Tools and challenges for diversity-driven proteomics in Brazil

Proteomics

Volumn 12, Issue 17, 2012, Pages 2601-2606

  Junqueira, Magno ^a   Carvalho, Paulo Costa ^b  

^a UNIVERSITY OF BRASILIA   (Brazil)

^b INSTITUTO CARLOS CHAGAS   (Brazil)

Author keywords

Bioinformatics; Diversity; Homology driven proteomics; Quantitative analysis; Sequence similarity search

Indexed keywords

PROTEIN; PROTEOME;

ALGORITHM; ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ARTICLE; BRAZIL; CELL LINE; CIRCULAR DICHROISM; COMPUTATIONAL FLUID DYNAMICS; DE NOVO PEPTIDE SEQUENCING; DERIVATIZATION; ELECTRON CAPTURE DETECTION; ELECTRON TRANSPORT; ENZYME METABOLISM; GENE MUTATION; GENE REGULATORY NETWORK; GENE SEQUENCE; GENOME; LARGE SCALE PRODUCTION; MASS SPECTROMETRY; MOLECULAR BIOLOGY; NEXT GENERATION SEQUENCING; PEPTIDE SPECTRUM MATCHING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN METABOLISM; PROTEIN PROCESSING; PROTEOMICS; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; SEQUENCE TAGGED SITE; SINGLE NUCLEOTIDE POLYMORPHISM; TAG SEARCHING;

ANIMALS; BRAZIL; HUMANS; PEPTIDES; PROTEINS; PROTEOMICS; SEQUENCE ANALYSIS;

THERMUS AQUATICUS;

EID: 84865545371     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200058     Document Type: Article

References (46)

