Introduction

Protein chemical cross-linking and mass spectrometry enable the analysis of protein-protein interactions and protein topologies; however, complicated cross-linked peptide spectra require specialized algorithms to identify interacting sites. The Kojak cross-linking software application is a new, efficient approach to identify cross-linked peptides, enabling large-scale analysis of protein-protein interactions by chemical cross-linking techniques. The algorithm integrates spectral processing and scoring schemes adopted from traditional database search algorithms and can identify cross-linked peptides using many different chemical cross-linkers with or without heavy isotope labels. Kojak was used to analyze both novel and existing data sets and was compared to existing cross-linking algorithms. The algorithm provided increased cross-link identifications over existing algorithms and, equally importantly, the results in a fraction of computational time. The Kojak algorithm is open-source, cross-platform, and freely available. This software provides both existing and new cross-linking researchers alike an effective way to derive additional cross-link identifications from new or existing data sets. For new users, it provides a simple analytical resource resulting in more cross-link identifications than other methods.

Publications

  1. Kojak: efficient analysis of chemically cross-linked protein complexes.
    Cite this
    Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL, 2015-05-01 - Journal of proteome research

Credits

  1. Michael R Hoopmann
    Developer

    †Institute for Systems Biology, 401 Terry Avenue North, United States of America

  2. Alex Zelter
    Developer

    ‡Department of Biochemistry, University of Washington, United States of America

  3. Richard S Johnson
    Developer

    §Department of Genome Sciences, University of Washington, United States of America

  4. Michael Riffle
    Developer

    ‡Department of Biochemistry, University of Washington, United States of America

  5. Michael J MacCoss
    Developer

    §Department of Genome Sciences, University of Washington, United States of America

  6. Trisha N Davis
    Developer

    ‡Department of Biochemistry, University of Washington, United States of America

  7. Robert L Moritz
    Investigator

    †Institute for Systems Biology, 401 Terry Avenue North, United States of America

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Summary
AccessionBT006929
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByRobert L Moritz