Finding Protein Sequences Using PROWL
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
PROWL is a collection of tools for the identification of protein sequences, using input data derived from mass spectrometry. Experimental data from various types of mass spectrometers can be input directly into PROWL's component software. This unit presents protocols for several of the individual PROWL tools. Specifically, PepFrag allows for the analysis of a single spectrum derived from tandem mass spectrometry. GPM, on the other hand, provides for the analysis of multiple MS/MS spectra. An additional protocol introduces ProFound for analyzing a single spectrum of peptide mass fingerprinting data.
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PDF or HTML at Wiley Online LibraryTable of Contents
- Basic Protocol 1: Using PROWL with the Web Interface from the Rockefeller Server with Tandem Mass Spectrometry (MS/MS) Data: PepFrag
- Basic Protocol 2: Using PROWL with the Web Interface from the Rockefeller Server with Tandem Mass Spectrometry (MS/MS) Data: GPM
- Support Protocol 1: Using Advanced Features for GPM Searches
- Basic Protocol 3: Using PROWL with the Web Interface from the Rockefeller Server with Peptide Fingerprinting Mass Spectrometry (MS) Data: ProFound
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
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Figure 13.2.1 The start page for a PepFrag session. View Image -
Figure 13.2.2 Results obtained from a PepFrag search. View Image -
Figure 13.2.3 The start page for a GPM session. View Image -
Figure 13.2.4 Initial results page obtained from a GPM search. View Image -
Figure 13.2.5 Homologue page for one protein. View Image -
Figure 13.2.6 Protein model page, upper section showing sequence coverage. View Image -
Figure 13.2.7 Protein model page, lower section showing spectrum assignments. View Image -
Figure 13.2.8 The peptide model display page. View Image -
Figure 13.2.9 The start page for a ProFound session. View Image -
Figure 13.2.10 Results obtained from a ProFound search. View Image -
Figure 13.2.11 Details of a match between the data and a protein sequence. View Image
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Literature Cited
| Literature Cited | |
| Aebersold, R. and Goodlett, D.R. 2001. Mass spectrometry in proteomics. Chem. Rev. 101:269‐295. | |
| Craig., R. and Beavis, R.C. 2003. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun. Mass Spectrom. 17:2310‐2316. | |
| Eriksson, J. and Fenyö, D. 2004. Probity: A protein identification algorithm with accurate assignment of the statistical significance of the results. J. Proteome Res. 3:32‐36. | |
| Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F., and Whitehouse, C.M. 1989. Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64‐71. | |
| Fenyö, D., Zhang, W., Chait, B.T., and Beavis, R.C. 1996. Internet‐based analytical chemistry resources: A model project. Anal. Chem. 68:721A‐726A | |
| Fenyö, D., Qin, J., and Chait, B.T. 1998. Protein identification using mass spectrometric information. Electrophoresis 19:998‐1005. | |
| Field, H.I., Fenyö, D., and Bevies, R.C. 2002. RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimizes protein identification and archives data in a relational database. Proteomics 2:36‐47. | |
| Hillenkamp, F., Karas, M., Beavis, R.C., and Chait, B.T. 1991. Matrix‐assisted laser desorption/ionization mass spectrometry of biopolymers. Anal. Chem. 63:1193A‐1203A. | |
| Karlin, S. and Altschul, S. 1990. Methods for assessing the statistical significance of molecular sequence features using general scoring schemes. Proc. Natl. Acad. Sci. U.S.A. 87:2264‐2268. | |
| Karlin, S. and Altschul, S. 1993. Applications and statistics for multiple high‐scoring segments in molecular sequences. Proc. Natl. Acad. Sci. U.S.A. 90:5873‐5877. | |
| Mann, M. and Pandey, A. 2001. Use of mass spectrometry–derived data to annotate nucleotide and protein sequence databases. Trends Biochem. Sci. 26:54‐61. | |
| Mann, M. and Wilm, M. 1994. Error‐tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66:4390‐4399. | |
| Nielsen, M.L., Bennett, K.L., Larsen, B., Moniatte, M., and Mann, M. 2002. Peptide end sequencing by orthogonal MALDI tandem mass spectrometry. J. Proteome Res. 1:63‐71. | |
| Parker, K.C. 2002. Scoring methods in MALDI peptide mass fingerprinting: ChemScore and the ChemApplex program. J. Am. Soc. Mass Spectrom. 13:22‐39. | |
| Perkins, D.N., Pappin, D.J., Creasy, D.M., and Cottrell, J.S. 1999. Probability‐based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551‐3567. | |
| Yates, J.R. III, Eng, J.K., McCormack, A.L., and Schietz, D. 1995. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67:1426‐1436. | |
| Zhang, W. and Chait, B.T. 2000. ProFound: An expert system for protein identification using mass spectrometric peptide mapping information. Anal. Chem. 72:2482‐2489. |
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