1. Lewinsohn, T. M., Prado, P. I., How many species are there in Brazil? Conserv. Biol. 2005, 19, 619-624.
2. Alho, C. J., Camargo, G., Fischer, E., Terrestrial and aquatic mammals of the Pantanal. Braz. J. Biol. 2011, 71, 297-310.
3. Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J. et al., Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 1988, 239, 487-491.
4. Ferreira, S. H., Bartelt, D. C., Greene, L. J., Isolation of bradykinin-potentiating peptides from Bothrops jararaca venom. Biochemistry 1970, 9, 2583-2593.
5. Opie, L. H., Kowolik, H., The discovery of captopril: from large animals to small molecules. Cardiovasc. Res. 1995, 30, 18-25.
6. Eng, J. K., L., McCormack, A, Yates, Yates, J. R., III., An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass. Spectrom. 1994, 5, 976-989.
7. Mortz, E., O'Connor, P. B., Roepstorff, P., Kelleher, N. L. et al., Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases. Proc. Natl. Acad. Sci. USA 1996, 93, 8264-8267.
8. Seidler, J., Zinn, N., Boehm, M. E., Lehmann, W. D., De novo sequencing of peptides by MS/MS. Proteomics 2010, 10, 634-649.
9. 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.
10. Craig, R., Beavis, R. C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
11. 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.
12. Barboza, R., Cociorva, D., Xu, T., Barbosa, V. C. et al., Can the false-discovery rate be misleading? Proteomics 2011, 11, 4105-4108.
13. Cociorva, D., Tabb, L., Yates, J. R., Validation of tandem mass spectrometry database search results using DTASelect. Curr. Protoc. Bioinformatics 2007 Jan; Chapter 13, Unit 13.4.
14. Ma, Z. Q., Dasari, S., Chambers, M. C., Litton, M. D. et al., IDPicker 2.0: improved protein assembly with high discrimination peptide identification filtering. J. Proteome Res. 2009, 8, 3872-3881.
15. Cox, J., Hubner, N. C., Mann, M., How much peptide sequence information is contained in ion trap tandem mass spectra? J. Am. Soc. Mass. Spectrom. 2008, 19, 1813-1820.
16. Mann, M., Wilm, M., Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 1994, 66, 4390-4399.
17. Dasari, S., Chambers, M. C., Slebos, R. J., Zimmerman, L. J. et al., TagRecon: high-throughput mutation identification through sequence tagging. J. Proteome Res. 2010, 9, 1716-1726.
18. Kuster, B., Mortensen, P., Andersen, J. S., Mann, M., Mass spectrometry allows direct identification of proteins in large genomes. Proteomics 2001, 1, 641-650.
19. Shevchenko, A., Keller, P., Scheiffele, P., Mann, M. et al., Identification of components of trans-Golgi network-derived transport vesicles and detergent-insoluble complexes by nanoelectrospray tandem mass spectrometry. Electrophoresis 1997, 18, 2591-2600.
20. Sunyaev, S., Liska, A. J., Golod, A., Shevchenko, A. et al., MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry. Anal. Chem. 2003, 75, 1307-1315.
21. Hung, C. W., Tholey, A. Tandem mass tag protein labeling for top-down identification and quantification. Anal. Chem. 2012, 84, 161-170.
22. Dancik, V., Addona, T. A., Clauser, K. R., Vath, J. E. et al., De novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 1999, 6, 327-342.
23. Chi, H., Sun, R. X., Yang, B., Song, C. Q. et al., pNovo: de novo peptide sequencing and identification using HCD spectra. J. Proteome Res. 2010, 9, 2713-2724.
24. Frank, A., Pevzner, P., PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem. 2005, 77, 964-973.
25. Fischer, B., Roth, V., Roos, F., Grossmann, J. et al., NovoHMM: a hidden Markov model for de novo peptide sequencing. Anal. Chem. 2005, 77, 7265-7273.
26. Pevtsov, S., Fedulova, I., Mirzaei, H., Buck, C. et al., Performance evaluation of existing de novo sequencing algorithms. J. Proteome Res. 2006, 5, 3018-3028.
27. Frank, A. M., Savitski, M. M., Nielsen, M. L., Zubarev, R. A. et al., De novo peptide sequencing and identification with precision mass spectrometry. J. Proteome Res. 2007, 6, 114-123.
28. Zubarev, R. A., Zubarev, A. R., Savitski, M. M., Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet? J. Am. Soc. Mass. Spectrom. 2008, 19, 753-761.
29. Junqueira, M., Spirin, V., Balbuena, T. S., Thomas, H. et al., Protein identification pipeline for the homology-driven proteomics. J. Proteomics 2008, 71, 346-356.
30. Valcu, C. M., Junqueira, M., Shevchenko, A., Schlink, K., Comparative proteomic analysis of responses to pathogen infection and wounding in Fagus sylvatica. J. Proteome Res. 2009, 8, 4077-4091.
31. Charneau, S., Junqueira, M., Costa, C. M., Pires, D. L., et al., The saliva proteome of the blood-feeding insect Triatoma infestans is rich in platelet-aggregation inhibitors. Int. J. Mass. Spectrom. 2007, 268, 265-276.
32. Bandeira, N. Spectral networks: a new approach to de novo discovery of protein sequences and posttranslational modifications. Biotechniques 2007, 42, 687-695.
33. Frank, A. M., Monroe, M. E., Shah, A. R., Carver, J. J., et al., Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat. Methods 2011, 8, 587-591.
34. Gouw, J. W., Krijgsveld, J., Heck, A. J. Quantitative proteomics by metabolic labeling of model organisms. Mol. Cell Proteomics 2010, 9, 11-24.
35. Thompson, A., Schafer, J., Kuhn, K., Kienle, S. et al., Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75, 1895-1904.
36. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 2004, 3, 1154-1169.
37. Liu, H., Sadygov, R. G., Yates, J. R., III, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
38. Carvalho, P. C., Hewel, J., Barbosa, V. C., Yates, J. R., III, Identifying differences in protein expression levels by spectral counting and feature selection. Genet. Mol. Res. 2008, 7, 342-356.
39. Bondarenko, P. V., Chelius, D., Shaler, T. A., Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal. Chem. 2002, 74, 4741-4749.
40. Carvalho, P. C., Fischer, J. S., Chen, E. I., Yates, J. R., III et al., PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics 2008; 9: 316. Published online July 21 2008.
41. Carvalho, P. C., Xu, T., Han, X., Cociorva, D., Barbosa, V. C. et al., YADA: a tool for taking the most out of high-resolution spectra. Bioinformatics 2009, 25, 2734-2736.
42. Carvalho, P. C., Yates, I. I. I., Jr., Barbosa, V. C., Analyzing shotgun proteomic data with PatternLab for proteomics. Curr. Protoc. Bioinformatics 2010 Jun; Chapter 13, Unit 13.13.1-15.
43. Collier, T. S., Sarkar, P., Franck, W. L., Rao, B. M. et al., Direct comparison of stable isotope labeling by amino acids in cell culture and spectral counting for quantitative proteomics. Anal. Chem. 2010, 82, 8696-8702.
44. Silva, J. C., Gorenstein, M. V., Li, G. Z., Vissers, J. P. et al., Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell Proteomics 2006, 5, 144-56.
45. Venable, J. D., Dong, M. Q., Wohlschlegel, J., Dillin, A. et al., Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 2004, 1, 39-45.
46. Carvalho, P. C., Han, X., Xu, T., Cociorva, D. et al., XDIA: improving on the label-free data-independent analysis. Bioinformatics 2010, 26, 847-848.