Differenzielle Proteomanalyse – Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges)

Zusammenfassung Nach den großen Genomprojekten steht nun die Erforschung der Genprodukte, der Proteome, an. Die Proteomik verspricht neben fundamentalen Einsichten in die Funktionsweise des menschlichen Organismus, eine endlose Vielfalt von Applikationen in der medizinischen Diagnostik und Therapie. Wir beschreiben die derzeit gängigen experimentellen Techniken in der Proteomik. Diese Techniken erzeugen große Mengen komplexer Daten, die ohne geeignete Informatikmethoden nicht zu analysieren sind. Unter anderem kommen dabei Techniken aus dem Bereich der Statistik, des maschinellen Lernens, der Graphentheorie und der Bildverarbeitung zum Einsatz.

[1]  Vineet Bafna,et al.  SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database , 2001, ISMB.

[2]  Mikhail S. Gelfand,et al.  Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors , 2001, Bioinform..

[3]  Ming-Yang Kao,et al.  A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry , 2000, SODA '00.

[4]  P. Righetti,et al.  Modern strategies for protein quantification in proteome analysis: advantages and limitations. , 2002, Mass spectrometry reviews.

[5]  J. Yates,et al.  Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis. , 1998, Analytical chemistry.

[6]  P. Rabinow,et al.  Iceland: the case of a national human genome project. , 1999, Anthropology today.

[7]  Ting Chen,et al.  Algorithms for Identifying Protein Cross-Links via Tandem Mass Spectrometry , 2001, J. Comput. Biol..

[8]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[9]  Vineet Bafna,et al.  On de novo interpretation of tandem mass spectra for peptide identification , 2003, RECOMB '03.

[10]  G. Gonnet,et al.  Protein identification by mass profile fingerprinting. , 1993, Biochemical and biophysical research communications.

[11]  F. Lottspeich.  Proteomanalyse – ein Weg zur Funktionsanalyse von Proteinen , 1999 .

[12]  M. Mann,et al.  Proteomics to study genes and genomes , 2000, Nature.

[13]  E. Petricoin,et al.  Use of proteomic patterns in serum to identify ovarian Cancer , 2002 .

[14]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[15]  E. Dalmasso,et al.  Contribution of Human α-Defensin 1, 2, and 3 to the Anti-HIV-1 Activity of CD8 Antiviral Factor , 2002, Science.

[16]  G. Kroemer,et al.  Mass spectrometric identification of proteins released from mitochondria undergoing permeability transition , 2000, Cell Death and Differentiation.

[17]  Pavel A. Pevzner,et al.  De Novo Peptide Sequencing via Tandem Mass Spectrometry , 1999, J. Comput. Biol..

[18]  Edmond J. Breen,et al.  Automatic Poisson peak harvesting for high throughput protein identification , 2000, Electrophoresis.

[19]  J. A. Taylor,et al.  Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. , 1997, Rapid communications in mass spectrometry : RCM.

[20]  A Bairoch,et al.  Multiple parameter cross‐species protein identification using MultiIdent ‐ a world‐wide web accessible tool , 1998, Electrophoresis.

[21]  A. F. Neuwald,et al.  Purification and biochemical characterization of interchromatin granule clusters , 1999, The EMBO journal.

[22]  M. Wilm,et al.  Error-tolerant identification of peptides in sequence databases by peptide sequence tags. , 1994, Analytical chemistry.

[23]  Pavel A. Pevzner,et al.  Mutation-tolerant protein identification by mass-spectrometry , 2000, RECOMB '00.

[24]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[25]  P. Højrup,et al.  Rapid identification of proteins by peptide-mass fingerprinting , 1993, Current Biology.

[26]  G. Kroemer,et al.  Simplification of complex peptide mixtures for proteomic analysis: Reversible biotinylation of cysteinyl peptides , 2000, Electrophoresis.

[27]  Robert A. Thompson,et al.  Comparative proteomics based on stable isotope labeling and affinity selection. , 2002, Journal of mass spectrometry : JMS.

[28]  S. Patterson,et al.  Optimization of capillary chromatography ion trap‐mass spectrometry for identification of gel‐separated proteins , 1998, Electrophoresis.

[29]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[30]  B. Chait,et al.  ProFound: an expert system for protein identification using mass spectrometric peptide mapping information. , 2000, Analytical chemistry.

[31]  B. Chait,et al.  Protein indentification using mass spectrometric information , 1998, Electrophoresis.

[32]  Jilin Sun,et al.  Identification of incompletely processed potential Carboxypeptidase E substrates from CpEfat/CpEfat mice , 2001, Proteomics.

[33]  S. Patterson,et al.  Identification and Characterization of proSAAS, a Granin-Like Neuroendocrine Peptide Precursor that Inhibits Prohormone Processing , 2000, The Journal of Neuroscience.

[34]  S. Fields,et al.  Protein analysis on a proteomic scale , 2003, Nature.

[35]  A. Burlingame,et al.  Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Andres Metspalu.  Estonian Genome Project - before the take-off and take-off , 2002, ECCB.