ACS Publications. Most Trusted. Most Cited. Most Read

OR SEARCH CITATIONS

My Activity
Publications
CONTENT TYPES

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Proteome Res. 2003, 2, 1, 23-35
RETURN TO ISSUEPREVArticleNEXT

Large-Scale Identification of Caenorhabditis elegans Proteins by Multidimensional Liquid Chromatography−Tandem Mass Spectrometry

View Author Information
Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan, Integrated Proteomics System Project, Pioneer Research on Genome the Frontier, MEXT, Japan, and Department of Applied Bioscience, United Graduate School of Agriculture Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
Cite this: Journal of Proteome Research 2003, 2, 1, 23–35
Publication Date (Web):October 16, 2002
https://doi.org/10.1021/pr025551y
Copyright © 2003 American Chemical Society
Request reuse permissions

    Article Views

    852

    Altmetric

    -

    Citations

    106
    LEARN ABOUT THESE METRICS
    Read OnlinePDF (1011 KB)
    Get e-Alerts
    Supporting Info (1)»
    SUBJECTS:

    Abstract

    A proteome of a model organism, Caenorhabditis elegans, was analyzed by an integrated liquid chromatography (LC)-based protein identification system, which was constructed by microscale two-dimensional liquid chromatography (2DLC) coupled with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) on a high-resolution hybrid mass spectrometer with an automated data analysis system. Soluble and insoluble protein fractions were prepared from a mixed growth phase culture of the worm C. elegans, digested with trypsin, and fractionated separately on the 2DLC system. The separated peptides were directly analyzed by on-line ESI−MS/MS in a data-dependent mode, and the resultant spectral data were automatically processed to search a genome sequence database, wormpep 66, for protein identification. The total number of proteins of the composite proteome identified in this method was 1616, including 110 secreted/targeted proteins and 242 transmembrane proteins. The codon adaptation indices of the identified proteins suggested that the system could identify proteins of relatively low abundance, which are difficult to identify by conventional 2D-gel electrophoresis (GE) followed by an offline mass spectrometric analysis such as peptide mass fingerprinting. Among the ∼5400 peptides assigned in this study, many peptides with post-translational modifications, such as N-terminal acetylation and phosphorylation, were detected. This expression profile of C. elegans, containing 571 hypothetical gene products, will serve as the basic data of a major proteome set expressed in the worm.

    Keywords: liquid chromatography • tandem mass spectrometry • peptide signature • C. elegans

    †

     Tokyo Metropolitan University.

    ‡

     These authors contributed equally to this work.

    *

     To whom correspondence should be addressed. Fax:  81-426-77-2525. E-mail:  [email protected].

    §

     MEXT.

    ‖

     Tokyo University of Agriculture and Technology.

    Supporting Information Available

    ARTICLE SECTIONS
    Jump To

    Table of C. elegans protein identified by the 2DLC−MS/MS system. This material is available free of charge via the Internet at http://pubs.acs.org.

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    This article is cited by 106 publications.

