A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Titulaer, Mark K ^a   Mustafa, Dana A N ^a   Siccama, Ivar ^a   Konijnenburg, Marco ^b   Burgers, Peter C ^a   Andeweg, Arno C ^a   Smitt, Peter A E Sillevis ^a   Kros, Johan M ^a   Luider, Theo M ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b FOM INSTITUTE AMOLF   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM BINDING PROTEINS; DOMAIN-CONTAINING PROTEINS; FATTY ACID-BINDING PROTEINS; GLIAL FIBRILLARY ACIDIC PROTEINS; HIER-ARCHICAL CLUSTERING; INTENSITY MATRIXES; NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN; SOFTWARE APPLICATIONS;

APPLICATION PROGRAMS; BLOOD VESSELS; CALCIUM; ISOTOPES; JAVA PROGRAMMING LANGUAGE; MASS SPECTROMETRY; MATRIX ALGEBRA; PEPTIDES; SOFTWARE TESTING;

TUMORS;

ALPHA ACTIN; BETA ACTIN; CYTOSKELETON PROTEIN; DESMIN; FATTY ACID BINDING PROTEIN; FIBRINOGEN; GLIAL FIBRILLARY ACIDIC PROTEIN; GROWTH HORMONE; HEMOGLOBIN ALPHA CHAIN; HEMOGLOBIN DELTA CHAIN; KERATIN; LIPOCORTIN 5; MITOCHONDRIAL PROTEIN; MYOSIN; NEUTROPHIL GELATINASE ASSOCIATED LIPOCALIN; PEPTIDYLTRANSFERASE; PROTEIN CDC42; PROTEIN DERIVATIVE; PROTEIN P22; PROTEINASE; RIBONUCLEASE; SERUM ALBUMIN; TRANSFER RNA; TUBULIN; VIMENTIN; ZINC FINGER PROTEIN; ANGIOGENIC PROTEIN; TUMOR MARKER; TUMOR PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CALCIUM SIGNALING; CARBOXY TERMINAL SEQUENCE; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; GLIOMA; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; LASER CAPTURE MICRODISSECTION; MATRIX ASSISTED LASER DESORPTION IONIZATION FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETRY; NEOVASCULARIZATION (PATHOLOGY); PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; RANK SUM TEST; UPREGULATION; CYCLOTRON; EVALUATION; INFRARED SPECTROSCOPY; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; PEPTIDE MAPPING; SENSITIVITY AND SPECIFICITY; VASCULARIZATION;

ALGORITHMS; ANGIOGENIC PROTEINS; CYCLOTRONS; GLIOMA; HUMANS; NEOPLASM PROTEINS; NEOVASCULARIZATION, PATHOLOGIC; PEPTIDE MAPPING; SENSITIVITY AND SPECIFICITY; SOFTWARE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; TUMOR MARKERS, BIOLOGICAL;

EID: 42449083752     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-133     Document Type: Article

References (32)

