Why complexity and entropy matter: Information, posttranslational modifications, and assay fidelity

Proteomics

Volumn 12, Issue 8, 2012, Pages 1147-1150

  Sherman, Jamie ^a,c   Molloy, Mark P ^b   Burlingame, Alma L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MACQUARIE UNIVERSITY   (Australia)

^c UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Bioinformatics; Identification; Molecular profiling; Post translational modification; Proteome profiling

Indexed keywords

PEPTIDE;

ARTICLE; BIOINFORMATICS; CONCEPTUAL FRAMEWORK; ENTROPY; HUMAN; MATHEMATICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEOMICS;

AMINO ACID SEQUENCE; DATABASES, PROTEIN; ENTROPY; HUMANS; INFORMATION THEORY; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SENSITIVITY AND SPECIFICITY; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 84860875400     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100459     Document Type: Article

References (12)

1. Tabb, D. L., Saraf, A., Yates, J. R., GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal. Chem. 2003, 75, 6415-6421.
2. Eng, J., McCormack, A., Yates, J., An approach to correlate tandem mass-spectral data of peptides with amino-acid sequences in a protein database. J. Am. Soc. Mass. Spectr. 1994, 5, 976-989.
3. Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
4. Craig, R., Beavis, R.C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
5. Elias, J. E., Gygi, S. P., Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 2007, 4, 207-214.
6. Shannon, C., A mathematical theory of communication. The Bell Systems Technical Journal, 1948, 27, 379-423, 623-656.
7. Ash, R. B., Information Theory, Dover Publications, New York, 1990.
8. Goñi, J., Aznárez-Sanado, M., Arrondo, G., Fernández-Seara, M., et al., The neural substrate and functional integration of uncertainty in decision making: an information theory approach. PLoS ONE 2011, 6, e17408.
9. Knudsen, G.M., Chalkley, R. J., The effect of using an inappropriate protein database for proteomic data analysis PLoS ONE 2011, 6, e20873.
10. Sherman, J., McKay, M. J., Ashman, K., Molloy, M. P., Unique ion signature mass spectrometry, a deterministic method to assign peptide identity. Mol. Cell. Proteomics 2009, 8, 2051-2062.
11. Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., et al., A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 2006, 24, 1285-1292.
12. Baker, P., Trinidad, J., Chalkley, R., Modification site localization scoring integrated into a search engine. Mol. Cell. Proteomics 2011, 10, M111.008078.