    1. Masato Taoka, Michihiko Fujii, Masahiro Tsuchiya, Takamasa Uekita, and Tohru Ichimura . A Sensitive Microbead-Based Organic Media-Assisted Method for Proteomics Sample Preparation from Dilute and Denaturing Solutions. ACS Applied Materials & Interfaces 2017, 9 (49) , 42661-42667. https://doi.org/10.1021/acsami.7b16095
    2. Aidan P. Tay, Chi Nam Ignatius Pang, Daniel L. Winter, and Marc R. Wilkins . PTMOracle: A Cytoscape App for Covisualizing and Coanalyzing Post-Translational Modifications in Protein Interaction Networks. Journal of Proteome Research 2017, 16 (5) , 1988-2003. https://doi.org/10.1021/acs.jproteome.6b01052
    3. Sameh Magdeldin, James J. Moresco, Tadashi Yamamoto, and John R. Yates, III . Off-Line Multidimensional Liquid Chromatography and Auto Sampling Result in Sample Loss in LC/LC–MS/MS. Journal of Proteome Research 2014, 13 (8) , 3826-3836. https://doi.org/10.1021/pr500530e
    4. Toshihiro Yoneyama, Sumio Ohtsuki, Masaya Ono, Ken Ohmine, Yasuo Uchida, Tesshi Yamada, Masanori Tachikawa, and Tetsuya Terasaki . Quantitative Targeted Absolute Proteomics-Based Large-Scale Quantification of Proline-Hydroxylated α-Fibrinogen in Plasma for Pancreatic Cancer Diagnosis. Journal of Proteome Research 2013, 12 (2) , 753-762. https://doi.org/10.1021/pr3008144
    5. Mercedes Pardo and Jyoti S. Choudhary . Assignment of Protein Interactions from Affinity Purification/Mass Spectrometry Data. Journal of Proteome Research 2012, 11 (3) , 1462-1474. https://doi.org/10.1021/pr2011632
    6. John K. Chik, David C. Schriemer, Sarah J. Childs, and James D. McGhee . Proteome of the Caenorhabditis elegans Oocyte. Journal of Proteome Research 2011, 10 (5) , 2300-2305. https://doi.org/10.1021/pr101124f
    7. Feng Zhou, Job D. Cardoza, Scott B. Ficarro, Guillaume O. Adelmant, Jean-Bernard Lazaro, and Jarrod A. Marto . Online Nanoflow RP−RP-MS Reveals Dynamics of Multicomponent Ku Complex in Response to DNA Damage. Journal of Proteome Research 2010, 9 (12) , 6242-6255. https://doi.org/10.1021/pr1004696
    8. Sameh Magdeldin, Huiping Li, Yutaka Yoshida, Ichiro Satokata, Yoshitaka Maeda, Munesuke Yokoyama, Shymaa Enany, Ying Zhang, Bo Xu, Hidehiko Fujinaka, Eishin Yaoita, and Tadashi Yamamoto . Differential Proteomic Shotgun Analysis Elucidates Involvement of Water Channel Aquaporin 8 in Presence of α-Amylase in the Colon. Journal of Proteome Research 2010, 9 (12) , 6635-6646. https://doi.org/10.1021/pr100789v
    9. Holger Husi, Fiona McAllister, Nicos Angelopoulos, Victoria J. Butler, Kevin R. Bailey, Kirk Malone, Logan MacKay, Paul Taylor, Antony P. Page, Nicholas J. Turner, Perdita E. Barran, and Malcolm Walkinshaw . Selective Chemical Intervention in the Proteome of Caenorhabditis elegans. Journal of Proteome Research 2010, 9 (11) , 6060-6070. https://doi.org/10.1021/pr100427c
    10. Lisa M. Wolfe, Spencer B. Mahaffey, Nicole A. Kruh, and Karen M. Dobos. Proteomic Definition of the Cell Wall of Mycobacterium tuberculosis. Journal of Proteome Research 2010, 9 (11) , 5816-5826. https://doi.org/10.1021/pr1005873
    11. 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
    12. 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
    13. Akira Motoyama, John R. Yates, III. Multidimensional LC Separations in Shotgun Proteomics. Analytical Chemistry 2008, 80 (19) , 7187-7193. https://doi.org/10.1021/ac8013669
    14. Mohammad Al-Ghoul, Thomas B. Brück, Janelle L. Lauer-Fields, Victor S. Asirvatham, Claudia Zapata, Russell G. Kerr and Gregg B. Fields. Comparative Proteomic Analysis of Matched Primary and Metastatic Melanoma Cell Lines. Journal of Proteome Research 2008, 7 (9) , 4107-4118. https://doi.org/10.1021/pr800174k
    15. Marjorie L. Fournier,, Joshua M. Gilmore,, Skylar A. Martin-Brown, and, Michael P. Washburn. Multidimensional Separations-Based Shotgun Proteomics. Chemical Reviews 2007, 107 (8) , 3654-3686. https://doi.org/10.1021/cr068279a
    16. Brett R. Wenner, Bert C. Lynn. Factors that affect ion trap data-dependent MS/MS in proteomics. Journal of the American Society for Mass Spectrometry 2004, 15 (2) , 150-157. https://doi.org/10.1016/j.jasms.2003.10.006
