. Deisenhammer, G. Deniz, G. Erten, M. Espino, E. Fainardi, D. Franciotta, M. S. Freedman, V. Giedraitis, N. E. Gilhus, G. Giovannoni, A. Glabinski, P. Grieb, H. P. Hartung, B. Hemmer, S. K. Herukka, R. Hintzen, M. Ingelsson, S. Jackson, S. Jacobsen, N. Jafari, M. Jalosinski, S. Jarius, E. Kapaki, B. C. Kieseier, M. J. Koel-Simmelink, J. Kornhuber, J. Kuhle, J. Kurzepa, P. H. Lalive, L. Lannfelt, V. Lehmensiek, P. Lewczuk, P. Livrea, F. Marnetto, D. Martino, T. Menge, N. Norgren, E. Papuc, G. P. Paraskevas, T. Pirttila, C. Rajda, K. Rejdak, J. Ricny, D. Ripova, L. Rosengren, M. Ruggieri, S. Schraen, G. Shaw, C. Sindic, A. Siva, T. Stigbrand, I. Stonebridge, B. Topcular, M. Trojano, H. Tumani, H. A. Twaalfhoven, L. Vecsei, V. Van Pesch, H. Vanderstichele, C. Vedeler, M. M. Verbeek, L. M. Villar, R. Weissert, B. Wildemann, C. Yang, K. Yao and C. E. Teunissen (2010). "Neurofilament ELISA validation." J Immunol Methods 352(1-2): 23-31.
Qian, W. J., M. E. Monroe, T. Liu, J. M. Jacobs, G. A. Anderson, Y. Shen, R. J. Moore, D. J. Anderson, R. Zhang, S. E. Calvano, S. F. Lowry, W. Xiao, L. L. Moldawer, R. W. Davis, R. G. Tompkins, D. G. Camp, 2nd, R. D. Smith, Inflammation and P. the Host Response to Injury Large Scale Collaborative Research (2005). "Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach." Mol Cell Proteomics 4(5): 700-709.
Qin, J. and B. T. Chait (1997). "Identification and characterization of posttranslational modifications of proteins by MALDI ion trap mass spectrometry." Anal Chem 69(19): 4002-4009.
Qin, J., D. Fenyo, Y. Zhao, W. W. Hall, D. M. Chao, C. J. Wilson, R. A. Young and B. T. Chait (1997). "A strategy for rapid, high-confidence protein identification." Anal Chem 69(19): 3995-4001.
Rauniyar, N. and J. R. Yates, 3rd (2014). "Isobaric labeling-based relative quantification in shotgun proteomics." J Proteome Res 13(12): 5293-5309.
Ross, P. L., Y. N. Huang, J. N. Marchese, B. Williamson, K. Parker, S. Hattan, N. Khainovski, S. Pillai, S. Dey, S. Daniels, S. Purkayastha, P. Juhasz, S. Martin, M. Bartlet-Jones, F. He, A. Jacobson and D. J. Pappin (2004). "Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents." Mol Cell Proteomics 3(12): 1154-1169.
Schubert, O. T., L. C. Gillet, B. C. Collins, P. Navarro, G. Rosenberger, W. E. Wolski, H. Lam, D. Amodei, P. Mallick, B. MacLean and R. Aebersold (2015). "Building high-quality assay libraries for targeted analysis of SWATH MS data." Nat Protoc 10(3): 426-441.
Sharma, M. P., M. Irshad and N. Verma (1989). "Serum alpha-feto protein in amoebic liver abscess." Indian J Med Res 90: 127-130.
Silva, J. C., R. Denny, C. A. Dorschel, M. Gorenstein, I. J. Kass, G. Z. Li, T. McKenna, M. J. Nold, K. Richardson, P. Young and S. Geromanos (2005). "Quantitative proteomic analysis by accurate mass retention time pairs." Anal Chem 77(7): 2187-2200.
Smith, L. M., N. L. Kelleher and P. Consortium for Top Down Proteomics (2013). "Proteoform: a single term describing protein complexity." Nat Methods 10(3): 186-187.
Sze, S. K., Y. Ge, H. Oh and F. W. McLafferty (2002). "Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue." Proc Natl Acad Sci U S A 99(4): 1774-1779.
Sze, S. K., Y. Ge, H. Oh and F. W. McLafferty (2003). "Plasma electron capture dissociation for the characterization of large proteins by top down mass spectrometry." Anal Chem 75(7): 1599-1603.
