PROTEOMICS

Cover image for Vol. 10 Issue 6

Special Issue: SPECIAL: PROTEOMICS DATA MANAGEMENT

No. 6 March 2010

Volume 10, Issue 6

Pages 1102–1327

Issue edited by: Lennart Martens, Henning Hermjakob

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
    9. Reviews
    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
    15. Technical Briefs
    16. Review
    17. Dataset Brief
    18. Technical Briefs
    19. Reviews
    20. Research Articles
    1. Cover Picture: Proteomics 6'10

      Version of Record online: 19 MAR 2010 | DOI: 10.1002/pmic.201090017

  2. Contents

    1. Top of page
    2. Cover Picture
    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
    9. Reviews
    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
    15. Technical Briefs
    16. Review
    17. Dataset Brief
    18. Technical Briefs
    19. Reviews
    20. Research Articles
    1. Contents – Proteomics 6'2010

      Version of Record online: 19 MAR 2010 | DOI: 10.1002/pmic.201090019

  3. In this issue

    1. Top of page
    2. Cover Picture
    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
    9. Reviews
    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
    15. Technical Briefs
    16. Review
    17. Dataset Brief
    18. Technical Briefs
    19. Reviews
    20. Research Articles
    1. In this issue

      Version of Record online: 19 MAR 2010 | DOI: 10.1002/pmic.201090018

  4. From Our Sister Journal

    1. Top of page
    2. Cover Picture
    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
    9. Reviews
    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
    15. Technical Briefs
    16. Review
    17. Dataset Brief
    18. Technical Briefs
    19. Reviews
    20. Research Articles
    1. From Our Sister Journal (page 1102)

      Version of Record online: 19 MAR 2010 | DOI: 10.1002/pmic.201090015

  5. Editorial

    1. Top of page
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    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
    9. Reviews
    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
    15. Technical Briefs
    16. Review
    17. Dataset Brief
    18. Technical Briefs
    19. Reviews
    20. Research Articles
  6. Review

    1. Top of page
    2. Cover Picture
    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
    9. Reviews
    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
    15. Technical Briefs
    16. Review
    17. Dataset Brief
    18. Technical Briefs
    19. Reviews
    20. Research Articles
    1. Free computational resources for designing selected reaction monitoring transitions (pages 1106–1126)

      Jennifer A. Cham (Mead), Luca Bianco and Conrad Bessant

      Version of Record online: 13 JAN 2010 | DOI: 10.1002/pmic.200900396

  7. Research Articles

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    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
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    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
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    1. Investigating protein isoforms via proteomics: A feasibility study (pages 1127–1140)

      Paul Blakeley, Jennifer A. Siepen, Craig Lawless and Simon J. Hubbard

      Version of Record online: 13 JAN 2010 | DOI: 10.1002/pmic.200900445

    2. Prediction of the human membrane proteome (pages 1141–1149)

      Linn Fagerberg, Kalle Jonasson, Gunnar von Heijne, Mathias Uhlén and Lisa Berglund

      Version of Record online: 19 FEB 2010 | DOI: 10.1002/pmic.200900258

  8. Reviews

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    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
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    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
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    17. Dataset Brief
    18. Technical Briefs
    19. Reviews
    20. Research Articles
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      A guided tour of the Trans-Proteomic Pipeline (pages 1150–1159)

      Eric W. Deutsch, Luis Mendoza, David Shteynberg, Terry Farrah, Henry Lam, Natalie Tasman, Zhi Sun, Erik Nilsson, Brian Pratt, Bryan Prazen, Jimmy K. Eng, Daniel B. Martin, Alexey I. Nesvizhskii and Ruedi Aebersold

      Version of Record online: 25 JAN 2010 | DOI: 10.1002/pmic.200900375

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      Data maximization by multipass analysis of protein mass spectra (pages 1160–1171)

      Ravi Tharakan, Nathan Edwards and David R. M. Graham

      Version of Record online: 15 JAN 2010 | DOI: 10.1002/pmic.200900433

  9. Research Article

    1. Top of page
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    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
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    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
    15. Technical Briefs
    16. Review
    17. Dataset Brief
    18. Technical Briefs
    19. Reviews
    20. Research Articles
    1. Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines (pages 1172–1189)

      Wen Yu, J. Alex Taylor, Michael T. Davis, Leo E. Bonilla, Kimberly A. Lee, Paul L. Auger, Chris C. Farnsworth, Andrew A. Welcher and Scott D. Patterson

      Version of Record online: 25 JAN 2010 | DOI: 10.1002/pmic.200900074

  10. Technical Brief

    1. Top of page
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    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
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    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
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    17. Dataset Brief
    18. Technical Briefs
    19. Reviews
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    1. Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets (pages 1190–1195)

      Eric W. Deutsch, David Shteynberg, Henry Lam, Zhi Sun, Jimmy K. Eng, Christine Carapito, Priska D. von Haller, Natalie Tasman, Luis Mendoza, Terry Farrah and Ruedi Aebersold

      Version of Record online: 15 JAN 2010 | DOI: 10.1002/pmic.200900567

  11. Rapid Communication

    1. Top of page
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    5. From Our Sister Journal
    6. Editorial
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    11. Technical Brief
    12. Rapid Communication
    13. Review
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    1. LysNDeNovo: An algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation (pages 1196–1201)