    17. Yunting WANG, Yutaka YOSHIDA, Junichi KAMIIE, Yukari SHIWAKU, Osamu SUZUKI, Maiko FURUYA, Kotone YOKOTA, Hiroyasu KANETAKA, Taishi YOKOI, Masakazu KAWASHITA. Proteomic identification of serum proteins to induce osteoconductivity of hydroxyapatite. Dental Materials Journal 2021, 40 (6) , 1428-1436. https://doi.org/10.4012/dmj.2021-120
    18. Hiroshi Koike, Maki Kanda, Hiroshi Hayashi, Yoko Matsushima, Yumi Ohba, Yukiko Nakagawa, Chieko Nagano, Kotaro Sekimura, Akihiko Hirai, Tetsuya Shindo, Kenji Otsuka, Junichi Kamiie, Takeo Sasamoto, Tsuneo Hashimoto. Quantification of staphylococcal enterotoxin type A in cow milk by using a stable isotope-labelled peptide via liquid chromatography–tandem mass spectrometry. Food Additives & Contaminants: Part A 2019, 36 (7) , 1098-1108. https://doi.org/10.1080/19440049.2019.1615641
    19. Prasad Minakshi, Rajesh Kumar, Mayukh Ghosh, Hari Mohan Saini, Koushlesh Ranjan, Basanti Brar, Gaya Prasad. Single-Cell Proteomics: Technology and Applications. 2019, 283-318. https://doi.org/10.1016/B978-0-12-814919-5.00014-2
    20. Xing Liu, Yong-Jian Yang, Zheng-Wu Wang. Structure characteristics of Coix seeds prolamins and physicochemical and mechanical properties of their films. Journal of Cereal Science 2018, 79 , 233-239. https://doi.org/10.1016/j.jcs.2017.11.002
    21. Mingming Xiao, Junjun Yang, Yuxin Feng, Yan Zhu, Xin Chai, Yuefei Wang. Metaproteomic strategies and applications for gut microbial research. Applied Microbiology and Biotechnology 2017, 101 (8) , 3077-3088. https://doi.org/10.1007/s00253-017-8215-7
    22. Max J. Dörfel, Gholson J. Lyon. The biological functions of Naa10 — From amino-terminal acetylation to human disease. Gene 2015, 567 (2) , 103-131. https://doi.org/10.1016/j.gene.2015.04.085
    23. Roberto Samperi, Anna Laura Capriotti, Chiara Cavaliere, Valentina Colapicchioni, Riccardo Zenezini Chiozzi, Aldo Laganà. Food Proteins and Peptides. 2015, 309-357. https://doi.org/10.1016/B978-0-444-63340-8.00006-6
    24. Junichi Kamiie, Naoto Shimoyama, Naoyuki Aihara, Masaharu Hisasue, Yuko Naya, Kikumi Ogihara, Kinji Shirota. Quantitative analysis of CD3ε in a cloned canine lymphoma cell line by selected reaction monitoring assay. Bioscience, Biotechnology, and Biochemistry 2014, 78 (2) , 271-275. https://doi.org/10.1080/09168451.2014.878216
    25. Jun Hirabayashi. Lectin-Based Glycomics: How and When Was the Technology Born?. 2014, 225-242. https://doi.org/10.1007/978-1-4939-1292-6_20
    26. Mehdi Moini. High-Throughput Capillary Electrophoresis–Mass Spectrometry: From Analysis of Amino Acids to Analysis of Protein Complexes. 2013, 79-119. https://doi.org/10.1007/978-1-62703-296-4_8
    27. Amit Sinha, Ralf J Sommer, Christoph Dieterich. Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans. BMC Genomics 2012, 13 (1) https://doi.org/10.1186/1471-2164-13-254
    28. Ken Ohmine, Kei Kawaguchi, Sumio Ohtsuki, Fuyuhiko Motoi, Shinichi Egawa, Michiaki Unno, Tetsuya Terasaki. Attenuation of Phosphorylation by Deoxycytidine Kinase is Key to Acquired Gemcitabine Resistance in a Pancreatic Cancer Cell Line: Targeted Proteomic and Metabolomic Analyses in PK9 Cells. Pharmaceutical Research 2012, 29 (7) , 2006-2016. https://doi.org/10.1007/s11095-012-0728-2
    29. Clelia De-la-Peña, Dayakar V. Badri, Víctor M. Loyola-Vargas. Plant Root Secretions and Their Interactions with Neighbors. 2012, 1-26. https://doi.org/10.1007/978-3-642-23047-9_1
    30. Hirofumi Kaneko, Junichi Kamiie, Hirotaka Kawakami, Takahisa Anada, Yoshitomo Honda, Naru Shiraishi, Shinji Kamakura, Tetsuya Terasaki, Hidetoshi Shimauchi, Osamu Suzuki. Proteome analysis of rat serum proteins adsorbed onto synthetic octacalcium phosphate crystals. Analytical Biochemistry 2011, 418 (2) , 276-285. https://doi.org/10.1016/j.ab.2011.07.022
    31. Masachika Fujiyoshi, Masanori Tachikawa, Sumio Ohtsuki, Shingo Ito, Yasuo Uchida, Shin-ichi Akanuma, Junichi Kamiie, Tadafumi Hashimoto, Ken-ichi Hosoya, Takeshi Iwatsubo, Tetsuya Terasaki. Amyloid-β peptide(1-40) elimination from cerebrospinal fluid involves low-density lipoprotein receptor-related protein 1 at the blood-cerebrospinal fluid barrier. Journal of Neurochemistry 2011, 118 (3) , 407-415. https://doi.org/10.1111/j.1471-4159.2011.07311.x
