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An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics

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Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, California 92121, and Department of Cell Biology SR11, 10550 North Torrey Pines Road, The Scripps Research Institute, La Jolla, California 92037
Cite this: Anal. Chem. 2001, 73, 23, 5683–5690
Publication Date (Web):October 25, 2001
https://doi.org/10.1021/ac010617e
Copyright © 2001 American Chemical Society

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    Abstract

    We describe an automated method for shotgun proteomics named multidimensional protein identification technology (MudPIT), which combines multidimensional liquid chromatography with electrospray ionization tandem mass spectrometry. The multidimensional liquid chromatography method integrates a strong cation-exchange (SCX) resin and reversed-phase resin in a biphasic column. We detail the improvements over a system described by Link et al. (Link, A. J.; Eng, J.; Schieltz, D. M.; Carmack, E.; Mize, G. J.; Morris, D. R.; Garvik, B. M.; Yates, J. R., III. Nat. Biotechnol. 1999, 17, 676−682) that separates and acquires tandem mass spectra for thousands of peptides. Peptides elute off the SCX phase by increasing pI, and elution off the SCX material is evenly distributed across an analysis. In addition, we describe the chromatographic benchmarks of MudPIT. MudPIT was reproducible within 0.5% between two analyses. Furthermore, a dynamic range of 10 000 to 1 between the most abundant and least abundant proteins/peptides in a complex peptide mixture has been demonstrated. By improving sample preparation along with separations, the method improves the overall analysis of proteomes by identifying proteins of all functional and physical classes.

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     Torrey Mesa Research Institute.

    *

     Corresponding author:  (e-mail) [email protected]; (phone) (858) 784-8862.

     The Scripps Research Institute.

