Table 3 |
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Cheminformatics and mass spectrometry software course as part of an experimental mass spectrometry class, some of the software was deployed using WIN XP virtual machines in the computer laboratory. |
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General course |
Topics covered |
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General Introduction |
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Fighting computer illiteracy -- bits, bytes, CPUs |
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Regular expressions as emergency helpers |
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Structures -- resonance forms, stereoisomers, tautomers |
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Mass spectrometry publications via Yahoo Pipes |
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Mass spectral and molecular data handling |
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Mass spectral data formats and conversion of mass spectra |
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Open exchange formats for mass spectra (mzData, mzXML, JCAMP-DX, netCDF) |
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Structure handling software and structure conversion (SMILES/SMARTS, SDF/MOL, InChI/InChIKey, PDB, CML) |
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Chemical structure handling (Instant-JChem, BioClipse) |
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Mass spectral and molecular database search |
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Mass spectral databases (EI, ESI, APCI) and search algorithms (PBM, dot product, mass spectral trees) and library conversion |
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Proteomics data analysis (database search, de-novo sequencing, hybrid methods) |
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Molecule search (exact search, substructure search, similarity search, Markush search) |
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Databases (PubChem, SciFinder, Beilstein, BlueObelisk) |
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Mass Spectrometry Tools & Concepts |
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Resolving power, mass accuracy, isotopic pattern, charge states, charge state deconvolution |
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Molecular formula space of small molecules |
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Isotopic abundances as orthogonal filter for elemental compositions |
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Molecular Isomer Generators, substructure predictions, simulation of mass spectra |
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Concepts for GC-MS |
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Automatic peak detection |
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Peak picking and mass spectral deconvolution |
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Comprehensive GCxGC-TOF-MS |
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Concepts for LC-MS |
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Deconvolution and evaluation of LC-MS data |
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Adduct removal and detection during ESI-LC-MS |
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Seven Golden Rules for generation of possible molecular formulas |
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Structural isomer lookup example in ChemSpider |
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Prediction and simulation of mass spectra |
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Dendral - Artificial intelligence and mass spectrometry |
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Prediction of the isomer substructures from a given mass spectrum |
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Simulation of mass spectra from given isomer structures |
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Kind et al. Journal of Cheminformatics 2009 1:18 doi:10.1186/1758-2946-1-18 |
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