    32. Sasisekhar Bennuru, Zhaojing Meng, José M. C. Ribeiro, Roshanak Tolouei Semnani, Elodie Ghedin, King Chan, David A. Lucas, Timothy D. Veenstra, Thomas B. Nutman. Stage-specific proteomic expression patterns of the human filarial parasite Brugia malayi and its endosymbiont Wolbachia. Proceedings of the National Academy of Sciences 2011, 108 (23) , 9649-9654. https://doi.org/10.1073/pnas.1011481108
    33. Xiaoming YANG, Xindu GENG. Recent development for purification of active proteins from bovine pancreas with liquid chromatography. Chinese Journal of Chromatography 2011, 29 (3) , 199-204. https://doi.org/10.3724/SP.J.1123.2011.00199
    34. Shingo Ito, Sumio Ohtsuki, Yuki Katsukura, Miho Funaki, Yusuke Koitabashi, Akihiko Sugino, Sho Murata, Tetsuya Terasaki. Atrial Natriuretic Peptide is Eliminated from the Brain by Natriuretic Peptide Receptor-C-Mediated Brain-to-Blood Efflux Transport at the Blood—Brain Barrier. Journal of Cerebral Blood Flow & Metabolism 2011, 31 (2) , 457-466. https://doi.org/10.1038/jcbfm.2010.108
    35. Laura M. Jones, Carla De Giorgi, Peter E. Urwin. C. elegans as a Resource for Studies on Plant Parasitic Nematodes. 2011, 175-220. https://doi.org/10.1007/978-94-007-0434-3_10
    36. Ying Zhang, Yutaka Yoshida, Bo Xu, Sameh Magdeldin, Hidehiko Fujinaka, Zan Liu, Masahito Miyamoto, Eishin Yaoita, Tadashi Yamamoto. Comparison of human glomerulus proteomic profiles obtained from low quantities of samples by different mass spectrometry with the comprehensive database. Proteome Science 2011, 9 (1) , 47. https://doi.org/10.1186/1477-5956-9-47
    37. Shin-ichi Akanuma, Yasuo Uchida, Sumio Ohtsuki, Jun-ichi Kamiie, Masanori Tachikawa, Tetsuya Terasaki, Ken-ichi Hosoya. Molecular-weight-dependent, Anionic-substrate-preferential Transport of β-Lactam Antibiotics via Multidrug Resistance-associated Protein 4. Drug Metabolism and Pharmacokinetics 2011, 26 (6) , 602-611. https://doi.org/10.2133/dmpk.DMPK-11-RG-063
    38. Kimberly M. Wegener, Abhay K. Singh, Jon M. Jacobs, Thanura Elvitigala, Eric A. Welsh, Nir Keren, Marina A. Gritsenko, Bijoy K. Ghosh, David G. Camp, Richard D. Smith, Himadri B. Pakrasi. Global Proteomics Reveal an Atypical Strategy for Carbon/Nitrogen Assimilation by a Cyanobacterium Under Diverse Environmental Perturbations. Molecular & Cellular Proteomics 2010, 9 (12) , 2678-2689. https://doi.org/10.1074/mcp.M110.000109
    39. Hualing Li, Changhong Ren, Jinping Shi, Xingyi Hang, Feilong Zhang, Yan Gao, Yonghong Wu, Langlai Xu, Changsheng Chen, Chenggang Zhang. A proteomic view of Caenorhabditis elegans caused by short-term hypoxic stress. Proteome Science 2010, 8 (1) https://doi.org/10.1186/1477-5956-8-49
    40. Sabine P. Schrimpf, Michael O. Hengartner. A worm rich in protein: Quantitative, differential, and global proteomics in Caenorhabditis elegans. Journal of Proteomics 2010, 73 (11) , 2186-2197. https://doi.org/10.1016/j.jprot.2010.03.014
    41. James J. Moresco, Paulo C. Carvalho, John R. Yates. Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry. Journal of Proteomics 2010, 73 (11) , 2198-2204. https://doi.org/10.1016/j.jprot.2010.05.008
    42. Duxin LI, Lingyi ZHANG, Tong LI, Yiping DU, Weibing ZHANG. Improvement of interface in comprehensive two-dimensional liquid chromatography and its application in the research of proteomics. Chinese Journal of Chromatography 2010, 28 (2) , 163-167. https://doi.org/10.3724/SP.J.1123.2012.00163
    43. Yupeng Zhao, Yen-Han Lin. Whole-Cell Protein Identification Using the Concept of Unique Peptides. Genomics, Proteomics & Bioinformatics 2010, 8 (1) , 33-41. https://doi.org/10.1016/S1672-0229(10)60004-6
    44. Rainer Malik, Kalyan Dulla, Erich A. Nigg, Roman Körner. From proteome lists to biological impact– tools and strategies for the analysis of large MS data sets. PROTEOMICS 2010, 10 (6) , 1270-1283. https://doi.org/10.1002/pmic.200900365
