Scientific Journal of Astana IT University
PROTEIN IDENTIFICATION USING SEQUENCE DATABASES
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Link, A.J., Eng, J., Schieltz, D.M., Carmack, E., Mize, G.J., Morris, D.R., ... & and Yates, J.R. (3). rd. (1999).
Direct analysis of protein complexes using mass spectrometry. Nature Biotechnology, 17, 676-82.
doi: 10.1038/10890.
Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M.H., & Aebersold, R. (1999). Quantitative analysis of
complex protein mixtures using isotope-coded affinity tags. Nature Biotechnology, 17 (10), 994-999.
Washburn, M.P., Wolters, D., & Yates, J.R. (2001). Large-scale analysis of the yeast proteome by
multidimensional protein identification technology. Nature Biotechnology, 19, 242-247.
Chung, T.W., & Tureček, F. (2010). Backbone and side-chain specific dissociations of z ions from nontryptic peptides. Journal of the American Society for Mass Spectrometry, 21, 1279-1295
Dancik, V., Addona, T.A., Clauser, K.R., Vath, J.E., & Pevzner, P.A. (1999). De novo peptide sequencing
via tandem mass spectrometry. Journal of Computational Biology, 6 (3-4), 327-342.
Taylor, J.A., & Johnson, R.S. (2001). Implementation and uses of automated de novo peptide
sequencing by tandem mass spectrometry. Analytical Chemistry, 73 (11), 2594-2604.
Chen, T., Kao, M.Y., Tepel, M., Rush, J., & Church, G.M. (2001). A dynamic programming approach to de
novo sequencing via tandem mass spectrometry, Journal of Computational Biology, 8 (3), 325-337.
Ma, B., Zhang, K., Hendrie, C., et al. (2003). PEAKS: powerful software for peptide de novo sequencing
by tandem mass spectrometry. Rapid communications in mass spectrometry, 17, 2337-2342.
Frank, A., & Pevzner, P. (2005). PepNovo: de novo peptide sequencing via probabilistic network
modeling. Analytical chemistry, 77 (4), 964-973.
Berizovskaya, E.I., Ichalaynen A.A., Antochin A.M. (2015). Methods of processing mass spectrometry
data for identification of the peptides and proteins. Vestnik Moskovskogo universiteta, 56, 266-278.
Chen, C., Huang, H., & Wu, C.H. (2017). Protein bioinformatics databases and resources. Protein
Bioinformatics, 3-39.
Nesvizhskii, A.I. (2007). Protein Identification by Tandem Mass Spectrometry and Sequence Database
Searching. Mass Spectrometry Data Analysis in Proteomics, 367, 87-119. doi: 10.1385/1-59745-275-0:87.
Aebersold, R. & Goodlett, D.R. (2001). Mass spectrometry in proteomics. Chemical Reviews, 101,
-295.
Keller, A., Nesvizhskii, A.I., Kolker, E., & Aebersold, R. (2002). Empirical statistical model to estimate
the accuracy of peptide identifications made by MS/MS and database search. Analytical Chemistry,
, 5383-5392.
Tabb, D.L., Smith, L.L., Breci, L.A., Wysocki, V.H., Lin, D., & Yates, J.R. (2003). Statistical characterization of
ion trap tandem mass spectra from doubly charged tryptic peptides. Analytical Chemistry, 75, 1155-1163.
Kapp, E.A., Schütz, F., Reid, G.E., Eddes, J.S., Moritz, R.L., O’Hair, R.A., & Simpson, R.J. (2003). Mining
a tandem mass spectrometry database to determine the trends and global factors influencing peptide
fragmentation, Analytical Chemistry, 75, 6251-6254.
Resing, K.A., Meyer-Arendt, K., Mendoza, A.M., et al. (2004). Improving reproducibility and sensitivity
in identifying human proteins by shotgun proteomics, Analytical Chemistry, 76, 3556-3568.
Keller, A., Nesvizhskii, A.I., Kolker, E., & Aebersold, R. (2002). ‘Empirical statistical model to estimate
the accuracy of peptide identifications made by MS/MS and database search. Analytical chemistry,
(20), 5383-5392.
Avtonomov D., Agron I., Kononikhin A., Nikolaev E. (2009). Sozdaniye bazy dannykh tochnykh massovo-vremennykh metok dlya kachestvennogo i kolichestvennogo podkhoda v issledovanii proteoma mochi
cheloveka s ispol‘zovaniyem izotopnogo mecheniya. Proceedings of Moscow Institute of Physics and
Technology, 1 (1), 24-29.
Eng, J., McCormack, A., Yates, J. (1994). An approach to correlate tandem mass spectral data of
peptides with amino acid sequences in a protein database. Journal of the American Society for Mass
Spectrometry, 5, 976-989.
Yates, J.R., Eng, J.K., & McCormack, A.L. (1995). Mining Genomes: Correlating Tandem Mass Spectra
of Modified and Unmodified Peptides to Sequences in Nucleotide Databases. Analytical Chemistry,
(18), 3202-3210. https://doi.org/10.1021/ac00114a016.
Lyutvinsky J. (2007). Method of recognition of amino acid sequences in mass spectra of peptides for
proteomics problems. Dissertation.
Craig, R., Beavis, R.C. (2004). TANDEM: matching proteins with tandem mass spectra. Bioinformatics, 20
(9), 1466-1467.
Fenyö, D., Beavis, R.C., (2003). A method for assessing the statistical significance of mass spectrometrybased protein identifications using general scoring schemes. Analytical Chemistry, 75, 768-774.
Nesvizhskii, A.I., Keller, A., Kolker, E., & Aebersold, R. (2003). A statistical model for identifying
proteins by tandem mass spectrometry. Analytical Chemistry, 75, 4646-4658.
Rappsilber, J., & Mann, M. (2002). What does it mean to identify a protein in proteomics? Trends in
Biochemical Sciences, 27 (2), 74-78.
DOI: http://dx.doi.org/10.37943/AITU.2020.91.98.002
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