Taguchi, A., K. Politi, S. J. Pitteri, W. W. Lockwood, V. M. Faca, K. Kelly-Spratt, C. H. Wong, Q. Zhang, A. Chin, K. S. Park, G. Goodman, A. F. Gazdar, J. Sage, D. M. Dinulescu, R. Kucherlapati, R. A. Depinho, C. J. Kemp, H. E. Varmus and S. M. Hanash (2011). "Lung cancer signatures in plasma based on proteome profiling of mouse tumor models." Cancer Cell 20(3): 289-299.
Tammen, H., I. Schulte, R. Hess, C. Menzel, M. Kellmann, T. Mohring and P. Schulz-Knappe (2005). "Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display." Proteomics 5(13): 3414-3422.
Thompson, A., J. Schafer, K. Kuhn, S. Kienle, J. Schwarz, G. Schmidt, T. Neumann, R. Johnstone, A. K. Mohammed and C. Hamon (2003). "Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS." Anal Chem 75(8): 1895-1904.
Wang, J., Y. Gu, L. Wang, X. Hang, Y. Gao, H. Wang and C. Zhang (2007). "HUPO BPP pilot study: a proteomics analysis of the mouse brain of different developmental stages." Proteomics 7(21): 4008-4015.
Wiener, M. C., J. R. Sachs, E. G. Deyanova and N. A. Yates (2004). "Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures." Anal Chem 76(20): 6085-6096.
Winter, D., J. Seidler, S. Ziv-Lehrman, Y. Shiloh and W. D. Lehmann (2009). "Simultaneous identification and quantification of proteins by differential (16)O/(18)O labeling and UPLC-MS/MS applied to mouse cerebellar phosphoproteome following irradiation." Anticancer Res 29(12): 4949-4958.
Zhou, G., H. Li, D. DeCamp, S. Chen, H. Shu, Y. Gong, M. Flaig, J. W. Gillespie, N. Hu, P. R. Taylor, M. R. Emmert-Buck, L. A. Liotta, E. F. Petricoin, 3rd and Y. Zhao (2002). "2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers." Mol Cell Proteomics 1(2): 117-124.
Zybailov, B., M. K. Coleman, L. Florens and M. P. Washburn (2005). "Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling." Anal Chem 77(19): 6218-6224.
Arntzen, M. O., C. J. Koehler, A. Treumann and B. Thiede (2011). "Quantitative proteome analysis using isobaric peptide termini labeling (IPTL)." Methods Mol Biol 753: 65-76.
Blonder, J., M. L. Hale, K. C. Chan, L. R. Yu, D. A. Lucas, T. P. Conrads, M. Zhou, M. R. Popoff, H. J. Issaq, B. G. Stiles and T. D. Veenstra (2005). "Quantitative profiling of the detergent-resistant membrane proteome of iota-b toxin induced vero cells." J Proteome Res 4(2): 523-531.
Boersema, P. J., T. T. Aye, T. A. van Veen, A. J. Heck and S. Mohammed (2008). "Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates." Proteomics 8(22): 4624-4632.
Carr, S. A., S. E. Abbatiello, B. L. Ackermann, C. Borchers, B. Domon, E. W. Deutsch, R. P. Grant, A. N. Hoofnagle, R. Huttenhain, J. M. Koomen, D. C. Liebler, T. Liu, B. MacLean, D. R. Mani, E. Mansfield, H. Neubert, A. G. Paulovich, L. Reiter, O. Vitek, R. Aebersold, L. Anderson, R. Bethem, J. Blonder, E. Boja, J. Botelho, M. Boyne, R. A. Bradshaw, A. L. Burlingame, D. Chan, H. Keshishian, E. Kuhn, C. Kinsinger, J. S. Lee, S. W. Lee, R. Moritz, J. Oses-Prieto, N. Rifai, J. Ritchie, H. Rodriguez, P. R. Srinivas, R. R. Townsend, J. Van Eyk, G. Whiteley, A. Wiita and S. Weintraub (2014). "Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach." Mol Cell Proteomics 13(3): 907-917.
el-Shabrawi, Y., C. Livir-Rallatos, W. Christen, S. Baltatzis and C. S. Foster (1998). "High levels of interleukin-12 in the aqueous humor and vitreous of patients with uveitis." Ophthalmology 105(9): 1659-1663.