1. Mustafa DA Burgers PC Dekker LJ Charif H Titulaer MK Smitt PA Luider TM Kros JM Identification of Glioma Neovascularization-related Proteins by Using MALDI-FTMS and Nano-LC Fractionation to Microdissected Tumor Vessels Mol Cell Proteomics 2007, 6(7):1147-1157. 10.1074/ mcp.M600295-MCP200 17360931
2. Titulaer MK Siccama I Dekker LJ van Rijswijk AL Heeren RM Sillevis Smitt PA Luider TM A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls BMC bioinformatics 2006, 7:403. 1594579 16953879 10.1186/1471-2105-7-403
3. The source for Java developers http://java.sun.com
4. Horn DM Zubarev RA McLafferty FW Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules Journal of the American Society for Mass Spectrometry 2000, 11(4):320-332. 10.1016/S1044-0305(99)00157-9 10757168
5. The MASCOT peptide mass fingerprint search engine http://www.matrixscience.com
6. Marshall AG Hendrickson CL Jackson GS Fourier transform ion cyclotron resonance mass spectrometry: A primer, Chapter VIII. Mass resolving power, mass resolution, and mass accuracy Mass spectrometry reviews 1998, 17(1):1-35. 10.1002/ (SICI)1098-2787(1998)17:1<1::AID-MAS1>3.0.CO;2-K 9768511
7. Comisarow MB Melka JD Error Estimates for Finite Zero-Filling in Fourier Transform Spectroscopy Analytical chemistry 1979, 51(13):2198-2203. 10.1021/ac50049a032
8. van der Burgt YE Taban IM Konijnenburg M Biskup M Duursma MC Heeren RM Rompp A van Nieuwpoort RV Bal HE Parallel processing of large datasets from NanoLC-FTICR-MS measurements Journal of the American Society for Mass Spectrometry 2007, 18(1):152-161. 10.1016/j.jasms.2006.09.005 17055738
9. Valkenborg D Assam P Thomas G Krols L Kas K Burzykowski T Using a Poisson approximation to predict the isotopic distribution of sulphur-containing peptides in a peptide-centric proteomic approach Rapid Commun Mass Spectrom 2007, 21(20):3387-3391. 10.1002/rcm.3237 17891751
10. CRC handbook of chemistry and physics 48th edition Cleveland, Ohio: CRC Press 1967
11. Gay S Binz PA Hochstrasser DF Appel RD Modeling peptide mass fingerprinting data using the atomic composition of peptides Electrophoresis 1999, 20(18):3527-3534. 10.1002/ (SICI)1522-2683(19991201)20:18<3527::AID-ELPS3527>3.0.CO;2-9 10612279
12. Samuelsson J Dalevi D Levander F Rognvaldsson T Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting Bioinformatics (Oxford, England) 2004, 20(18):3628-3635. 10.1093/ bioinformatics/bth460 15297302
13. Michael W Senko SCB McLafferty W Fred Determination of Monoisotopic Masses and Ion Populations for Large Biomolecules from Resolved Isotopic Distributions J American Society for Mass Spectrometry 1995, 6:229-233. 10.1016/1044-0305(95)00017-8
14. The R project for statistical computing http://www.r-project.org
15. The open source database MySQL http://www.mysql.com
16. The enterprise distributions technologies free Java FTP library http://www.enterprisedt.com
17. The Apache XML project http://xml.apache.org
18. The Spotfire enterprise analytics platform http://www.spotfire.com
19. Caprioli R United States Patent 20070031900 Diagnosing and Grading Gliomas Using a Proteomics Approach 2006 http://www.freepatentsonline.com/20070031900.html In., vol. 20070031900
20. Schwartz SA Weil RJ Thompson RC Shyr Y Moore JH Toms SA Johnson MD Caprioli RM Proteomic-based prognosis of brain tumor patients using direct-tissue matrix-assisted laser desorption ionization mass spectrometry Cancer research 2005, 65(17):7674-7681. 16140934
21. Human Kegg (Kyoto Encyclopedia of Genes and Genomes) Pathway Calcium signaling pathway hsa04020 http://www.t1dbase.org/page/Kegg/display/ path_id/294
22. Dekker LJ
23. Szymanski PT Tao T Localization of protein regions involved in the interaction between calponin and myosin The Journal of biological chemistry 1997, 272(17):11142-11146. 10.1074/jbc.272.17.11142 9111011
24. Ikeda K Kundu RK Ikeda S Kobara M Matsubara H Quertermous T Glia maturation factor-gamma is preferentially expressed in microvascular endothelial and inflammatory cells and modulates actin cytoskeleton reorganization Circulation research 2006, 99(4):424-433. 10.1161/ 01.RES.0000237662.23539.0b 16873721
25. Boquest AC Shahdadfar A Fronsdal K Sigurjonsson O Tunheim SH Collas P Brinchmann JE Isolation and transcription profiling of purified uncultured human stromal stem cells: Alteration of gene expression after in vitro cell culture Molecular biology of the cell 2005, 16(3):1131-1141. 551479 15635089 10.1091/mbc.E04-10-0949
26. Strittmatter EF Rodriguez N Smith RD High mass measurement accuracy determination for proteomics using multivariate regression fitting: application to electrospray ionization time-of-flight mass spectrometry Analytical chemistry 2003, 75(3):460-468. 10.1021/ac026057g 12585471
27. The multinomial distribution http://en.wikipedia.org/wiki/ Multinomial_distribution
28. The maximum likelihood http://en.wikipedia.org/wiki/Maximum_likelihood
29. Bernt Schiele http://www.mis.informatik.tu-darmstadt.de/Education/ Courses/ml/tutorials/ml_mean.pdf Maximum Likelihood - Mixture of Gaussians
30. The mixture model http://en.wikipedia.org/wiki/Gaussian_mixture_model
31. Andrew W. Moore, Gaussian mixture modeling algebra http://www.cs.cmu.edu/ ~awm/doc/gmm-algebra.pdf
32. Yergey JA A General Approach to Calculating Isotopic Distributions for Mass International Journal of Mass Spectrometry and Ion Physics 1983, 52:337-349. 10.1016/0020-7381(83)85053-0