    45. Masato Taoka, Yoshio Yamauchi, Yuko Nobe, Shunpei Masaki, Hiroshi Nakayama, Hideaki Ishikawa, Nobuhiro Takahashi, Toshiaki Isobe. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes. Nucleic Acids Research 2009, 37 (21) , e140-e140. https://doi.org/10.1093/nar/gkp732
    46. Motohiro Nozumi, Tetsuya Togano, Kazuko Takahashi-Niki, Jia Lu, Atsuko Honda, Masato Taoka, Takashi Shinkawa, Hisashi Koga, Kosei Takeuchi, Toshiaki Isobe, Michihiro Igarashi. Identification of functional marker proteins in the mammalian growth cone. Proceedings of the National Academy of Sciences 2009, 106 (40) , 17211-17216. https://doi.org/10.1073/pnas.0904092106
    47. Jing Li, Tanxi Cai, Peng Wu, Ziyou Cui, Xiulan Chen, Junjie Hou, Zhensheng Xie, Peng Xue, Linan Shi, Pingsheng Liu, John R. Yates, Fuquan Yang. Proteomic analysis of mitochondria from Caenorhabditis elegans. PROTEOMICS 2009, 9 (19) , 4539-4553. https://doi.org/10.1002/pmic.200900101
    48. Anat Ben-Zvi, Elizabeth A. Miller, Richard I. Morimoto. Collapse of proteostasis represents an early molecular event in Caenorhabditis elegans aging. Proceedings of the National Academy of Sciences 2009, 106 (35) , 14914-14919. https://doi.org/10.1073/pnas.0902882106
    49. Harry Schachter. Paucimannose N-glycans in Caenorhabditis elegans and Drosophila melanogaster. Carbohydrate Research 2009, 344 (12) , 1391-1396. https://doi.org/10.1016/j.carres.2009.04.028
    50. Sabine P Schrimpf, Manuel Weiss, Lukas Reiter, Christian H Ahrens, Marko Jovanovic, Johan Malmström, Erich Brunner, Sonali Mohanty, Martin J Lercher, Peter E Hunziker, Ruedi Aebersold, Christian von Mering, Michael O Hengartner, . Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes. PLoS Biology 2009, 7 (3) , e1000048. https://doi.org/10.1371/journal.pbio.1000048
    51. Harry Schachter. The functions of paucimannose N-glycans in Caenorhabditis elegans. Trends in Glycoscience and Glycotechnology 2009, 21 (119) , 131-148. https://doi.org/10.4052/tigg.21.131
    52. András Mádi, Stefan Mikkat, Cornelia Koy, Bruno Ringel, Hans-Jürgen Thiesen, Michael O. Glocker. Mass spectrometric proteome analysis suggests anaerobic shift in metabolism of Dauer larvae of Caenorhabditis elegans. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2008, 1784 (11) , 1763-1770. https://doi.org/10.1016/j.bbapap.2008.05.017
    53. Junichi Kamiie, Sumio Ohtsuki, Ryo Iwase, Ken Ohmine, Yuki Katsukura, Kazunari Yanai, Yumi Sekine, Yasuo Uchida, Shingo Ito, Tetsuya Terasaki. Quantitative Atlas of Membrane Transporter Proteins: Development and Application of a Highly Sensitive Simultaneous LC/MS/MS Method Combined with Novel In-silico Peptide Selection Criteria. Pharmaceutical Research 2008, 25 (6) , 1469-1483. https://doi.org/10.1007/s11095-008-9532-4
    54. Jon Barbour, Sebastian Wiese, Helmut E. Meyer, Bettina Warscheid, Andreas Tholey, Matthias Glückmann, Kerstin Seemann, Michael Karas, Cloud P. Paweletz, Nathan A. Yates, Ronald C. Hendrickson, Josef Kellermann, Kathryn S. Lilley, Tom Dunkley, Pawel Sadowski. Mass Spectrometry. 2008, 41-128. https://doi.org/10.1002/9783527622832.ch4
    55. Hiroyuki Kaji, Jun-ichi Kamiie, Hirotaka Kawakami, Kazuki Kido, Yoshio Yamauchi, Takashi Shinkawa, Masato Taoka, Nobuhiro Takahashi, Toshiaki Isobe. Proteomics Reveals N-Linked Glycoprotein Diversity in Caenorhabditis elegans and Suggests an Atypical Translocation Mechanism for Integral Membrane Proteins. Molecular & Cellular Proteomics 2007, 6 (12) , 2100-2109. https://doi.org/10.1074/mcp.M600392-MCP200
    56. Jing Zhao, Tomonori Izumi, Kazuto Nunomura, Shinya Satoh, Sumiko Watanabe. MARCKS-like protein, a membrane protein identified for its expression in developing neural retina, plays a role in regulating retinal cell proliferation. Biochemical Journal 2007, 408 (1) , 51-59. https://doi.org/10.1042/BJ20070826
    57. King Wai Lau, Andrew R. Jones, Neil Swainston, Jennifer A. Siepen, Simon J. Hubbard. Capture and analysis of quantitative proteomic data. PROTEOMICS 2007, 7 (16) , 2787-2799. https://doi.org/10.1002/pmic.200700127
