MassSorter: A tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Barsnes, Harald ^a,b   Mikalsen, Svein Ole ^c   Eidhammer, Ingvar ^a  

^a UNIVERSITY OF BERGEN   (Norway)

^b UNIFOB/UIB   (Norway)

^c OSLO UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; CELLULAR PROCESS; PEPTIDE MASS FINGERPRINTING; POST-TRANSLATIONAL MODIFICATIONS; PROTEIN CHARACTERIZATION; PROTEIN IDENTIFICATION; PROTEOLYTIC CLEAVAGE; SEQUENCE COVERAGES;

AMINO ACIDS; EXPERIMENTS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; TOOLS;

PROTEINS;

KERATIN; PROTEINASE; PROTEOME; PROTEIN;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPUTER PROGRAM; DATA ANALYSIS; DATA BASE; MASS SPECTROMETRY; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN PROCESSING; PROTEOMICS; UNIMOD; ALGORITHM; CHEMISTRY; COMPUTER INTERFACE; MOLECULAR GENETICS; PEPTIDE MAPPING; PROCEDURES; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDE MAPPING; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 33645023826     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-42     Document Type: Article

References (28)

1. Aebersold R, Mann M: Mass spectrometry-based proteomics. Nature 2003, 422:198-207.
2. Cristoni S, Bernardi L: Bioinformatics in mass spectrometry data analysis for proteomics studies. Exp Rev Prot 2004, 1:469-483.
3. Steen H, Mann M: The abc's (and xyz's) of peptide sequencing. Nat Rev Mol Cell Biol 2004, 5:699-711.
4. Reinders J, Lewandrowski U, Moebius J, Wagner Y, Sickmann A: Challenges in mass spectrometry-based proteomics. Proteomics 2004, 4:3686-3703.
5. Protein Prospector [http:/prospector.ucsf.edu/]
6. Perkins D, Pappin D, Creasy D, Cottrell J: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
7. Zhang W, Chait B: ProFound - an expert system for protein identification using mass spectrometric peptide mapping information. Anal Chem 2000, 72:2482-2489.
8. Tuloup M, Hernandez C, Coro I, Hoogland C, Binz PA, Appel R: Aldente and BioGraph: An improved peptide mass fingerprinting protein identification environment. In Understanding Biological Systems through Proteomics, Basel, Switzerland Edited by: FontisMedia. Swiss Proteomics Society; 2003:174-176.
9. Phenyx [http://www.phenyx-ms.com/]
10. Peri S, Steen H, Pandey A: GPMAW - a software tool for analyzing proteins and peptides. Trends Biochem Sci 2001, 11:687-689.
11. Schmidt F, Schmid M, Jungblut P, Mattow J, Facius A, Pleissner KP: Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis. J Am Soc Mass Spectrom 2003, 14:943-956.
12. FindMod [http://au.expasy.org/tools/findmod/]
13. Gattiker A, Bienvenut WV, Bairoch A, Gasteiger E: FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification. Proteomics 2002, 2:1435-1444.
14. Ceasy DM, Cottrell JS: UniMod: Protein modifications for mass spectrometry. Proteomics 2004, 4:1534-1536.
15. UniMod [http://www/unimod.org/]
16. Clauser KR, Baker PR, Burlingame AL: Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem 1999, 71:2871-2882.
17. PeptideCutter [http://au.expasy.org/tools/peptidecutter/]
18. Deshpande N, Addess KJ, Bluhm WF, Merino-Ott JC, Townsend-Merino W, Zhang Q, Knezevich C, Xie L, Chen L, Feng F, Green RK, Flippen-Anderson JL, Westbrook J, Berman HM, Bourne PE: The RCSB Protein Data bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res 2005, 33:D233-D237.
19. Pasha S: Visualization Tools for Bioinformatics, Master thesis, University of Bergen, Department of informatics. 2004.
20. Can T, Wang Y, Wang YF, Su J: FPV: fast protein visualization using Java 3D™. Bioinformatics 2003, 19:913-922.
21. Valero ML, Giralt E, Andreu D: An investigation of residue-specific contributions to peptide desorption in MALDI-TOF mass spectrometry. Lett Pept Sci 1999, 6:109-115.
22. Gay S, Binz PA, Hochstrasser DF, Appel RD: Peptide mass fingerprinting peak intensity prediction: Extracting knowledge from spectra. Proteomics 2002, 2:1374-1391.
23. Baumgart S, Lindner Y, Kühne R, Oberemm A, Wenschuh H, Krause E: The contributions of specific amino acid side chains to signal intensities of peptides in matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 2004, 18:863-868.
24. Wool A, Smilansky Z: Precalibration of matrix-assisted laser desorption/ ionization-time of flight spectra for peptide mass fingerprinting. Proteomics 2002, 2:1365-1373.
25. Shneiderman B: Designing the User Interface Addison Wesley 1998.
26. Lindstad RI, Sylte I, Mikalsen SO, Seglen PO, Berg E, Winberg JO: Pancreatic trypsin activates human promatrix metalloproteinase-2. J Mol Biol 2005, 350:682-698.
27. Stetler-Stevenson WG, Krutzsch HC, Wacher MP, Margulies IM, Liotta LA: The activation of human type IV collagenase proenzyme. Sequence identification of the major conversion product following organomercurial activation. J Biol Chem 1989, 264:1353-1356.
28. Netbeans [http://www.netbeans.org/]