Applications of graph theory in protein structure identification. Peptide charge state determination of tandem mass spectra from low-resolution collision induced dissociation. A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry.
How to design, execute, and interpret experiments for protein sequencing using mass spectrometry. The rapid expansion of searchable protein. How to design, execute, and interpret experiments for protein sequencing using mass spectrometry The rapid expansion of searchable protein and DNA.
Proteomic studies of plant—bacterial interactions. Proteomic characterization of lignocellulose-degrading enzymes secreted by Phanerochaete carnosa grown on spruce and microcrystalline cellulose. LysNDeNovo: An algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation.
Mass spectrometry of peptides and proteins from human blood. Proteomics Facing the Combinatorial Problem. De Novo Sequencing Methods in Proteomics. Isotope pattern vector based tandem mass spectral data calibration for improved peptide and protein identification. Generalized lattice graphs for 2D-visualization of biological information.
Reinterpretation of the protein identification process for proteomics data. Mass spectrometric top-down analysis of proteins. Ritendra Datta and Marshall Bern. A combined database related and de novo MS-identification of yeast mannosephosphate guanyltransferase PSA1 interaction partners at different phases of batch cultivation.
Identification and characterization of INMAP, a novel interphase nucleus and mitotic apparatus protein that is involved in spindle formation and cell cycle progression. An application of the metric access methods to the mass spectrometry data. PTMap—A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites.
Spectral Dictionaries. Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences.
Comparison of Spectra in Unsequenced Species. Algorithms and Databases. Part 1: Finding biomarkers of organic drugs with mean Markov connectivity indices of spiral networks of blood mass spectra.
Stochastic molecular descriptors for polymers. Study of complex mixtures with topological indices of mass spectra spiral and star networks: The blood proteome case. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification.
Proteome analysis of non-model plants: A challenging but powerful approach. Identification of a novel centrosomal protein CrpF46 involved in cell cycle progression and mitosis.
Solving peptide sequencing as satisfiability. Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification. De novo sequencing of peptides. Analysis of Mass Spectrometry Data in Proteomics. Mass spectra alignments and their significance. A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data. Detection, quantification and identification of fungal extracellular laccases using polyclonal antibody and mass spectrometry.
Evaluation of the influence of amino acid composition on the propensity for collision-induced dissociation of model peptides using molecular dynamics simulations. A robust algorithm for identification of proteins in a database. Methods, algorithms and tools in computational proteomics: A practical point of view. Shotgun Protein Sequencing. Protein identification by spectral networks analysis.
De novo peptide identification via mixed-integer linear optimization and tandem mass spectrometry. A mixed-integer optimization framework for de novo peptide identification. Insights into chloroplast proteomics: from basic principles to new horizons. Introduction Strategies in Drug Discovery and Evaluation. Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways inChlamydomonas reinhardtii.
Advances in the analysis of dynamic protein complexes by proteomics and data processing. De novo peptide sequencing using exhaustive enumeration of peptide composition. Software for computational peptide identification from MS—MS data. Mathematical tools in analytical mass spectrometry.
Sabareesh, RSC Adv. Mass spectrometry-based protein identification by integrating de novo sequencing with database searching. Open Access. Reviews "[the authors] present their own laboratory-tested protocols for the analysis of a wide variety of samples, providing sufficient detail for duplication of their methods Mass spectra alignments and their significance. Introduction Strategies in Drug Discovery and Evaluation.
Protein identification and expression analysis using mass spectrometry. Marshall Bern and David Goldberg. Automated protein identification by tandem mass spectrometry: Issues and strategies. Manufacturing of recombinant therapeutic proteins in microbial systems. Peptide Identification via Tandem Mass Spectrometry. A preliminary work on evolutionary identification of protein variants and new proteins on grids. Statistical Methods in Proteomics.
Peptide identification via constrained multi-objective optimization: Pareto-based genetic algorithms. Increasing peptide identification in tandem mass spectrometry through automatic function switching optimization. ProbIDtree: An automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines.
Jason M. Fragmentation pathways of protonated peptides. Research challenges, opportunities and synergism in systems engineering and computational biology. Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined. Determination of partial amino acid composition from tandem mass spectra for use in peptide identification strategies.
Interpreting tandem mass spectra of peptides. Mass spectrometric data mining for protein sequences. Tandem mass spectrometry database searching. On peptidede novo sequencing: a new approach. Proteomic LC—MS systems using nanoscale liquid chromatography with tandem mass spectrometry.
A graph-theoretic approach for the separation of b and y ions in tandem mass spectra. Chapter 9 Mass spectrometry for protein identification. Identification of post-translational modifications via blind search of mass-spectra. Peptide charge state determination for low-resolution tandem mass spectra. Algorithms and databases in bioinformatics: towards a proteomic ontology.
Mass Spectra Alignments and Their Significance. Matching Peptide Sequences with Mass Spectra. Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book. Mass spectrometry and computational proteomics. De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by fourier transform ion cyclotron resonance mass spectrometry. Mass spectrometry has married statistics: uncle is functionality, children are selectivity and sensitivity. Algorithms for de novo peptide sequencing using tandem mass spectrometry.
Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS.
Proteomic Informatics. Hardware and software systems for accelerating common bioinformatics sequence analysis algorithms. Ryan H. Lilien , Hany Farid , and Bruce R. Bioinformatics support for high-throughput proteomics. PEAKS: powerful software for peptidede novo sequencing by tandem mass spectrometry. Proteomic analysis of the synaptic plasma membrane fraction isolated from rat forebrain.
Improved peptide sequencing using isotope information inherent in tandem mass spectra. Stable isotopic labeling and mass spectrometry as a means to determine differences in protein expression. Large-scale protein identification using mass spectrometry. Bingwen Lu and Ting Chen.
ProbID: A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Getting More from Less.