Citing Kojak

Please use the following citations:

Hoopmann MR, Shteynberg DD, Zelter A, Riffle M, Lyon AS, Agard DA, Luan Q, Nolen BJ, MacCoss MJ, Davis TN, and Moritz RL. “Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline” J Proteome Res 2023 Feb 3;22(2):647-655. Link

Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, and Moritz RL. “Kojak: Efficient analysis of chemically cross-linked protein complexes” J Proteome Res 2015 May 1;14(5):2190-8. Link

If you use the Kojak Spectrum Viewer, please cite:

Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, and Moritz RL. “An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results” J Am Soc Mass Spectrom 2016 July 28 (web) Link

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Software tools that integrate Kojak

ProXL Website Publication

CLMSVault Website Publication

Crux Website Publication

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Additional publications using Kojak

Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. “Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure.” J Struct Biol 2016 194(3):303-10 Link

Kudalkar EM, Scarborough EA, Umbreit NT, Zelter A, Gestaut DR, Riffle M, Johnson RS, MacCoss MJ, Asbury CL, Davis TN. “Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex.” Proc Natl Acad Sci U S A 2015 112(41):E5583-9. Link

Zelter A, Bonomi M, Kim JO, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, and Davis TN. “The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling.” Nat Commun 2015 6:8673 Link

Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR 3rd, MacCoss MJ, Moritz RL, Asbury CL, and Davis TN. “Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex.” Genetics 2014 198(4):1483-93 Link