Engwegen, J. Y., H. H. Helgason, A. Cats, N. Harris, J. M. Bonfrer, J. H. Schellens and J. H. Beijnen (2006). "Identification of serum proteins discriminating colorectal cancer patients and healthy controls using surface-enhanced laser desorption ionisation-time of flight mass spectrometry." World J Gastroenterol 12(10): 1536-1544.
Fenyo, D., J. Qin and B. T. Chait (1998). "Protein identification using mass spectrometric information." Electrophoresis 19(6): 998-1005.
Fuhrman, B. J., C. Schairer, M. H. Gail, J. Boyd-Morin, X. Xu, L. Y. Sue, S. S. Buys, C. Isaacs, L. K. Keefer, T. D. Veenstra, C. D. Berg, R. N. Hoover and R. G. Ziegler (2012). "Estrogen metabolism and risk of breast cancer in postmenopausal women." J Natl Cancer Inst 104(4): 326-339.
Gharbi, S., P. Gaffney, A. Yang, M. J. Zvelebil, R. Cramer, M. D. Waterfield and J. F. Timms (2002). "Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system." Mol Cell Proteomics 1(2): 91-98.
Gillet, L. C., P. Navarro, S. Tate, H. Rost, N. Selevsek, L. Reiter, R. Bonner and R. Aebersold (2012). "Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis." Mol Cell Proteomics 11(6): O111 016717.
Gygi, S. P., B. Rist, S. A. Gerber, F. Turecek, M. H. Gelb and R. Aebersold (1999). "Quantitative analysis of complex protein mixtures using isotope-coded affinity tags." Nat Biotechnol 17(10): 994-999.
Hamacher, M., R. Apweiler, G. Arnold, A. Becker, M. Bluggel, O. Carrette, C. Colvis, M. J. Dunn, T. Frohlich, M. Fountoulakis, A. van Hall, F. Herberg, J. Ji, H. Kretzschmar, P. Lewczuk, G. Lubec, K. Marcus, L. Martens, N. Palacios Bustamante, Y. M. Park, S. R. Pennington, J. Robben, K. Stuhler, K. A. Reidegeld, P. Riederer, J. Rossier, J. C. Sanchez, M. Schrader, C. Stephan, D. Tagle, H. Thiele, J. Wang, J. Wiltfang, J. S. Yoo, C. Zhang, J. Klose and H. E. Meyer (2006). "HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy." Proteomics 6(18): 4890-4898.
Hood, B. L., D. A. Lucas, G. Kim, K. C. Chan, J. Blonder, H. J. Issaq, T. D. Veenstra, T. P. Conrads, I. Pollet and A. Karsan (2005). "Quantitative analysis of the low molecular weight serum proteome using 18O stable isotope labeling in a lung tumor xenograft mouse model." J Am Soc Mass Spectrom 16(8): 1221-1230.
Jones, K. A., P. D. Kim, B. B. Patel, S. G. Kelsen, A. Braverman, D. J. Swinton, P. R. Gafken, L. A. Jones, W. S. Lane, J. M. Neveu, H. C. Leung, S. A. Shaffer, J. D. Leszyk, B. A. Stanley, T. E. Fox, A. Stanley, M. J. Hall, H. Hampel, C. D. South, A. de la Chapelle, R. W. Burt, D. A. Jones, L. Kopelovich and A. T. Yeung (2013). "Immunodepletion plasma proteomics by tripleTOF 5600 and Orbitrap elite/LTQ-Orbitrap Velos/Q exactive mass spectrometers." J Proteome Res 12(10): 4351-4365.
Klose, J. and H. Spielmann (1975). "Gel isoelectric focusing of mouse lactate dehydrogenase: heterogeneity of the isoenzymes A4 and X4." Biochem Genet 13(9-10): 707-720.
Listgarten, J. and A. Emili (2005). "Practical proteomic biomarker discovery: taking a step back to leap forward." Drug Discov Today 10(23-24): 1697-1702.
Listgarten, J. and A. Emili (2005). "Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry." Mol Cell Proteomics 4(4): 419-434.
Listgarten, J., R. M. Neal, S. T. Roweis, P. Wong and A. Emili (2007). "Difference detection in LC-MS data for protein biomarker discovery." Bioinformatics 23(2): e198-204.
