Bioinformatic methods to exploit mass spectrometric data for proteomic applications.

The new technologies in mass spectrometric analysis of peptides and proteins necessary to accommodate proteomics-scale analyses require, in turn, concomitant development of informatics technologies suitable for very large-scale data handling and analysis. This chapter focuses on the data analysis tools available to the community for analysis of mass spectrometric proteomics data. Different database searching strategies are discussed for peptide and protein identification, and approaches and tools available for comparative quantitative analysis of samples are outlined.

[1]  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.

[2]  K. Biemann.  Appendix 5. Nomenclature for peptide fragment ions (positive ions). , 1990, Methods in enzymology.

[3]  A. Burlingame,et al.  Functional Assignment of the 20 S Proteasome from Trypanosoma brucei Using Mass Spectrometry and New Bioinformatics Approaches* , 2001, The Journal of Biological Chemistry.

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

[5]  F. Cross,et al.  Accurate quantitation of protein expression and site-specific phosphorylation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Cathy H. Wu,et al.  Protein sequence databases. , 2004, Current opinion in chemical biology.

[7]  N. Kelleher,et al.  Web and database software for identification of intact proteins using "top down" mass spectrometry. , 2003, Analytical chemistry.

[8]  K. Resing,et al.  Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. , 2004, Analytical chemistry.

[9]  B. Chait,et al.  Automatic identification of proteins with a MALDI-quadrupole ion trap mass spectrometer. , 2001, Analytical chemistry.

[10]  P. Højrup,et al.  Use of mass spectrometric molecular weight information to identify proteins in sequence databases. , 1993, Biological mass spectrometry.

[11]  J. Yates,et al.  Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides , 1996, Journal of the American Society for Mass Spectrometry.

[12]  Ming Li,et al.  PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. , 2003, Rapid communications in mass spectrometry : RCM.

[13]  Gordon A Anderson,et al.  Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. , 2003, Analytical chemistry.

[14]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[15]  S F Altschul,et al.  Protein database searches for multiple alignments. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Ruedi Aebersold,et al.  The Need for Guidelines in Publication of Peptide and Protein Identification Data , 2004, Molecular & Cellular Proteomics.

[17]  D. Arnott,et al.  An integrated approach to proteome analysis: identification of proteins associated with cardiac hypertrophy. , 1998, Analytical biochemistry.

[18]  Alma L. Burlingame,et al.  The Advantages and Versatility of a High-Energy Collision-Induced Dissociation-Based Strategy for the Sequence and Structural Determination of Proteins , 1994 .

[19]  J. Yates,et al.  Probability-based validation of protein identifications using a modified SEQUEST algorithm. , 2002, Analytical chemistry.

[20]  A. Podtelejnikov,et al.  Identification of the components of simple protein mixtures by high-accuracy peptide mass mapping and database searching. , 1997, Analytical chemistry.

[21]  Eugene A. Kapp,et al.  Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. , 2003, Analytical chemistry.

[22]  P Berndt,et al.  Reliable automatic protein identification from matrix‐assisted laser desorption/ionization mass spectrometric peptide fingerprints , 1999, Electrophoresis.

[23]  T. Hunkapiller,et al.  Peptide mass maps: a highly informative approach to protein identification. , 1993, Analytical biochemistry.

[24]  A. P. Land,et al.  Application of liquid chromatography-mass spectrometry(n) analyses to the characterization of novel glyburide metabolites formed in vitro. , 1998, Journal of chromatography. A.

[25]  David Fenyö,et al.  RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database , 2002, Proteomics.

[26]  Nikola Tolić,et al.  High throughput proteome-wide precision measurements of protein expression using mass spectrometry , 1999 .

[27]  J. Yates,et al.  Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. , 2004, Analytical chemistry.

[28]  S. Altschul.  Amino acid substitution matrices from an information theoretic perspective , 1991, Journal of Molecular Biology.

[29]  Lan Huang,et al.  Comprehensive Analysis of a Multidimensional Liquid Chromatography Mass Spectrometry Dataset Acquired on a Quadrupole Selecting, Quadrupole Collision Cell, Time-of-flight Mass Spectrometer , 2005, Molecular & Cellular Proteomics.

[30]  J. A. Taylor,et al.  Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. , 2001, Analytical chemistry.

[31]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[32]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[33]  R. Aebersold,et al.  Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. , 2003, Analytical chemistry.

[34]  F. McLafferty,et al.  Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. , 2000, Analytical chemistry.

[35]  Aaron J Mackey,et al.  Getting More from Less , 2002, Molecular & Cellular Proteomics.

[36]  J. Yates,et al.  Direct analysis of protein complexes using mass spectrometry , 1999, Nature Biotechnology.

[37]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

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

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

[40]  R. Aebersold,et al.  A statistical model for identifying proteins by tandem mass spectrometry. , 2003, Analytical chemistry.

[41]  Peter R. Baker,et al.  Comprehensive Analysis of a Multidimensional Liquid Chromatography Mass Spectrometry Dataset Acquired on a Quadrupole Selecting, Quadrupole Collision Cell, Time-of-flight Mass Spectrometer , 2005, Molecular & Cellular Proteomics.

[42]  Robert J Chalkley,et al.  Mass Spectrometric Analysis of Protein Mixtures at Low Levels Using Cleavable 13C-Isotope-coded Affinity Tag and Multidimensional Chromatography* , 2003, Molecular & Cellular Proteomics.

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

[44]  Peter R Baker,et al.  The Identification of Protein-Protein Interactions of the Nuclear Pore Complex of Saccharomyces cerevisiae Using High Throughput Matrix-assisted Laser Desorption Ionization Time-of-Flight Tandem Mass Spectrometry* , 2002, Molecular & Cellular Proteomics.

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

[46]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[47]  J. Blake,et al.  Creating the Gene Ontology Resource : Design and Implementation The Gene Ontology Consortium 2 , 2001 .

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

[49]  M. Wilm,et al.  Analytical properties of the nanoelectrospray ion source. , 1996, Analytical chemistry.

[50]  Rolf Apweiler,et al.  Advances in the development of common interchange standards for proteomic data , 2004, Proteomics.

[51]  Peter R. Baker,et al.  Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. , 1999, Analytical chemistry.

[52]  Alexey I Nesvizhskii,et al.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.

[53]  C. Watanabe,et al.  Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Roger E. Moore,et al.  Qscore: An algorithm for evaluating SEQUEST database search results , 2002, Journal of the American Society for Mass Spectrometry.

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

[56]  B. Cargile,et al.  Immobilized pH gradients as a first dimension in shotgun proteomics and analysis of the accuracy of pI predictability of peptides , 2004, Electrophoresis.

[57]  A. Shevchenko,et al.  The Power and the Limitations of Cross-Species Protein Identification by Mass Spectrometry-driven Sequence Similarity Searches*S , 2004, Molecular & Cellular Proteomics.

[58]  R Kaufmann,et al.  Peptide sequencing by matrix-assisted laser-desorption mass spectrometry. , 1992, Rapid communications in mass spectrometry : RCM.

[59]  Chris F. Taylor,et al.  A common open representation of mass spectrometry data and its application to proteomics research , 2004, Nature Biotechnology.