Начало семинаров — 4 июля 2011 (понедельник).
Подробное расписание опубликовано здесь.
Материалы лекций:
- 05/07/2011: Intro to computational MS (Pavel) — slides (pptx)
- 06/07/2011: Spectral probabilities and spectral dictionaries (Pavel) — slides (ppt)
- 07/07/2011: Target-Decoy Search in MS: When things may go wrong (Kira) — slides (pdf), paper: Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong (Gupta et al., 2011) (including supplement)
- 08/07/2011: Deconvolution and Database Search of Complex Top-Down Tandem Mass Spectra — slides (ppt), paper: Protein Identification Using Top-Down Spectra (Liu et al. 2011) (including supplement)
- 11/07/2011: Block Pattern Matching and its Applications in Proteomics (Kira) — slides (ppt), paper: Blocked Pattern Matching Problem and its Applications in Proteomics (Ng et al., 2011)
- 12/07/2011: Gapped Spectral Dictionaries (Max Gladkih) — slides (odp), paper: Gapped spectral dictionaries and their applications for database searches of tandem mass spectra (Jeong et al. 2011) http://www.ncbi.nlm.nih.gov/pubmed/21444829
- 26/07/2011: TBA (Alexey Nezhvinsky, University of Michigan) — slides (TBA), paper (TBA).
- 27/07/2011: De Novo peptide sequencing (Sergey Nikolenko) — slides (pdf), papers: De novo peptide sequencing via tandem mass spectrometry (Dancik et al. 1999), A ranking-based scoring function for peptide-spectrum matches (Frank. 2009).
Освещаемые статьи:
- Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis. Liu et al. 2010.
- Blocked Pattern Matching Problem and its Applications in Proteomics. Ng et al., 2011
- Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applicationsfor de Novo Peptide Sequencing andIdentification. Kim et al. 2009.
- Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Kim et al. 2009.
- Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. Kim et al. 2008.
- Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Bandeira et al. 2007.
- Protein identification by spectral networks analysis. Bandeira et al. 2007.
- Identification of post-translational modifications by blind search of mass spectra. Tsur et al. 2005. http://www.ncbi.nlm.nih.gov/pubmed/16311586
- InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Tanner et al. 2005.
- De novo peptide sequencing via tandem mass spectrometry. Dancik et al. 1999.
- A ranking-based scoring function for peptide-spectrum matches. Frank. 2009.