Little, R. R. and W. L. Roberts (2009). "A review of variant hemoglobins interfering with hemoglobin A1c measurement." J Diabetes Sci Technol 3(3): 446-451.
Liu, H., R. G. Sadygov and J. R. Yates, 3rd (2004). "A model for random sampling and estimation of relative protein abundance in shotgun proteomics." Anal Chem 76(14): 4193-4201.
Lundgren, D. H., S. I. Hwang, L. Wu and D. K. Han (2010). "Role of spectral counting in quantitative proteomics." Expert Rev Proteomics 7(1): 39-53.
Mann, M. (2006). "Functional and quantitative proteomics using SILAC." Nat Rev Mol Cell Biol 7(12): 952-958.
Moore, L. E., R. M. Pfeiffer, Z. Zhang, K. H. Lu, E. T. Fung and R. C. Bast, Jr. (2012). "Proteomic biomarkers in combination with CA 125 for detection of epithelial ovarian cancer using prediagnostic serum samples from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial." Cancer 118(1): 91-100.
Neher, S. B., J. Villen, E. C. Oakes, C. E. Bakalarski, R. T. Sauer, S. P. Gygi and T. A. Baker (2006). "Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon." Mol Cell 22(2): 193-204.
Neubert, T. A. and P. Tempst (2010). "Super-SILAC for tumors and tissues." Nat Methods 7(5): 361-362.
Omenn, G. S. (2004). "Advancement of biomarker discovery and validation through the HUPO plasma proteome project." Dis Markers 20(3): 131-134.
Omenn, G. S. (2007). "THE HUPO Human Plasma Proteome Project." Proteomics Clin Appl 1(8): 769-779.
Ong, S. E., L. J. Foster and M. Mann (2003). "Mass spectrometric-based approaches in quantitative proteomics." Methods 29(2): 124-130.
Petzold, A., A. Altintas, L. Andreoni, A. Bartos, A. Berthele, M. A. Blankenstein, L. Buee, M. Castellazzi, S. Cepok, M. Comabella, C. S. Constantinescu, F. Deisenhammer, G. Deniz, G. Erten, M. Espino, E. Fainardi, D. Franciotta, M. S. Freedman, V. Giedraitis, N. E. Gilhus, G. Giovannoni, A. Glabinski, P. Grieb, H. P. Hartung, B. Hemmer, S. K. Herukka, R. Hintzen, M. Ingelsson, S. Jackson, S. Jacobsen, N. Jafari, M. Jalosinski, S. Jarius, E. Kapaki, B. C. Kieseier, M. J. Koel-Simmelink, J. Kornhuber, J. Kuhle, J. Kurzepa, P. H. Lalive, L. Lannfelt, V. Lehmensiek, P. Lewczuk, P. Livrea, F. Marnetto, D. Martino, T. Menge, N. Norgren, E. Papuc, G. P. Paraskevas, T. Pirttila, C. Rajda, K. Rejdak, J. Ricny, D. Ripova, L. Rosengren, M. Ruggieri, S. Schraen, G. Shaw, C. Sindic, A. Siva, T. Stigbrand, I. Stonebridge, B. Topcular, M. Trojano, H. Tumani, H. A. Twaalfhoven, L. Vecsei, V. Van Pesch, H. Vanderstichele, C. Vedeler, M. M. Verbeek, L. M. Villar, R. Weissert, B. Wildemann, C. Yang, K. Yao and C. E. Teunissen (2010). "Neurofilament ELISA validation." J Immunol Methods 352(1-2): 23-31.
Qian, W. J., M. E. Monroe, T. Liu, J. M. Jacobs, G. A. Anderson, Y. Shen, R. J. Moore, D. J. Anderson, R. Zhang, S. E. Calvano, S. F. Lowry, W. Xiao, L. L. Moldawer, R. W. Davis, R. G. Tompkins, D. G. Camp, 2nd, R. D. Smith, Inflammation and P. the Host Response to Injury Large Scale Collaborative Research (2005). "Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach." Mol Cell Proteomics 4(5): 700-709.
Qin, J. and B. T. Chait (1997). "Identification and characterization of posttranslational modifications of proteins by MALDI ion trap mass spectrometry." Anal Chem 69(19): 4002-4009.
Qin, J., D. Fenyo, Y. Zhao, W. W. Hall, D. M. Chao, C. J. Wilson, R. A. Young and B. T. Chait (1997). "A strategy for rapid, high-confidence protein identification." Anal Chem 69(19): 3995-4001.