    58. Benito Cañas, Carmen Piñeiro, Enrique Calvo, Daniel López-Ferrer, Jose Manuel Gallardo. Trends in sample preparation for classical and second generation proteomics. Journal of Chromatography A 2007, 1153 (1-2) , 235-258. https://doi.org/10.1016/j.chroma.2007.01.045
    59. Masaaki Oyama, Hiroko Kozuka-Hata, Yutaka Suzuki, Kentaro Semba, Tadashi Yamamoto, Sumio Sugano. Diversity of Translation Start Sites May Define Increased Complexity of the Human Short ORFeome. Molecular & Cellular Proteomics 2007, 6 (6) , 1000-1006. https://doi.org/10.1074/mcp.M600297-MCP200
    60. Masahiro Hosaka, Tsuyoshi Watanabe, Yoshio Yamauchi, Yuko Sakai, Masayuki Suda, Shin Mizutani, Toshiyuki Takeuchi, Toshiaki Isobe, Tetsuro Izumi. A Subset of p23 Localized on Secretory Granules in Pancreatic β-cells. Journal of Histochemistry & Cytochemistry 2007, 55 (3) , 235-245. https://doi.org/10.1369/jhc.6A7093.2006
    61. Robert L. J. Graham, Catherine E. Pollock, S. Naomi O'Loughlin, Nigel G. Ternan, D. Brent Weatherly, Rick L. Tarleton, Geoff McMullan. Multidimensional analysis of the insoluble sub-proteome ofOceanobacillus iheyensis HTE831, an alkaliphilic and halotolerant deep-sea bacterium isolated from the Iheya ridge. PROTEOMICS 2007, 7 (1) , 82-91. https://doi.org/10.1002/pmic.200600665
    62. H. Schachter. Glycobiology of Caenorhabditis elegans. 2007, 81-100. https://doi.org/10.1016/B978-044451967-2/00083-0
    63. Chunli Liu, Xiangmin Zhang. Multidimensional capillary array liquid chromatography and matrix-assisted laser desorption/ionization tandem mass spectrometry for high-throughput proteomic analysis. Journal of Chromatography A 2007, 1139 (2) , 191-198. https://doi.org/10.1016/j.chroma.2006.11.019
    64. Zhicong Wang, Qinghe Zhang, Tong Li, Zhongyi Zhao, Weibing Zhang. On-line parallel reversed phase two-dimensional liquid chromatography for high-throughput analysis of complex proteomic samples. Science in China Series B: Chemistry 2006, 49 (6) , 527-533. https://doi.org/10.1007/s11426-006-2024-7
    65. Hiroyuki Kaji, Yoshio Yamauchi, Nobuhiro Takahashi, Toshiaki Isobe. Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site–specific stable isotope tagging. Nature Protocols 2006, 1 (6) , 3019-3027. https://doi.org/10.1038/nprot.2006.444
    66. CHRISTIAN V. FORST, LAWRENCE CABUSORA, KWASI G. MAWUENYEGA, XIAN CHEN. BIOLOGICAL SYSTEMS ANALYSIS BY A NETWORK PROTEOMICS APPROACH AND SUBCELLULAR PROTEIN PROFILING. Advances in Complex Systems 2006, 09 (04) , 299-314. https://doi.org/10.1142/S0219525906000835
    67. Mingxia Gao, Na Li, Jie Zhang, Pengyuan Yang, Xiangmin Zhang. The study of three extraction methods for pre-separation and enrichment: Application to the complex proteome separation in rat liver. Separation and Purification Technology 2006, 52 (1) , 170-176. https://doi.org/10.1016/j.seppur.2006.04.006
    68. Christian Schley, Matthias O. Altmeyer, Remco Swart, Rolf Müller, Christian G. Huber. Proteome Analysis of Myxococcus x anthus by Off-Line Two-Dimensional Chromatographic Separation Using Monolithic Poly-(styrene-divinylbenzene) Columns Combined with Ion-Trap Tandem Mass Spectrometry. Journal of Proteome Research 2006, 5 (10) , 2760-2768. https://doi.org/10.1021/pr0602489
    69. Selynda Garza, Mehdi Moini. Analysis of Complex Protein Mixtures with Improved Sequence Coverage Using (CE−MS/MS) n . Analytical Chemistry 2006, 78 (20) , 7309-7316. https://doi.org/10.1021/ac0612269
    70. Mei Huang, Tong Chen, ZhuLong Chan. An evaluation for cross-species proteomics research by publicly available expressed sequence tag database search using tandem mass spectral data. Rapid Communications in Mass Spectrometry 2006, 20 (18) , 2635-2640. https://doi.org/10.1002/rcm.2631
    71. Robert Leslie James Graham, S. Naomi O'Loughlin, Catherine E. Pollock, Nigel G. Ternan, D. Brent Weatherly, Philip J. Jackson, Rick L. Tarleton, Geoff McMullan. A Combined Shotgun and Multidimensional Proteomic Analysis of the Insoluble Subproteome of the Obligate Thermophile, Geobacillus t hermoleovorans T80. Journal of Proteome Research 2006, 5 (9) , 2465-2473. https://doi.org/10.1021/pr0602444
