Rovshan Sadygov, Ph.D.

Assistant Professor, Dept. of Biochemistry and Molecular Biology, Scientist, Sealy Center for Molecular Medicine

University of Texas Medical Branch
301 University Blvd. Galveston, TX 77555-0647
6.630 Basic Science Building
(409) 772-3287

Research Summary

Our research interests are in computational analysis of mass spectral data from proteomics experiments to infer biological information. For these purposes we adopt methods of probability/statistics, signal processing and pattern recognition to analyze mass spectral data and use biological knowledge base for interpretations. Proteomics research plays important role in the studies of primary structure of proteins, protein interaction networks, biomarker discovery, post-translational modifications and signaling pathways.
Proteomics experiments generate large amounts of data relevant to the protein content and complexity of a sample. The interpretation of these data requires efficient bioinformatics tools to process, store, visualize and disseminate the data. We develop algorithms for error tolerant database search, protein grouping, spectral quality assessment, in silico sequence hybridization (to reduce sequence redundancy), spectral library search, elemental composition determination and for processing chromatographic surfaces for alignments in time and mass-to-charge ratio domains and normalization in abundance domain, peak detection, background subtraction and peak area integration. These algorithms will serve as a base for inferring primary protein content information of a biological sample. We will then use this information to generate probabilistic models for protein interaction networks, signaling pathways, statistical models for potential biomarker discovery and validation, for absolute and relative protein quantification.

Selected Publications

  1. Charger: a combination of signal processing and statistical learning algorithms for charge state determination from MS/MS. R.G. Sadygov, Z. Hao, A. FR. Huhmer. Anal. Chem., 2008:80:376-386.
  2. ChromAlign: A Two-Step Algorithmic Procedure for Time Alignment of Three Dimensional LC-MS Chromatographic Surfaces. R.G. Sadygov, F. M. Maroto, A. Huhmer. Anal. Chem. 2006;78:8207-8217.
  3. Assigning in vivo Carbamylation and Acetylation in Human Lens Proteins using Tandem Mass Spectrometry and Database Searching. Z.-Y. Park, R. Sadygov, J. Clark, J.R. Yates. International Journal of Mass Spectrometry;2007:259:161-173
  4. Central Limit Theorem as an Approximation for Intensity-Based Scoring Function. R.G. Sadygov, J. Wohlschlegel, S.K. Park, T. Xu and J.R. Yates III, Anal. Chem. 2006;78:89-95.
  5. Large-scale Database Searching using Tandem Mass Spectra: Looking up the answer in the Back of the Book. R.G. Sadygov, D. Cociorva, J.R. Yates III, Nature Methods 2004;1:195-202.
  6. MS1, MS2, and SQT – three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. W.H. McDonald, D.L. Tabb, R.G. Sadygov, M.J. MacCoss, J. Venable, J. Grauman, J.R. Johnson, D. Cociorva and J.R. Yates III, Rapid Communications in Mass Spectrometry, 2004;18:2162-2168.
  7. A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics, R.G. Sadygov, H. Liu, and J.R. Yates III, Analytical Chemistry, 2004;76:4193-4201.
  8. Statistical Models for Protein Validation using Tandem Mass Spectral Data and Protein Amino Acid Sequence Databases, R.G. Sadygov, H. Liu, and J.R. Yates III, Analytical Chemistry, 2004;76:1664-1671.
  9. A Hypergeometric Probability Model for Protein Identification and Validation using Tandem Mass Spectral Data and Protein Sequence Databases, R.G. Sadygov, and J. R. Yates III, Analytical Chemistry 2003;75:3792-3798.
  10. A Correlation Algorithm for the Automated Quantitative Analysis of Shotgun Proteomics Data, M. J. MacCoss, C. C. Wu, H. Liu, R.G. Sadygov, J. R. Yates, III, Analytical Chemistry 2003;75:6912-6921.
  11. Code Developments to Improve the Efficiency of Automated MS/MS Spectra Interpretation, R.G. Sadygov, J. Eng, E. Durr, A. Saraf, H.W. McDonald, J.M. MacCoss, and J.R. Yates III,  J. Proteome Res., 2002:1:211.
  12. Shotgun identification of protein modifications from protein complexes and lens tissue, M.J. MacCoss, W.H. McDonald, A. Saraf, R.G. Sadygov, J.M. Clark, J.J. Tasto, K.L. Gould, D. Wolters, M. Washburn, A. Weiss, J.I. Clark, and J.R. Yates III,  Proc. Natl. Acad. Sci. USA, 2002;99:7900-7905.
  13. Dynamics of primary charge separation in bacterial photosynthesis using the multilevel Redfield-Davies secular approach, R.G. Sadygov, and D. Neuhauser, International Journal of Quantum Chemistry  2002;87:254-263.
  14. Unusual conical intersections in the Jahn-Teller effect: The electronically excited states of $Li_3$, R.G. Sadygov, and D.R. Yarkony, J. Chem. Phys. 1999:110:3639. 
  15. On the Adiabatic to Diabatic States Transformation in the Presence of a Conical Intersection: A Most Diabatic Basis from the Solution to a Poisson's Equation. 1, R.G. Sadygov, and D.R. Yarkony, J. Chem. Phys. 1998;109:20.
  16. Electronic structure aspects of the spin-forbidden reaction CH3(X 2A2//)+N(4S) -> HCN(X 1Σ+) + H2(X 1Σg+), R.G. Sadygov, and D.R. Yarkony, J. Chem. Phys. 1997;107:4994.
  17. Resonances  in the predissociation of the A{^2} state of MgBr, R.G. Sadygov, J. Rostas, G. Taieb and D.R. Yarkony, J. Chem. Phys. 1997;106:10.
  18. Intramolecular charge-transfer and solvent-polarity dependence of radiative decay-rate in photoexcited dinaphthylamines, S.J. Wang, J.J. Cai, R.G. Sadygov, and E.C. Lim, J. Physical Chem. 1995; 99:7416.
  19. A Theoretical Study of the Structure and Energetics of Stacked Dimers of Polycyclic Aromatic Hydrocarbons: Application of INDO 1/S Method to Singlet Excimers of Naphthalene and Phenanthrene, R.G. Sadygov, and E.C. Lim, Chem. Phys. Lett. 1994;225:441.
  20. An Influence of Asymmetry of Reaction Center Dimer Polar Environment on the Electron Transfer Process, O.V. Parush, R.G. Sadygov, and A.K. Kukushkin, Biophysics 1994;39:875.
  21. Intramolecular Photoassociation and Photoinduced Charge Transfer in Bridged Diaryl Compounds: A Semiempirical MO Study of Intramolecular Charge Transfer in the Excited Singlet States of Dinaphthylamines, D. Chen, R.G. Sadygov, and E.C. Lim, J. Phys. Chem. 1994;98:2018.
  22. The Effect of Broadening of Vibrational Levels on the Primary Charge Separation Processes in Bacterial Photosynthesis, R.G. Sadygov and A.K. Kukushkin, Biofizika 1991;36: 990 .
  23. Activationless Electron Transfer in the Primary Charge Separation of Bacterial Photosynthesis, A.K. Kukushkin, and R.G. Sadygov, Vestnik MGU, Ser. 3 Physics and Astronomy 1991;32:84.