Rauniyar, N. and J. R. Yates, 3rd (2014). "Isobaric labeling-based relative quantification in shotgun proteomics." J Proteome Res 13(12): 5293-5309.
Ross, P. L., Y. N. Huang, J. N. Marchese, B. Williamson, K. Parker, S. Hattan, N. Khainovski, S. Pillai, S. Dey, S. Daniels, S. Purkayastha, P. Juhasz, S. Martin, M. Bartlet-Jones, F. He, A. Jacobson and D. J. Pappin (2004). "Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents." Mol Cell Proteomics 3(12): 1154-1169.
Schubert, O. T., L. C. Gillet, B. C. Collins, P. Navarro, G. Rosenberger, W. E. Wolski, H. Lam, D. Amodei, P. Mallick, B. MacLean and R. Aebersold (2015). "Building high-quality assay libraries for targeted analysis of SWATH MS data." Nat Protoc 10(3): 426-441.
Sharma, M. P., M. Irshad and N. Verma (1989). "Serum alpha-feto protein in amoebic liver abscess." Indian J Med Res 90: 127-130.
Silva, J. C., R. Denny, C. A. Dorschel, M. Gorenstein, I. J. Kass, G. Z. Li, T. McKenna, M. J. Nold, K. Richardson, P. Young and S. Geromanos (2005). "Quantitative proteomic analysis by accurate mass retention time pairs." Anal Chem 77(7): 2187-2200.
Smith, L. M., N. L. Kelleher and P. Consortium for Top Down Proteomics (2013). "Proteoform: a single term describing protein complexity." Nat Methods 10(3): 186-187.
Sze, S. K., Y. Ge, H. Oh and F. W. McLafferty (2002). "Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue." Proc Natl Acad Sci U S A 99(4): 1774-1779.
Sze, S. K., Y. Ge, H. Oh and F. W. McLafferty (2003). "Plasma electron capture dissociation for the characterization of large proteins by top down mass spectrometry." Anal Chem 75(7): 1599-1603.
Taguchi, A., K. Politi, S. J. Pitteri, W. W. Lockwood, V. M. Faca, K. Kelly-Spratt, C. H. Wong, Q. Zhang, A. Chin, K. S. Park, G. Goodman, A. F. Gazdar, J. Sage, D. M. Dinulescu, R. Kucherlapati, R. A. Depinho, C. J. Kemp, H. E. Varmus and S. M. Hanash (2011). "Lung cancer signatures in plasma based on proteome profiling of mouse tumor models." Cancer Cell 20(3): 289-299.
Tammen, H., I. Schulte, R. Hess, C. Menzel, M. Kellmann, T. Mohring and P. Schulz-Knappe (2005). "Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display." Proteomics 5(13): 3414-3422.
Thompson, A., J. Schafer, K. Kuhn, S. Kienle, J. Schwarz, G. Schmidt, T. Neumann, R. Johnstone, A. K. Mohammed and C. Hamon (2003). "Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS." Anal Chem 75(8): 1895-1904.
Wang, J., Y. Gu, L. Wang, X. Hang, Y. Gao, H. Wang and C. Zhang (2007). "HUPO BPP pilot study: a proteomics analysis of the mouse brain of different developmental stages." Proteomics 7(21): 4008-4015.
Wiener, M. C., J. R. Sachs, E. G. Deyanova and N. A. Yates (2004). "Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures." Anal Chem 76(20): 6085-6096.
Winter, D., J. Seidler, S. Ziv-Lehrman, Y. Shiloh and W. D. Lehmann (2009). "Simultaneous identification and quantification of proteins by differential (16)O/(18)O labeling and UPLC-MS/MS applied to mouse cerebellar phosphoproteome following irradiation." Anticancer Res 29(12): 4949-4958.
Zhou, G., H. Li, D. DeCamp, S. Chen, H. Shu, Y. Gong, M. Flaig, J. W. Gillespie, N. Hu, P. R. Taylor, M. R. Emmert-Buck, L. A. Liotta, E. F. Petricoin, 3rd and Y. Zhao (2002). "2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers." Mol Cell Proteomics 1(2): 117-124.
Zybailov, B., M. K. Coleman, L. Florens and M. P. Washburn (2005). "Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling." Anal Chem 77(19): 6218-6224.