    72. Young-Ki Paik, Seul-Ki Jeong, Eun-Young Lee, Pan-Young Jeong, Yhong-Hee Shim. C. elegans : an invaluable model organism for the proteomics studies of the cholesterol-mediated signaling pathway. Expert Review of Proteomics 2006, 3 (4) , 439-453. https://doi.org/10.1586/14789450.3.4.439
    73. Robert Leslie James Graham, Catherine E. Pollock, Nigel G. Ternan, Geoff McMullan. Top-Down Proteomic Analysis of the Soluble Sub-Proteome of the Obligate Thermophile, Geobacillus t hermoleovorans T80:  Insights into Its Cellular Processes. Journal of Proteome Research 2006, 5 (4) , 822-828. https://doi.org/10.1021/pr0504642
    74. Hui Shi, Jenny Tan, Harry Schachter. N‐Glycans Are Involved in the Response of Caenorhabditis elegans to Bacterial Pathogens. 2006, 359-389. https://doi.org/10.1016/S0076-6879(06)17022-6
    75. Ayse Dosemeci, Jung-Hwa Tao-Cheng, Lucia Vinade, Howard Jaffe. Preparation of postsynaptic density fraction from hippocampal slices and proteomic analysis. Biochemical and Biophysical Research Communications 2006, 339 (2) , 687-694. https://doi.org/10.1016/j.bbrc.2005.11.069
    76. Kazuto Nunomura, Kohji Nagano, Chiharu Itagaki, Masato Taoka, Nobuko Okamura, Yoshio Yamauchi, Sumio Sugano, Nobuhiro Takahashi, Tomonori Izumi, Toshiaki Isobe. Cell Surface Labeling and Mass Spectrometry Reveal Diversity of Cell Surface Markers and Signaling Molecules Expressed in Undifferentiated Mouse Embryonic Stem Cells. Molecular & Cellular Proteomics 2005, 4 (12) , 1968-1976. https://doi.org/10.1074/mcp.M500216-MCP200
    77. Takashi Shinkawa, Masato Taoka, Yoshio Yamauchi, Tohru Ichimura, Hiroyuki Kaji, Nobuhiro Takahashi, Toshiaki Isobe. STEM:  A Software Tool for Large-Scale Proteomic Data Analyses. Journal of Proteome Research 2005, 4 (5) , 1826-1831. https://doi.org/10.1021/pr050167x
    78. Viviane Tschäppät, Emmanuel Varesio, Luca Signor, Gérard Hopfgartner. The application of 2‐D dual nanoscale liquid chromatography and triple quadrupole‐linear ion trap system for the identification of proteins. Journal of Separation Science 2005, 28 (14) , 1704-1711. https://doi.org/10.1002/jssc.200500149
    79. Alexander Gottschalk, Ruta B Almedom, Thorsten Schedletzky, Scott D Anderson, John R Yates, William R Schafer. Identification and characterization of novel nicotinic receptor-associated proteins in Caenorhabditis elegans. The EMBO Journal 2005, 24 (14) , 2566-2578. https://doi.org/10.1038/sj.emboj.7600741
    80. Yo Tabuse, Takuji Nabetani, Akira Tsugita. Proteomic analysis of protein expression profiles duringCaenorhabditis elegans development using two-dimensional difference gel electrophoresis. PROTEOMICS 2005, 5 (11) , 2876-2891. https://doi.org/10.1002/pmic.200401154
    81. Scott L. Hooper, Jeffrey B. Thuma. Invertebrate Muscles: Muscle Specific Genes and Proteins. Physiological Reviews 2005, 85 (3) , 1001-1060. https://doi.org/10.1152/physrev.00019.2004
    82. D. Brent Weatherly, James A. Atwood, Todd A. Minning, Cameron Cavola, Rick L. Tarleton, Ron Orlando. A Heuristic Method for Assigning a False-discovery Rate for Protein Identifications from Mascot Database Search Results. Molecular & Cellular Proteomics 2005, 4 (6) , 762-772. https://doi.org/10.1074/mcp.M400215-MCP200
    83. Christian Ihling, Andrea Sinz. Proteome analysis ofEscherichia coli using high-performance liquid chromatography and Fourier transform ion cyclotron resonance mass spectrometry. PROTEOMICS 2005, 5 (8) , 2029-2042. https://doi.org/10.1002/pmic.200401122
    84. Selene K. Swanson, Michael P. Washburn. The continuing evolution of shotgun proteomics. Drug Discovery Today 2005, 10 (10) , 719-725. https://doi.org/10.1016/S1359-6446(05)03450-1
    85. Kohji Nagano, Masato Taoka, Yoshio Yamauchi, Chiharu Itagaki, Takashi Shinkawa, Kazuto Nunomura, Nobuko Okamura, Nobuhiro Takahashi, Tomonori Izumi, Toshiaki Isobe. Large-scale identification of proteins expressed in mouse embryonic stem cells. PROTEOMICS 2005, 5 (5) , 1346-1361. https://doi.org/10.1002/pmic.200400990
