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Correlation of Relative Abundance Ratios Derived from Peptide Ion Chromatograms and Spectrum Counting for Quantitative Proteomic Analysis Using Stable Isotope Labeling

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Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110
Cite this: Anal. Chem. 2005, 77, 19, 6218–6224
Publication Date (Web):August 31, 2005
https://doi.org/10.1021/ac050846r
Copyright © 2005 American Chemical Society

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    Abstract

    In this study, S. cerevisiae crude membrane fractions were prepared using the acid-labile detergent RapiGest from cells grown under rich and minimal media conditions using 14N and 15N ammonium sulfate as the sole nitrogen source. Four independent MudPIT analyses of 1:1 mixtures of sample were prepared and analyzed via quantitative multidimensional protein identification technology on a two-dimensional ion trap mass spectrometer. Using the method described in this study, low-abundance integral membrane proteins with up to 14 transmembrane domains were identified and their protein expression determined when sufficient spectrum counting and ion chromatogram information was generated. We demonstrate that spectrum counting and mass spectrometry derived ion chromatograms strongly correlate for determining quantitative changes in protein expression. Spectrum counting proved more reproducible and has a wider dynamic range contributing to the deviation of the two quantitative approaches from a perfect positive correlation.

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    70. Kyle Mangano, Tanja Florin, Xinhao Shao, Dorota Klepacki, Irina Chelysheva, Zoya Ignatova, Yu Gao, Alexander S Mankin, Nora Vázquez-Laslop. Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria. eLife 2020, 9 https://doi.org/10.7554/eLife.62655
    71. Thomas L. Williams, Stephen L. Senft, Jingjie Yeo, Francisco J. Martín-Martínez, Alan M. Kuzirian, Camille A. Martin, Christopher W. DiBona, Chun-Teh Chen, Sean R. Dinneen, Hieu T. Nguyen, Conor M. Gomes, Joshua J. C. Rosenthal, Matthew D. MacManes, Feixia Chu, Markus J. Buehler, Roger T. Hanlon, Leila F. Deravi. Dynamic pigmentary and structural coloration within cephalopod chromatophore organs. Nature Communications 2019, 10 (1) https://doi.org/10.1038/s41467-019-08891-x
    72. Hiroko Otake, Tetushi Yamamoto, Saori Deguchi, Atushi Taga, Noriaki Nagai. Retinal proteomic evaluation of rats following streptozotocin‑injection using shotgun proteomics. Molecular Medicine Reports 2019, 78 https://doi.org/10.3892/mmr.2019.10801
    73. Haruhiko Nakamura, Kiyonaga Fujii, Vipul Gupta, Hiroko Hata, Hirotaka Koizumu, Masahiro Hoshikawa, Saeko Naruki, Yuka Miyata, Ikuya Takahashi, Tomoyuki Miyazawa, Hiroki Sakai, Kouhei Tsumoto, Masayuki Takagi, Hisashi Saji, Toshihide Nishimura, . Identification of key modules and hub genes for small-cell lung carcinoma and large-cell neuroendocrine lung carcinoma by weighted gene co-expression network analysis of clinical tissue-proteomes. PLOS ONE 2019, 14 (6) , e0217105. https://doi.org/10.1371/journal.pone.0217105
    74. Susan T. Weintraub, Nurul Humaira Mohd Redzuan, Melissa K. Barton, Nur Amira Md Amin, Maxim I. Desmond, Lily E. Adams, Bazla Ali, Sammy Pardo, Dana Molleur, Weimin Wu, William W. Newcomb, Michael V. Osier, Lindsay W. Black, Alasdair C. Steven, Julie A. Thomas, . Global Proteomic Profiling of Salmonella Infection by a Giant Phage. Journal of Virology 2019, 93 (5) https://doi.org/10.1128/JVI.01833-18
    75. Boris L. Zybailov, Galina V. Glazko, Yasir Rahmatallah, Dmitri S. Andreyev, Taylor McElroy, Oleg Karaduta, Stephanie D. Byrum, Lisa Orr, Alan J. Tackett, Samuel G. Mackintosh, Ricky D. Edmondson, Dorothy A. Kieffer, R. J. Martin, Sean H. Adams, Nosratola D. Vaziri, John M. Arthur, . Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats. PLOS ONE 2019, 14 (1) , e0199274. https://doi.org/10.1371/journal.pone.0199274