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    76. Fangjun Wang, Chunxia Song, Kai Cheng, Xinning Jiang, Mingliang Ye, and Hanfa Zou . Perspectives of Comprehensive Phosphoproteome Analysis Using Shotgun Strategy. Analytical Chemistry 2011, 83 (21) , 8078-8085. https://doi.org/10.1021/ac201833j
    77. Liyan Chen, Lei Zhou, Eric C.Y. Chan, Jason Neo, and Roger W. Beuerman . Characterization of The Human Tear Metabolome by LC–MS/MS. Journal of Proteome Research 2011, 10 (10) , 4876-4882. https://doi.org/10.1021/pr2004874
    78. Haichuan Liu, Lee Yang, Nikita Khainovski, Ming Dong, Steven C. Hall, Susan J. Fisher, Mark D. Biggin, Jian Jin, and H. Ewa Witkowska . Automated Iterative MS/MS Acquisition: A Tool for Improving Efficiency of Protein Identification Using a LC–MALDI MS Workflow. Analytical Chemistry 2011, 83 (16) , 6286-6293. https://doi.org/10.1021/ac200911v
    79. Adrian P. Brown, Johan T. M. Kroon, Jennifer F. Topping, Joanne L. Robson, William J. Simon, and Antoni R. Slabas . Components of Complex Lipid Biosynthetic Pathways in Developing Castor (Ricinus communis) Seeds Identified by MudPIT Analysis of Enriched Endoplasmic Reticulum. Journal of Proteome Research 2011, 10 (8) , 3565-3577. https://doi.org/10.1021/pr2002066
    80. Sven Nahnsen, Andreas Bertsch, Jörg Rahnenführer, Alfred Nordheim, and Oliver Kohlbacher . Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification. Journal of Proteome Research 2011, 10 (8) , 3332-3343. https://doi.org/10.1021/pr2002879
    81. Bryan R. Fonslow, Paulo C. Carvalho, Katrina Academia, Steve Freeby, Tao Xu, Aleksey Nakorchevsky, Aran Paulus, and John R. Yates, III . Improvements in Proteomic Metrics of Low Abundance Proteins through Proteome Equalization Using ProteoMiner Prior to MudPIT. Journal of Proteome Research 2011, 10 (8) , 3690-3700. https://doi.org/10.1021/pr200304u
    82. Xudong Yao . Derivatization or Not: A Choice in Quantitative Proteomics. Analytical Chemistry 2011, 83 (12) , 4427-4439. https://doi.org/10.1021/ac200925p
    83. Stephen J. Valentine, Michael A. Ewing, Jonathan M. Dilger, Matthew S. Glover, Scott Geromanos, Chris Hughes, and David E. Clemmer . Using Ion Mobility Data to Improve Peptide Identification: Intrinsic Amino Acid Size Parameters. Journal of Proteome Research 2011, 10 (5) , 2318-2329. https://doi.org/10.1021/pr1011312
    84. Paola Donato, Francesco Cacciola, Eduardo Sommella, Chiara Fanali, Laura Dugo, Marina Dachà, Pietro Campiglia, Ettore Novellino, Paola Dugo, and Luigi Mondello . Online Comprehensive RPLC × RPLC with Mass Spectrometry Detection for the Analysis of Proteome Samples. Analytical Chemistry 2011, 83 (7) , 2485-2491. https://doi.org/10.1021/ac102656b
    85. Thomas Köcher, Remco Swart, and Karl Mechtler . Ultra-High-Pressure RPLC Hyphenated to an LTQ-Orbitrap Velos Reveals a Linear Relation between Peak Capacity and Number of Identified Peptides. Analytical Chemistry 2011, 83 (7) , 2699-2704. https://doi.org/10.1021/ac103243t
    86. Yuhong Wei, Jiefei Tong, Paul Taylor, Dan Strumpf, Vladimir Ignatchenko, Nhu-An Pham, Naoki Yanagawa, Geoffrey Liu, Igor Jurisica, Frances A. Shepherd, Ming-Sound Tsao, Thomas Kislinger, and Michael F. Moran . Primary Tumor Xenografts of Human Lung Adeno and Squamous Cell Carcinoma Express Distinct Proteomic Signatures. Journal of Proteome Research 2011, 10 (1) , 161-174. https://doi.org/10.1021/pr100491e
    87. Jian-Ying Zhou, Athena A. Schepmoes, Xu Zhang, Ronald J. Moore, Matthew E. Monroe, Jung Hwa Lee, David G. Camp, II, Richard D. Smith, and Wei-Jun Qian . Improved LC−MS/MS Spectral Counting Statistics by Recovering Low-Scoring Spectra Matched to Confidently Identified Peptide Sequences. Journal of Proteome Research 2010, 9 (11) , 5698-5704. https://doi.org/10.1021/pr100508p
    88. Timothy S. Collier, Prasenjit Sarkar, William L. Franck, Balaji M. Rao, Ralph A. Dean, and David C. Muddiman . Direct Comparison of Stable Isotope Labeling by Amino Acids in Cell Culture and Spectral Counting for Quantitative Proteomics. Analytical Chemistry 2010, 82 (20) , 8696-8702. https://doi.org/10.1021/ac101978b
    89. Flaubert Mbeunkui, Elizabeth H. Scholl, Charles H. Opperman, Michael B. Goshe, and David McK. Bird. Proteomic and Bioinformatic Analysis of the Root-Knot Nematode Meloidogyne hapla: The Basis for Plant Parasitism. Journal of Proteome Research 2010, 9 (10) , 5370-5381. https://doi.org/10.1021/pr1006069
    90. Urs Lewandrowski and Albert Sickmann. Online Dual Gradient Reversed-Phase/Porous Graphitized Carbon nanoHPLC for Proteomic Applications. Analytical Chemistry 2010, 82 (12) , 5391-5396. https://doi.org/10.1021/ac100853w
    91. Kamila Chughtai and Ron M. A. Heeren. Mass Spectrometric Imaging for Biomedical Tissue Analysis. Chemical Reviews 2010, 110 (5) , 3237-3277. https://doi.org/10.1021/cr100012c
    92. Jisheng Liu, Sichun Zheng, Lin Liu, Ling Li and Qili Feng. Protein Profiles of the Midgut of Spodoptera litura Larvae at the Sixth Instar Feeding Stage by Shotgun ESI−MS Approach. Journal of Proteome Research 2010, 9 (5) , 2117-2147. https://doi.org/10.1021/pr900826f
    93. Yong-Ak Song, Michael Chan, Chris Celio, Steven R. Tannenbaum, John S. Wishnok and Jongyoon Han . Free-Flow Zone Electrophoresis of Peptides and Proteins in PDMS Microchip for Narrow pI Range Sample Prefractionation Coupled with Mass Spectrometry. Analytical Chemistry 2010, 82 (6) , 2317-2325. https://doi.org/10.1021/ac9025219
    94. Adina S. Chuang, Yang Oh Jin, Laura S. Schmidt, Yalan Li, Samuel Fogel, Donna Smoler and Timothy E. Mattes . Proteomic Analysis of Ethene-Enriched Groundwater Microcosms from a Vinyl Chloride-Contaminated Site. Environmental Science & Technology 2010, 44 (5) , 1594-1601. https://doi.org/10.1021/es903033r
    95. Paul A. Grimsrud, Danielle L. Swaney, Craig D. Wenger, Nicole A. Beauchene and Joshua J. Coon . Phosphoproteomics for the Masses. ACS Chemical Biology 2010, 5 (1) , 105-119. https://doi.org/10.1021/cb900277e
    96. Nora V. Fernbach, Melanie Planyavsky, André Müller, Florian P. Breitwieser, Jacques Colinge, Uwe Rix and Keiryn L. Bennett. Acid Elution and One-Dimensional Shotgun Analysis on an Orbitrap Mass Spectrometer: An Application to Drug Affinity Chromatography. Journal of Proteome Research 2009, 8 (10) , 4753-4765. https://doi.org/10.1021/pr900455x
    97. Andreas Leinenbach, Ralf Hartmer, Markus Lubeck, Benny Kneissl, Yasser A. Elnakady, Carsten Baessmann, Rolf Müller and Christian G. Huber . Proteome Analysis of Sorangium cellulosum Employing 2D-HPLC-MS/MS and Improved Database Searching Strategies for CID and ETD Fragment Spectra. Journal of Proteome Research 2009, 8 (9) , 4350-4361. https://doi.org/10.1021/pr9004647
    98. Paul Drogaris, J. C. Yves Le Blanc, Jennifer E. Fitzgerald, Noel F. Lowndes, Alain Verreault and Pierre Thibault . Enhanced Protein Detection Using a Trapping Mode on a Hybrid Quadrupole Linear Ion Trap (Q-Trap). Analytical Chemistry 2009, 81 (15) , 6300-6309. https://doi.org/10.1021/ac9004259
    99. Carl A. White, Nicodemus Oey and Andrew Emili . Global Quantitative Proteomic Profiling through 18O-Labeling in Combination with MS/MS Spectra Analysis. Journal of Proteome Research 2009, 8 (7) , 3653-3665. https://doi.org/10.1021/pr8009098
    100. Sharon Gauci, Liesbeth M. Veenhoff, Albert J. R. Heck and Jeroen Krijgsveld . Orthogonal Separation Techniques for the Characterization of the Yeast Nuclear Proteome. Journal of Proteome Research 2009, 8 (7) , 3451-3463. https://doi.org/10.1021/pr9000948
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