pepReap: A Peptide Identification Algorithm Using Support Vector Machines

[1]  A. Masselot,et al.  OLAV: Towards high‐throughput tandem mass spectrometry data identification , 2003, Proteomics.

[2]  Zhongqi Zhang,et al.  De novo peptide sequencing based on a divide-and-conquer algorithm and peptide tandem spectrum simulation. , 2004, Analytical chemistry.

[3]  Ying Xu,et al.  A computational method for assessing peptide‐ identification reliability in tandem mass spectrometry analysis with SEQUEST , 2004 .

[4]  Adam Buciński,et al.  Artificial neural network analysis for evaluation of peptide MS/MS spectra in proteomics. , 2004, Analytical chemistry.

[5]  Joshua E. Elias,et al.  Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. , 2003, Journal of proteome research.

[6]  Wen Gao,et al.  Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry , 2004, Bioinform..

[7]  P. Pevzner,et al.  PepNovo: de novo peptide sequencing via probabilistic network modeling. , 2005, Analytical chemistry.

[8]  J. Yates.  Mass spectrometry and the age of the proteome. , 1998, Journal of mass spectrometry : JMS.

[9]  Bin Ma,et al.  PEAKS: Powerful Software for Peptide De Novo Sequencing by MS/MS , 2003 .

[10]  A. Shevchenko,et al.  MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry. , 2003, Analytical chemistry.

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

[12]  Vladimir Vapnik,et al.  The Nature of Statistical Learning , 1995 .

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

[14]  Jayson Falkner,et al.  Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined , 2005, Bioinform..

[15]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[16]  R. Aebersold,et al.  ProbID: A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data , 2002, Proteomics.

[17]  Steven P Gygi,et al.  Intensity-based protein identification by machine learning from a library of tandem mass spectra , 2004, Nature Biotechnology.

[18]  A. Nesvizhskii,et al.  Experimental protein mixture for validating tandem mass spectral analysis. , 2002, Omics : a journal of integrative biology.

[19]  Zhongqi Zhang.  Prediction of low-energy collision-induced dissociation spectra of peptides. , 2004, Analytical chemistry.

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

[21]  Wei Sun,et al.  RScore: a peptide randomicity score for evaluating tandem mass spectra. , 2004, Rapid communications in mass spectrometry : RCM.

[22]  Vladimir Vapnik,et al.  Statistical learning theory , 1998 .

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

[24]  Z. Smilansky,et al.  Intensity-based statistical scorer for tandem mass spectrometry. , 2003, Analytical chemistry.

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

[26]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[27]  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.

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

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

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

[31]  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.

[32]  Pei Hao,et al.  A High-throughput Approach for Subcellular Proteome , 2004, Molecular & Cellular Proteomics.

[33]  William Stafford Noble,et al.  A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. , 2003, Journal of proteome research.

[34]  J. Yates,et al.  GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. , 2003, Analytical chemistry.

[35]  J. Yates,et al.  DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. , 2002, Journal of proteome research.