    76. Tetsushi Yamamoto, Tomoyo Nishita, Atsushi Taga. Dark‑colored maple syrup treatment induces S‑phase cell cycle arrest via reduced proliferating cell nuclear antigen expression in colorectal cancer cells. Oncology Letters 2019, 13 https://doi.org/10.3892/ol.2019.9928
    77. Bradley J. Smith, Daniel Martins-de-Souza, Mariana Fioramonte. A Guide to Mass Spectrometry-Based Quantitative Proteomics. 2019, 3-39. https://doi.org/10.1007/978-1-4939-8994-2_1
    78. Inderjeet Kaur, Jasbir Kaur, K. Sooraj, Sandeep Goswami, Rohit Saxena, Virander Singh Chauhan, Ramanjit Sihota. Comparative evaluation of the aqueous humor proteome of primary angle closure and primary open angle glaucomas and age-related cataract eyes. International Ophthalmology 2019, 39 (1) , 69-104. https://doi.org/10.1007/s10792-017-0791-0
    79. Joseph C. Genereux. Mass spectrometric approaches for profiling protein folding and stability. 2019, 111-144. https://doi.org/10.1016/bs.apcsb.2019.09.006
    80. Chen Zou, Changjing Han, Minjie Zhao, Jingjing Yu, Lin Bai, Yuan Yao, Shuaixin Gao, Hui Cao, Zhi Zheng. Change of ranibizumab-induced human vitreous protein profile in patients with proliferative diabetic retinopathy based on proteomics analysis. Clinical Proteomics 2018, 15 (1) https://doi.org/10.1186/s12014-018-9187-z
    81. Tetsushi Yamamoto, Hiroko Otake, Noriko Hiramatsu, Naoki Yamamoto, Atsushi Taga, Noriaki Nagai. A Proteomic Approach for Understanding the Mechanisms of Delayed Corneal Wound Healing in Diabetic Keratopathy Using Diabetic Model Rat. International Journal of Molecular Sciences 2018, 19 (11) , 3635. https://doi.org/10.3390/ijms19113635
    82. Tetsushi Yamamoto, Saori Nakanishi, Kuniko Mitamura, Atsushi Taga. Shotgun label‐free proteomic analysis for identification of proteins in HaCaT human skin keratinocytes regulated by the administration of collagen from soft‐shelled turtle. Journal of Biomedical Materials Research Part B: Applied Biomaterials 2018, 106 (6) , 2403-2413. https://doi.org/10.1002/jbm.b.34034
    83. Z. Cui, A. Agarwal, B. F. da Silva, R. Sharma, E. Sabanegh. Evaluation of seminal plasma proteomics and relevance of FSH in identification of nonobstructive azoospermia: A preliminary study. Andrologia 2018, 50 (5) https://doi.org/10.1111/and.12999
    84. Xiaomeng Shen, Shichen Shen, Jun Li, Qiang Hu, Lei Nie, Chengjian Tu, Xue Wang, David J. Poulsen, Benjamin C. Orsburn, Jianmin Wang, Jun Qu. IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts. Proceedings of the National Academy of Sciences 2018, 115 (21) https://doi.org/10.1073/pnas.1800541115
    85. Tetsushi Yamamoto, Saori Nakanishi, Kuniko Mitamura, Atsushi Taga. Collagen peptides from soft‑shelled turtle induce calpain‑1 expression and regulate inflammatory cytokine expression in HaCaT human skin keratinocytes. International Journal of Molecular Medicine 2018, 55 https://doi.org/10.3892/ijmm.2018.3659
    86. David Morse, Sirius P.K Tse, Samuel C.L. Lo. Exploring dinoflagellate biology with high-throughput proteomics. Harmful Algae 2018, 75 , 16-26. https://doi.org/10.1016/j.hal.2018.03.010
    87. Varahenage R. Perera, John D. Lapek, Gerald L. Newton, David J. Gonzalez, Kit Pogliano, . Identification of the S-transferase like superfamily bacillithiol transferases encoded by Bacillus subtilis. PLOS ONE 2018, 13 (2) , e0192977. https://doi.org/10.1371/journal.pone.0192977
    88. Jonathan N. Wells, Joseph A. Marsh. Experimental Characterization of Protein Complex Structure, Dynamics, and Assembly. 2018, 3-27. https://doi.org/10.1007/978-1-4939-7759-8_1
    89. Javier Soria, Arantxa Acera, Jesús Merayo-LLoves, Juan A. Durán, Nerea González, Sandra Rodriguez, Nikitas Bistolas, Soeren Schumacher, Frank F. Bier, Harald Peter, Walter Stöcklein, Tatiana Suárez. Tear proteome analysis in ocular surface diseases using label-free LC-MS/MS and multiplexed-microarray biomarker validation. Scientific Reports 2017, 7 (1) https://doi.org/10.1038/s41598-017-17536-2