    86. Wei-Jun Qian, Jon M. Jacobs, David G. Camp, Matthew E. Monroe, Ronald J. Moore, Marina A. Gritsenko, Steve E. Calvano, Stephen F. Lowry, Wenzhong Xiao, Lyle L. Moldawer, Ronald W. Davis, Ronald G. Tompkins, Richard D. Smith. Comparative proteome analyses of human plasma followingin vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry. PROTEOMICS 2005, 5 (2) , 572-584. https://doi.org/10.1002/pmic.200400942
    87. Wei-Jun Qian, Tao Liu, Matthew E. Monroe, Eric F. Strittmatter, Jon M. Jacobs, Lars J. Kangas, Konstantinos Petritis, David G. Camp, Richard D. Smith. Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis:  The Human Proteome. Journal of Proteome Research 2005, 4 (1) , 53-62. https://doi.org/10.1021/pr0498638
    88. Kwasi G. Mawuenyega, Christian V. Forst, Karen M. Dobos, John T. Belisle, Jin Chen, E. Morton Bradbury, Andrew R.M. Bradbury, Xian Chen. Mycobacterium tuberculosis Functional Network Analysis by Global Subcellular Protein Profiling. Molecular Biology of the Cell 2005, 16 (1) , 396-404. https://doi.org/10.1091/mbc.e04-04-0329
    89. S. Vaidyanathan, R. Goodacre. Understanding the behaviour of pathogenic cells: proteome and metabolome analyses. 2005, 3-52. https://doi.org/10.1533/9781845690229.1.3
    90. Harry Schachter. Protein glycosylation lessons from Caenorhabditis elegans. Current Opinion in Structural Biology 2004, 14 (5) , 607-616. https://doi.org/10.1016/j.sbi.2004.09.005
    91. Masato Taoka, Yoshio Yamauchi, Takashi Shinkawa, Hiroyuki Kaji, Wakana Motohashi, Hiroshi Nakayama, Nobuhiro Takahashi, Toshiaki Isobe. Only a Small Subset of the Horizontally Transferred Chromosomal Genes in Escherichia coli Are Translated into Proteins. Molecular & Cellular Proteomics 2004, 3 (8) , 780-787. https://doi.org/10.1074/mcp.M400030-MCP200
    92. Patricia B. Maguire, Niamh Moran, Gerard Cagney, Desmond J. Fitzgerald. Application of Proteomics to the Study of Platelet Regulatory Mechanisms. Trends in Cardiovascular Medicine 2004, 14 (6) , 207-220. https://doi.org/10.1016/j.tcm.2004.06.001
    93. Edgar Nägele, Martin Vollmer, Patric Hörth, Cornelia Vad. 2D-LC/MS techniques for the identification of proteins in highly complex mixtures. Expert Review of Proteomics 2004, 1 (1) , 37-46. https://doi.org/10.1586/14789450.1.1.37
    94. Wei-Jun Qian, David G Camp II, Richard D Smith. High-throughput proteomics using Fourier transform ion cyclotron resonance mass spectrometry. Expert Review of Proteomics 2004, 1 (1) , 87-95. https://doi.org/10.1586/14789450.1.1.87
    95. Xiao-Sheng Jiang, Hu Zhou, Lei Zhang, Quan-Hu Sheng, Su-Jun Li, Long Li, Pei Hao, Yi-Xue Li, Qi-Chang Xia, Jia-Rui Wu, Rong Zeng. A High-throughput Approach for Subcellular Proteome. Molecular & Cellular Proteomics 2004, 3 (5) , 441-455. https://doi.org/10.1074/mcp.M300117-MCP200
    96. György Marko-Varga, Thomas E. Fehniger. Proteomics and Disease The Challenges for Technology and Discovery. Journal of Proteome Research 2004, 3 (2) , 167-178. https://doi.org/10.1021/pr049958+
    97. D.P. Knox. Technological advances and genomics in metazoan parasites. International Journal for Parasitology 2004, 34 (2) , 139-152. https://doi.org/10.1016/j.ijpara.2003.10.013
    98. Yoshiyuki Yoshimura, Yoshio Yamauchi, Takashi Shinkawa, Masato Taoka, Hitomi Donai, Nobuhiro Takahashi, Toshiaki Isobe, Takashi Yamauchi. Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry. Journal of Neurochemistry 2004, 88 (3) , 759-768. https://doi.org/10.1046/j.1471-4159.2003.02136.x
    99. Jon M. Jacobs, Heather M. Mottaz, Li-Rong Yu, David J. Anderson, Ronald J. Moore, Wan-Nan U. Chen, Kenneth J. Auberry, Eric F. Strittmatter, Matthew E. Monroe, Brian D. Thrall, David G. Camp, Richard D. Smith. Multidimensional Proteome Analysis of Human Mammary Epithelial Cells. Journal of Proteome Research 2004, 3 (1) , 68-75. https://doi.org/10.1021/pr034062a
    100. Brett R. Wenner, Mark A. Lovell, Bert C. Lynn. Proteomic Analysis of Human Ventricular Cerebrospinal Fluid from Neurologically Normal, Elderly Subjects Using Two-Dimensional LC−MS/MS. Journal of Proteome Research 2004, 3 (1) , 97-103. https://doi.org/10.1021/pr034070r
    Load all citations
    Download PDF

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    MENDELEY PAIRING EXPIRED
    Your Mendeley pairing has expired. Please reconnect