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Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis:  The Yeast Proteome

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Department of Cell Biology, and Taplin Biological Mass Spectrometry Facility, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115
Cite this: Journal of Proteome Research 2003, 2, 1, 43–50
Publication Date (Web):October 15, 2002
https://doi.org/10.1021/pr025556v
Copyright © 2003 American Chemical Society

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    Abstract

    Highly complex protein mixtures can be directly analyzed after proteolysis by liquid chromatography coupled with tandem mass spectrometry (LC−MS/MS). In this paper, we have utilized the combination of strong cation exchange (SCX) and reversed-phase (RP) chromatography to achieve two-dimensional separation prior to MS/MS. One milligram of whole yeast protein was proteolyzed and separated by SCX chromatography (2.1 mm i.d.) with fraction collection every minute during an 80-min elution. Eighty fractions were reduced in volume and then re-injected via an autosampler in an automated fashion using a vented-column (100 μm i.d.) approach for RP-LC−MS/MS analysis. More than 162 000 MS/MS spectra were collected with 26 815 matched to yeast peptides (7537 unique peptides). A total of 1504 yeast proteins were unambiguously identified in this single analysis. We present a comparison of this experiment with a previously published yeast proteome analysis by Yates and colleagues (Washburn, M. P.; Wolters, D.; Yates, J. R., III. Nat. Biotechnol.2001, 19, 242−7). In addition, we report an in-depth analysis of the false-positive rates associated with peptide identification using the Sequest algorithm and a reversed yeast protein database. New criteria are proposed to decrease false-positives to less than 1% and to greatly reduce the need for manual interpretation while permitting more proteins to be identified.

    Keywords: proteome • tandem mass spectrometry • LC−MS/MS • vented column • Sequest criteria

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     Department of Cell Biology.

     Taplin Biological Mass Spectrometry Facility.

    *

     To whom correspondence should be addressed. E-mail:  steven_gygi@ hms.harvard.edu.

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    Table of unique peptide sequences. This material is available free of charge via the Internet at http://pubs.acs.org.