      Bas van Breukelen, Alexandros Georgiou, Madalina M. Drugan, Nadia Taouatas, Shabaz Mohammed and Albert J. R. Heck

      Version of Record online: 13 JAN 2010 | DOI: 10.1002/pmic.200900405

  12. Review

    1. Top of page
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    3. Contents
    4. In this issue
    5. From Our Sister Journal
    6. Editorial
    7. Review
    8. Research Articles
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    10. Research Article
    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
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    17. Dataset Brief
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    1. Missing values in gel-based proteomics (pages 1202–1211)

      Daniela Albrecht, Olaf Kniemeyer, Axel A. Brakhage and Reinhard Guthke

      Version of Record online: 13 JAN 2010 | DOI: 10.1002/pmic.200800576

  13. Research Article

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    5. From Our Sister Journal
    6. Editorial
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    11. Technical Brief
    12. Rapid Communication
    13. Review
    14. Research Article
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    17. Dataset Brief
    18. Technical Briefs
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  14. Technical Briefs

    1. Top of page
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    4. In this issue
    5. From Our Sister Journal
    6. Editorial
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    11. Technical Brief
    12. Rapid Communication
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    1. jTraqX: A free, platform independent tool for isobaric tag quantitation at the protein level (pages 1223–1225)

      Thilo Muth, Daniela Keller, Stephanie Michaela Puetz, Lennart Martens, Albert Sickmann and Andreas M. Boehm

      Version of Record online: 7 JAN 2010 | DOI: 10.1002/pmic.200900374

    2. Rover: A tool to visualize and validate quantitative proteomics data from different sources (pages 1226–1229)

      Niklaas Colaert, Kenny Helsens, Francis Impens, Joël Vandekerckhove and Kris Gevaert

      Version of Record online: 7 JAN 2010 | DOI: 10.1002/pmic.200900379

  15. Review

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    6. Editorial
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    11. Technical Brief
    12. Rapid Communication
    13. Review
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    17. Dataset Brief
    18. Technical Briefs
    19. Reviews
    20. Research Articles
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      Using Laboratory Information Management Systems as central part of a proteomics data workflow (pages 1230–1249)

      Christian Stephan, Michael Kohl, Michael Turewicz, Katharina Podwojski, Helmut E. Meyer and Martin Eisenacher

      Version of Record online: 13 JAN 2010 | DOI: 10.1002/pmic.200900420

  16. Dataset Brief

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    6. Editorial
    7. Review
    8. Research Articles
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    10. Research Article
    11. Technical Brief
    12. Rapid Communication
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    14. Research Article
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    1. Data management and functional annotation of the Korean reference plasma proteome (pages 1250–1255)

      Seul-Ki Jeong, Eun-Young Lee, Jin-Young Cho, Hyoung-Joo Lee, An-Sung Jeong, Sang Yun Cho and Young-Ki Paik

      Version of Record online: 19 FEB 2010 | DOI: 10.1002/pmic.200900371

  17. Technical Briefs

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    6. Editorial
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    12. Rapid Communication
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    1. Semi-automatic tool to describe, store and compare proteomics experiments based on MIAPE compliant reports (pages 1256–1260)

      Salvador Martínez-Bartolomé, J. Alberto Medina-Aunon, Andrew R. Jones and Juan P. Albar

      Version of Record online: 13 JAN 2010 | DOI: 10.1002/pmic.200900367

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      ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics (pages 1261–1264)

      Kenny Helsens, Niklaas Colaert, Harald Barsnes, Thilo Muth, Kristian Flikka, An Staes, Evy Timmerman, Steffi Wortelkamp, Albert Sickmann, Joël Vandekerckhove, Kris Gevaert and Lennart Martens

      Version of Record online: 7 JAN 2010 | DOI: 10.1002/pmic.200900409

  18. Reviews

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    6. Editorial
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    8. Research Articles
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    11. Technical Brief
    12. Rapid Communication
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    1. From proteome lists to biological impact– tools and strategies for the analysis of large MS data sets (pages 1270–1283)

      Rainer Malik, Kalyan Dulla, Erich A. Nigg and Roman Körner

      Version of Record online: 13 JAN 2010 | DOI: 10.1002/pmic.200900365

    2. MS-driven protease substrate degradomics (pages 1284–1296)

      Francis Impens, Niklaas Colaert, Kenny Helsens, Kim Plasman, Petra Van Damme, Joël Vandekerckhove and Kris Gevaert

      Version of Record online: 7 JAN 2010 | DOI: 10.1002/pmic.200900418

  19. Research Articles

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    12. Rapid Communication
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    1. Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome (pages 1297–1306)

      Manuel Weiss, Sabine Schrimpf, Michael O. Hengartner, Martin J. Lercher and Christian von Mering

      Version of Record online: 13 JAN 2010 | DOI: 10.1002/pmic.200900414

    2. Network generation enhances interpretation of proteomic data from induced apoptosis (pages 1307–1315)

      Ruth F. Deighton, Lorraine E. Kerr, Duncan M. Short, Mike Allerhand, Ian R. Whittle and James McCulloch

      Version of Record online: 25 JAN 2010 | DOI: 10.1002/pmic.200900112

    3. Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps (pages 1316–1327)

      Ruth Isserlin, Daniele Merico, Rasoul Alikhani-Koupaei, Anthony Gramolini, Gary D. Bader and Andrew Emili

      Version of Record online: 1 FEB 2010 | DOI: 10.1002/pmic.200900412

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