    90. Julia Wattacheril, Kristie L. Rose, Salisha Hill, Christian Lanciault, Clark R. Murray, Kay Washington, Brandon Williams, Wayne English, Matthew Spann, Ronald Clements, Naji Abumrad, Charles Robb Flynn. Non‐alcoholic fatty liver disease phosphoproteomics: A functional piece of the precision puzzle. Hepatology Research 2017, 47 (13) , 1469-1483. https://doi.org/10.1111/hepr.12885
    91. Bazla Ali, Maxim I. Desmond, Sara A. Mallory, Andrea D. Benítez, Larry J. Buckley, Susan T. Weintraub, Michael V. Osier, Lindsay W. Black, Julie A. Thomas. To Be or Not To Be T4: Evidence of a Complex Evolutionary Pathway of Head Structure and Assembly in Giant Salmonella Virus SPN3US. Frontiers in Microbiology 2017, 8 https://doi.org/10.3389/fmicb.2017.02251
    92. Noriaki Nagai, Tetsushi Yamamoto, Kuniko Mitamura, Atsushi Taga. Proteomic profile of the lens in a streptozotocin-induced diabetic rat model using shotgun proteomics. Biomedical Reports 2017, 7 (5) , 445-450. https://doi.org/10.3892/br.2017.988
    93. Lara Marcus, Patti Virtue, Peter D. Nichols, Mark G. Meekan, Heidi Pethybridge. Effects of sample treatment on the analysis of stable isotopes of carbon and nitrogen in zooplankton, micronekton and a filter-feeding shark. Marine Biology 2017, 164 (6) https://doi.org/10.1007/s00227-017-3153-6
    94. Jianfang Li, Matteo M. E. Metruccio, David J. Evans, Suzanne M. J. Fleiszig, . Mucosal fluid glycoprotein DMBT1 suppresses twitching motility and virulence of the opportunistic pathogen Pseudomonas aeruginosa. PLOS Pathogens 2017, 13 (5) , e1006392. https://doi.org/10.1371/journal.ppat.1006392
    95. Tetsuya Fukuda, Masaharu Nomura, Yasufumi Kato, Hiromasa Tojo, Kiyonaga Fujii, Toshitaka Nagao, Yasuhiko Bando, Thomas E. Fehniger, György Marko-Varga, Haruhiko Nakamura, Harubumi Kato, Toshihide Nishimura, . A selected reaction monitoring mass spectrometric assessment of biomarker candidates diagnosing large-cell neuroendocrine lung carcinoma by the scaling method using endogenous references. PLOS ONE 2017, 12 (4) , e0176219. https://doi.org/10.1371/journal.pone.0176219
    96. Sayem Miah, Charles A. S. Banks, Mark K. Adams, Laurence Florens, Kiven E. Lukong, Michael P. Washburn. Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer. Molecular BioSystems 2017, 13 (1) , 42-55. https://doi.org/10.1039/C6MB00639F
    97. Hideyuki Takata, Mitsuhiro Kudo, Tetsushi Yamamoto, Junji Ueda, Kousuke Ishino, Wei-Xia Peng, Ryuichi Wada, Nobuhiko Taniai, Hiroshi Yoshida, Eiji Uchida, Zenya Naito. Increased expression of PDIA3 and its association with cancer cell proliferation and poor prognosis in hepatocellular carcinoma. Oncology Letters 2016, 12 (6) , 4896-4904. https://doi.org/10.3892/ol.2016.5304
    98. Tetsushi Yamamoto, Mitsuhiro Kudo, Wei-Xia Peng, Hideyuki Takata, Hideki Takakura, Kiyoshi Teduka, Takenori Fujii, Kuniko Mitamura, Atsushi Taga, Eiji Uchida, Zenya Naito. Identification of aldolase A as a potential diagnostic biomarker for colorectal cancer based on proteomic analysis using formalin-fixed paraffin-embedded tissue. Tumor Biology 2016, 37 (10) , 13595-13606. https://doi.org/10.1007/s13277-016-5275-8
    99. Alicia K. Byrd, Boris L. Zybailov, Leena Maddukuri, Jun Gao, John C. Marecki, Mihir Jaiswal, Matthew R. Bell, Wezley C. Griffin, Megan R. Reed, Shubeena Chib, Samuel G. Mackintosh, Angus M. MacNicol, Giulia Baldini, Robert L. Eoff, Kevin D. Raney. Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress. Journal of Biological Chemistry 2016, 291 (34) , 18041-18057. https://doi.org/10.1074/jbc.M116.718478
    100. Xu Li, Wenqi Wang, Yuanxin Xi, Min Gao, MyKim Tran, Kathryn E. Aziz, Jun Qin, Wei Li, Junjie Chen. FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis. Cell Reports 2016, 16 (2) , 487-497. https://doi.org/10.1016/j.celrep.2016.06.004
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