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    71. Thomas A. Hansen, Fedor Kryuchkov, and Frank Kjeldsen . Reduction in Database Search Space by Utilization of Amino Acid Composition Information from Electron Transfer Dissociation and Higher-Energy Collisional Dissociation Mass Spectra. Analytical Chemistry 2012, 84 (15) , 6638-6645. https://doi.org/10.1021/ac3010007
    72. Jung Hwa Lee, Seok-Won Hyung, Dong-Gi Mun, Hee-Jung Jung, Hokeun Kim, Hangyeore Lee, Su-Jin Kim, Kyong Soo Park, Ronald J. Moore, Richard D. Smith, and Sang-Won Lee . Fully Automated Multifunctional Ultrahigh Pressure Liquid Chromatography System for Advanced Proteome Analyses. Journal of Proteome Research 2012, 11 (8) , 4373-4381. https://doi.org/10.1021/pr3004166
    73. Nicholas T. Seyfried, Yair M. Gozal, Laura E. Donovan, Jeremy H. Herskowitz, Eric B. Dammer, Qiangwei Xia, Li Ku, Jianjun Chang, Duc M. Duong, Howard D. Rees, Deborah S. Cooper, Jonathan D. Glass, Marla Gearing, Malú G. Tansey, James J. Lah, Yue Feng, Allan I. Levey, and Junmin Peng . Quantitative Analysis of the Detergent-Insoluble Brain Proteome in Frontotemporal Lobar Degeneration Using SILAC Internal Standards. Journal of Proteome Research 2012, 11 (5) , 2721-2738. https://doi.org/10.1021/pr2010814
    74. Ming-Xia Gu, Yi Fu, Xiao-Li Sun, Yu-Zhu Ding, Cheng-Hong Li, Wei Pang, Songqin Pan, and Yi Zhu . Proteomic Analysis of Endothelial Lipid Rafts Reveals a Novel Role of Statins in Antioxidation. Journal of Proteome Research 2012, 11 (4) , 2365-2373. https://doi.org/10.1021/pr300098f
    75. Zhou Li, Rachel M. Adams, Karuna Chourey, Gregory B. Hurst, Robert L. Hettich, and Chongle Pan . Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos. Journal of Proteome Research 2012, 11 (3) , 1582-1590. https://doi.org/10.1021/pr200748h
    76. Liudy G. Hernández, Bingwen Lu, Gabriel C. N. da Cruz, Luciana K. Calábria, Natalia F. Martins, Roberto Togawa, Foued S. Espindola, John R. Yates, III, Ricardo B. Cunha, and Marcelo V. de Sousa . Worker Honeybee Brain Proteome. Journal of Proteome Research 2012, 11 (3) , 1485-1493. https://doi.org/10.1021/pr2007818
    77. Piliang Hao, Jingru Qian, Bamaprasad Dutta, Esther Sok Hwee Cheow, Kae Hwan Sim, Wei Meng, Sunil S. Adav, Andrew Alpert, and Siu Kwan Sze . Enhanced Separation and Characterization of Deamidated Peptides with RP-ERLIC-Based Multidimensional Chromatography Coupled with Tandem Mass Spectrometry. Journal of Proteome Research 2012, 11 (3) , 1804-1811. https://doi.org/10.1021/pr201048c
    78. Chen Li, Hong-Qiang Ruan, Yan-Sheng Liu, Meng-Jie Xu, Jie Dai, Quan-Hu Sheng, Ye-Xiong Tan, Zhen-Zhen Yao, Hong-Yang Wang, Jia-Rui Wu, and Rong Zeng . Quantitative Proteomics Reveal up-regulated Protein Expression of the SET Complex Associated with Hepatocellular Carcinoma. Journal of Proteome Research 2012, 11 (2) , 871-885. https://doi.org/10.1021/pr2006999
    79. Heike Stephanowitz, Sabine Lange, Diana Lang, Christian Freund, and Eberhard Krause . Improved Two-Dimensional Reversed Phase-Reversed Phase LC-MS/MS Approach for Identification of Peptide-Protein Interactions. Journal of Proteome Research 2012, 11 (2) , 1175-1183. https://doi.org/10.1021/pr200900s
    80. Lujian Liao, Richard C. Sando, III, John B. Farnum, Peter W. Vanderklish, Anton Maximov, and John R. Yates, III . 15N-Labeled Brain Enables Quantification of Proteome and Phosphoproteome in Cultured Primary Neurons. Journal of Proteome Research 2012, 11 (2) , 1341-1353. https://doi.org/10.1021/pr200987h
    81. Paul Abraham, Rachel Adams, Richard J. Giannone, Udaya Kalluri, Priya Ranjan, Brian Erickson, Manesh Shah, Gerald A. Tuskan, and Robert L. Hettich . Defining the Boundaries and Characterizing the Landscape of Functional Genome Expression in Vascular Tissues of Populus using Shotgun Proteomics. Journal of Proteome Research 2012, 11 (1) , 449-460. https://doi.org/10.1021/pr200851y
    82. Meng M. Rowland, Heidi E. Bostic, Denghuang Gong, Anna E. Speers, Nathan Lucas, Wonhwa Cho, Benjamin F. Cravatt, and Michael D. Best . Phosphatidylinositol 3,4,5-Trisphosphate Activity Probes for the Labeling and Proteomic Characterization of Protein Binding Partners. Biochemistry 2011, 50 (51) , 11143-11161. https://doi.org/10.1021/bi201636s
    83. Jong Hyuk Yoon, Parkyong Song, Jin-Hyeok Jang, Dae-Kyum Kim, Sunkyu Choi, Jaeyoon Kim, Jaewang Ghim, Dayea Kim, Sehoon Park, Hyeongji Lee, Dongoh Kwak, Kyungmoo Yea, Daehee Hwang, Pann-Ghill Suh, and Sung Ho Ryu . Proteomic Analysis of Tumor Necrosis Factor-Alpha (TNF-α)-Induced L6 Myotube Secretome Reveals Novel TNF-α-Dependent Myokines in Diabetic Skeletal Muscle. Journal of Proteome Research 2011, 10 (12) , 5315-5325. https://doi.org/10.1021/pr200573b
    84. Huan Wang, Hsin-Yao Tang, Glenn C. Tan, and David W. Speicher . Data Analysis Strategy for Maximizing High-Confidence Protein Identifications in Complex Proteomes Such as Human Tumor Secretomes and Human Serum. Journal of Proteome Research 2011, 10 (11) , 4993-5005. https://doi.org/10.1021/pr200464c
