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