    85. Yong-Yook Lee, Kimberly Q. McKinney, Sriparna Ghosh, David A. Iannitti, John B. Martinie, F. Ryan Caballes, Mark W. Russo, William A. Ahrens, Deborah H. Lundgren, David K. Han, Herbert L. Bonkovsky, and Sun-Il Hwang . Subcellular Tissue Proteomics of Hepatocellular Carcinoma for Molecular Signature Discovery. Journal of Proteome Research 2011, 10 (11) , 5070-5083. https://doi.org/10.1021/pr2005204
    86. Yong Yang, Xu Qiang, Katherine Owsiany, Sheng Zhang, Theodore W. Thannhauser, and Li Li . Evaluation of Different Multidimensional LC–MS/MS Pipelines for Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)-Based Proteomic Analysis of Potato Tubers in Response to Cold Storage. Journal of Proteome Research 2011, 10 (10) , 4647-4660. https://doi.org/10.1021/pr200455s
    87. Feng Zhou, Timothy W. Sikorski, Scott B. Ficarro, James T. Webber, and Jarrod A. Marto . Online Nanoflow Reversed Phase-Strong Anion Exchange-Reversed Phase Liquid Chromatography–Tandem Mass Spectrometry Platform for Efficient and In-Depth Proteome Sequence Analysis of Complex Organisms. Analytical Chemistry 2011, 83 (18) , 6996-7005. https://doi.org/10.1021/ac200639v
    88. Xu Wang, Paul A. Stewart, Qiang Cao, Qing-Xiang Amy Sang, Leland W. K. Chung, Mark R. Emmett, and Alan G. Marshall . Characterization of the Phosphoproteome in Androgen-Repressed Human Prostate Cancer Cells by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Journal of Proteome Research 2011, 10 (9) , 3920-3928. https://doi.org/10.1021/pr2000144
    89. Yufeng Shen, Nikola Tolić, Fang Xie, Rui Zhao, Samuel O. Purvine, Athena A. Schepmoes, Ronald, J. Moore, Gordon A. Anderson, and Richard D. Smith . Effectiveness of CID, HCD, and ETD with FT MS/MS for Degradomic-Peptidomic Analysis: Comparison of Peptide Identification Methods. Journal of Proteome Research 2011, 10 (9) , 3929-3943. https://doi.org/10.1021/pr200052c
    90. 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
    91. Genna L. Andrews, Ralph A. Dean, Adam M. Hawkridge, David C. Muddiman. Improving Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments. Journal of the American Society for Mass Spectrometry 2011, 22 (4) , 773-783. https://doi.org/10.1007/s13361-011-0075-2
    92. Juliana de Saldanha da Gama Fischer, Paulo Costa Carvalho, Clovis Orlando da Fonseca, Lujian Liao, Wim M. Degrave, Maria da Gloria da Costa Carvalho, John R. Yates, III, and Gilberto B. Domont . Chemo-Resistant Protein Expression Pattern of Glioblastoma Cells (A172) to Perillyl Alcohol. Journal of Proteome Research 2011, 10 (1) , 153-160. https://doi.org/10.1021/pr100677g
    93. Jeremy H. Herskowitz, Nicholas T. Seyfried, Duc M. Duong, Qiangwei Xia, Howard D. Rees, Marla Gearing, Junmin Peng, James J. Lah, and Allan I. Levey . Phosphoproteomic Analysis Reveals Site-Specific Changes in GFAP and NDRG2 Phosphorylation in Frontotemporal Lobar Degeneration. Journal of Proteome Research 2010, 9 (12) , 6368-6379. https://doi.org/10.1021/pr100666c
    94. Kiran S. Ambatipudi, Fred K. Hagen, Claire M. Delahunty, Xuemei Han, Rubina Shafi, Jennifer Hryhorenko, Stacy Gregoire, Robert E. Marquis, James E. Melvin, Hyun Koo, and John R. Yates, III . Human Common Salivary Protein 1 (CSP-1) Promotes Binding of Streptococcus mutans to Experimental Salivary Pellicle and Glucans Formed on Hydroxyapatite Surface. Journal of Proteome Research 2010, 9 (12) , 6605-6614. https://doi.org/10.1021/pr100786y
    95. Mikhail M. Savitski, Frank Fischer, Toby Mathieson, Gavain Sweetman, Manja Lang, Marcus Bantscheff. Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays. Journal of the American Society for Mass Spectrometry 2010, 21 (10) , 1668-1679. https://doi.org/10.1016/j.jasms.2010.01.012
    96. Jian-Ying Zhou, Leila Afjehi-Sadat, Seneshaw Asress, Duc M. Duong, Merit Cudkowicz, Jonathan D. Glass, and Junmin Peng. Galectin-3 Is a Candidate Biomarker for Amyotrophic Lateral Sclerosis: Discovery by a Proteomics Approach. Journal of Proteome Research 2010, 9 (10) , 5133-5141. https://doi.org/10.1021/pr100409r
    97. 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
    98. Roslyn N. Brown, Margaret F. Romine, Athena A. Schepmoes, Richard D. Smith and Mary S. Lipton. Mapping the Subcellular Proteome of Shewanella oneidensis MR-1 using Sarkosyl-Based Fractionation and LC−MS/MS Protein Identification. Journal of Proteome Research 2010, 9 (9) , 4454-4463. https://doi.org/10.1021/pr100215h
    99. Rovshan G. Sadygov, Yingxin Zhao, Sigmund J. Haidacher, Jonathan M. Starkey, Ronald G. Tilton and Larry Denner . Using Power Spectrum Analysis to Evaluate 18O-Water Labeling Data Acquired from Low Resolution Mass Spectrometers. Journal of Proteome Research 2010, 9 (8) , 4306-4312. https://doi.org/10.1021/pr100642q
    100. Xinning Jiang, Mingliang Ye, Guanghui Han, Xiaoli Dong and Hanfa Zou . Classification Filtering Strategy to Improve the Coverage and Sensitivity of Phosphoproteome Analysis. Analytical Chemistry 2010, 82 (14) , 6168-6175. https://doi.org/10.1021/ac100975t
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